This structure has broken O3'[i] to P[i+1] linkages **************************************************************************** 3DNA v2.4.5-2021may19, created and maintained by xiangjun@x3dna.org **************************************************************************** 1. The list of the parameters given below correspond to the 5' to 3' direction of strand I and 3' to 5' direction of strand II. 2. All angular parameters, except for the phase angle of sugar pseudo- rotation, are measured in degrees in the range of [-180, +180], and all displacements are measured in Angstrom units. **************************************************************************** File name: 1gax.pdb Date and time: Mon Sep 23 16:13:31 2024 Number of base-pairs: 55 Number of atoms: 17368 **************************************************************************** HEADER LIGASE/RNA 23-JUN-00 1GAX TITLE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE TITLE 2 COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA(VAL); COMPND 3 CHAIN: C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VALYL-TRNA SYNTHETASE; COMPND 7 CHAIN: A, B; COMPND 8 SYNONYM: VALRS; COMPND 9 EC: 6.1.1.9; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE FROM THERMUS THERMOPHILUS; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 6 ORGANISM_TAXID: 274; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PK7 KEYWDS PROTEIN-RNA COMPLEX, ROSSMANN FOLD, COILED COIL, TRNA, RIKEN KEYWDS 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, STRUCTURAL KEYWDS 3 GENOMICS, LIGASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.FUKAI,O.NUREKI,S.SEKINE,A.SHIMADA,J.TAO,D.G.VASSYLYEV,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 27-DEC-23 1GAX 1 REMARK LINK REVDAT 2 24-FEB-09 1GAX 1 VERSN REVDAT 1 06-DEC-00 1GAX 0 JRNL AUTH S.FUKAI,O.NUREKI,S.SEKINE,A.SHIMADA,J.TAO,D.G.VASSYLYEV, JRNL AUTH 2 S.YOKOYAMA JRNL TITL STRUCTURAL BASIS FOR DOUBLE-SIEVE DISCRIMINATION OF L-VALINE JRNL TITL 2 FROM L-ISOLEUCINE AND L-THREONINE BY THE COMPLEX OF JRNL TITL 3 TRNA(VAL) AND VALYL-TRNA SYNTHETASE. JRNL REF CELL(CAMBRIDGE,MASS.) V. 103 793 2000 JRNL REFN ISSN 0092-8674 JRNL PMID 11114335 JRNL DOI 10.1016/S0092-8674(00)00182-3 HELIX 1 1 ASP A 8 SER A 11 5 4 HELIX 2 2 VAL A 12 ASN A 23 1 12 HELIX 3 3 HIS A 50 MET A 69 1 20 HELIX 4 4 GLY A 84 ARG A 93 1 10 HELIX 5 5 GLU A 108 LEU A 132 1 25 HELIX 6 6 ASP A 137 GLU A 141 5 5 HELIX 7 7 ASP A 146 HIS A 162 1 17 HELIX 8 8 SER A 184 LEU A 186 5 3 HELIX 9 9 PRO A 217 PHE A 221 5 5 HELIX 10 10 THR A 272 HIS A 275 5 4 HELIX 11 11 ASP A 276 HIS A 286 1 11 HELIX 12 12 PHE A 315 GLU A 327 1 13 HELIX 13 13 ARG A 362 GLY A 377 1 16 HELIX 14 14 ARG A 385 ASN A 396 1 12 HELIX 15 15 ARG A 427 TYR A 431 5 5 HELIX 16 16 ASP A 454 ALA A 460 1 7 HELIX 17 17 LEU A 464 GLY A 468 5 5 HELIX 18 18 THR A 473 PHE A 479 1 7 HELIX 19 19 ASP A 490 LEU A 492 5 3 HELIX 20 20 TRP A 495 MET A 507 1 13 HELIX 21 21 ASP A 538 GLY A 547 1 10 HELIX 22 22 GLY A 547 ALA A 559 1 13 HELIX 23 23 ASP A 568 ARG A 593 1 26 HELIX 24 24 THR A 604 GLU A 626 1 23 HELIX 25 25 ASP A 629 PHE A 645 1 17 HELIX 26 26 TRP A 648 ALA A 659 1 12 HELIX 27 27 ASN A 661 HIS A 680 1 20 HELIX 28 28 MET A 683 GLY A 696 1 14 HELIX 29 29 GLU A 699 GLU A 703 5 5 HELIX 30 30 ASP A 712 GLY A 737 1 26 HELIX 31 31 THR A 752 ASN A 758 1 7 HELIX 32 32 ASN A 758 ARG A 767 1 10 HELIX 33 33 ASP A 797 ALA A 824 1 28 HELIX 34 34 GLU A 835 ILE A 861 1 27 HELIX 35 35 ASP B 8 SER B 11 5 4 HELIX 36 36 VAL B 12 ASN B 23 1 12 HELIX 37 37 HIS B 50 ARG B 70 1 21 HELIX 38 38 GLY B 84 ARG B 93 1 10 HELIX 39 39 GLY B 106 LEU B 132 1 27 HELIX 40 40 ASP B 137 GLU B 141 5 5 HELIX 41 41 ASP B 146 HIS B 162 1 17 HELIX 42 42 SER B 184 LEU B 186 5 3 HELIX 43 43 PRO B 217 PHE B 221 5 5 HELIX 44 44 GLU B 231 TYR B 235 5 5 HELIX 45 45 ASP B 276 GLY B 287 1 12 HELIX 46 46 ALA B 317 VAL B 322 1 6 HELIX 47 47 VAL B 322 GLU B 327 1 6 HELIX 48 48 ARG B 362 GLY B 377 1 16 HELIX 49 49 ARG B 385 ASN B 396 1 12 HELIX 50 50 ARG B 427 TYR B 431 5 5 HELIX 51 51 ASP B 454 ALA B 460 1 7 HELIX 52 52 LEU B 464 GLY B 468 5 5 HELIX 53 53 GLU B 474 PHE B 479 1 6 HELIX 54 54 GLY B 488 LEU B 492 5 5 HELIX 55 55 TRP B 495 HIS B 505 1 11 HELIX 56 56 ASP B 538 TYR B 546 1 9 HELIX 57 57 GLY B 547 ALA B 559 1 13 HELIX 58 58 LEU B 569 GLU B 594 1 26 HELIX 59 59 THR B 604 ALA B 627 1 24 HELIX 60 60 ASP B 629 TRP B 642 1 14 HELIX 61 61 TRP B 648 ALA B 659 1 12 HELIX 62 62 ASN B 661 HIS B 680 1 20 HELIX 63 63 MET B 683 GLY B 696 1 14 HELIX 64 64 GLU B 699 GLU B 703 5 5 HELIX 65 65 ASP B 712 GLY B 737 1 26 HELIX 66 66 THR B 752 ASN B 758 1 7 HELIX 67 67 ASN B 758 ARG B 767 1 10 HELIX 68 68 ASP B 797 SER B 825 1 29 HELIX 69 69 GLY B 827 ALA B 832 1 6 HELIX 70 70 PRO B 833 ILE B 861 1 29 SHEET 1 A 2 PRO A 35 PHE A 39 0 SHEET 2 A 2 GLU A 73 LEU A 77 1 O GLU A 73 N PHE A 36 SHEET 1 B 2 GLY A 79 THR A 80 0 SHEET 2 B 2 ALA A 142 PHE A 143 1 O ALA A 142 N THR A 80 SHEET 1 C 2 ALA A 166 ALA A 169 0 SHEET 2 C 2 GLN A 358 LEU A 361 -1 N GLN A 358 O ALA A 169 SHEET 1 D 3 THR A 181 LEU A 183 0 SHEET 2 D 3 LEU A 172 CYS A 176 -1 O ASN A 174 N LEU A 183 SHEET 3 D 3 TYR A 353 ILE A 355 -1 O ALA A 354 N VAL A 173 SHEET 1 E 2 VAL A 188 THR A 190 0 SHEET 2 E 2 ALA A 342 CYS A 344 -1 N THR A 343 O GLU A 189 SHEET 1 F 3 GLU A 211 THR A 214 0 SHEET 2 F 3 THR A 193 ARG A 201 -1 O TYR A 198 N THR A 214 SHEET 3 F 3 LEU A 331 ILE A 339 -1 N VAL A 332 O THR A 199 SHEET 1 G 3 ILE A 254 ALA A 256 0 SHEET 2 G 3 ILE A 226 VAL A 228 1 O ILE A 226 N LEU A 255 SHEET 3 G 3 ALA A 268 LYS A 270 -1 O LEU A 269 N ALA A 227 SHEET 1 H 3 ALA A 380 PHE A 381 0 SHEET 2 H 3 THR A 514 HIS A 518 1 N VAL A 515 O ALA A 380 SHEET 3 H 3 LEU A 485 GLY A 488 1 N LEU A 485 O THR A 514 SHEET 1 I 3 VAL A 423 ASN A 424 0 SHEET 2 I 3 TRP A 415 CYS A 417 -1 O TRP A 415 N ASN A 424 SHEET 3 I 3 LEU A 446 ARG A 448 -1 O LYS A 447 N TYR A 416 SHEET 1 J 2 VAL A 521 LEU A 522 0 SHEET 2 J 2 ILE A 565 ARG A 566 1 O ILE A 565 N LEU A 522 SHEET 1 K 4 ALA A 768 LEU A 770 0 SHEET 2 K 4 VAL A 744 GLY A 750 1 O VAL A 744 N ASP A 769 SHEET 3 K 4 VAL A 786 PRO A 791 -1 N THR A 787 O GLU A 749 SHEET 4 K 4 ALA A 778 ALA A 782 -1 O LEU A 779 N MET A 790 SHEET 1 L 2 PRO B 35 PHE B 39 0 SHEET 2 L 2 GLU B 73 LEU B 77 1 O GLU B 73 N PHE B 36 SHEET 1 M 2 GLY B 79 THR B 80 0 SHEET 2 M 2 ALA B 142 PHE B 143 1 O ALA B 142 N THR B 80 SHEET 1 N 3 ALA B 166 ALA B 169 0 SHEET 2 N 3 GLN B 358 LEU B 361 -1 N GLN B 358 O ALA B 169 SHEET 3 N 3 TRP B 400 ASN B 401 -1 N TRP B 400 O LEU B 361 SHEET 1 O 2 LEU B 172 VAL B 173 0 SHEET 2 O 2 ALA B 354 ILE B 355 -1 O ALA B 354 N VAL B 173 SHEET 1 P 2 VAL B 188 THR B 190 0 SHEET 2 P 2 ALA B 342 CYS B 344 -1 N THR B 343 O GLU B 189 SHEET 1 Q 2 THR B 193 GLY B 195 0 SHEET 2 Q 2 TYR B 337 ILE B 339 -1 O TYR B 337 N GLY B 195 SHEET 1 R 3 GLU B 211 THR B 214 0 SHEET 2 R 3 TYR B 198 ARG B 201 -1 O TYR B 198 N THR B 214 SHEET 3 R 3 LEU B 331 GLU B 334 -1 N VAL B 332 O THR B 199 SHEET 1 S 3 ILE B 254 ALA B 256 0 SHEET 2 S 3 ILE B 226 VAL B 228 1 O ILE B 226 N LEU B 255 SHEET 3 S 3 ALA B 268 LYS B 270 -1 O LEU B 269 N ALA B 227 SHEET 1 T 3 ALA B 380 PHE B 381 0 SHEET 2 T 3 PHE B 512 LEU B 517 1 O LYS B 513 N ALA B 380 SHEET 3 T 3 GLY B 482 THR B 487 1 O GLY B 482 N LYS B 513 SHEET 1 U 3 VAL B 423 ASN B 424 0 SHEET 2 U 3 TRP B 415 CYS B 417 -1 O TRP B 415 N ASN B 424 SHEET 3 U 3 LEU B 446 ARG B 448 -1 O LYS B 447 N TYR B 416 SHEET 1 V 2 VAL B 521 LEU B 522 0 SHEET 2 V 2 ILE B 565 ARG B 566 1 O ILE B 565 N LEU B 522 SHEET 1 W 4 ASP B 769 LEU B 771 0 SHEET 2 W 4 ARG B 745 GLY B 750 1 O VAL B 746 N LEU B 771 SHEET 3 W 4 VAL B 786 PRO B 791 -1 N THR B 787 O GLU B 749 SHEET 4 W 4 ALA B 778 ALA B 782 -1 O LEU B 779 N MET B 790 **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.005) ....>C:.901_:[..G]G-----C[..C]:.971_:C<.... (0.004) | 2 (0.003) ....>C:.902_:[..G]G-----C[..C]:.970_:C<.... (0.007) | 3 (0.005) ....>C:.903_:[..G]G-----C[..C]:.969_:C<.... (0.005) | 4 (0.005) ....>C:.904_:[..C]C-----G[..G]:.968_:C<.... (0.006) | 5 (0.006) ....>C:.905_:[..G]G-----C[..C]:.967_:C<.... (0.002) | 6 (0.008) ....>C:.906_:[..G]G-----C[..C]:.966_:C<.... (0.004) | 7 (0.005) ....>C:.907_:[..C]C-----G[..G]:.965_:C<.... (0.007) | 8 (0.005) ....>C:.948_:[..G]G-----C[..C]:.964_:C<.... (0.007) | 9 (0.004) ....>C:.949_:[..U]U-----A[..A]:.963_:C<.... (0.003) | 10 (0.009) ....>C:.950_:[..A]A-----U[..U]:.962_:C<.... (0.003) | 11 (0.003) ....>C:.951_:[..G]G-----C[..C]:.961_:C<.... (0.001) | 12 (0.008) ....>C:.952_:[..G]G-----C[..C]:.960_:C<.... (0.004) | 13 (0.002) ....>C:.953_:[..U]U-**--A[..A]:.957_:C<.... (0.006) | 14 (0.005) ....>C:.954_:[..U]U-**+-G[..G]:.917_:C<.... (0.007) x 15 (0.004) ....>C:.938_:[..G]G-----C[..C]:.930_:C<.... (0.004) | 16 (0.006) ....>C:.939_:[..C]C-----G[..G]:.929_:C<.... (0.007) | 17 (0.004) ....>C:.940_:[..G]G-----C[..C]:.928_:C<.... (0.004) | 18 (0.008) ....>C:.941_:[..A]A-----U[..U]:.927_:C<.... (0.006) | 19 (0.007) ....>C:.942_:[..G]G-----C[..C]:.926_:C<.... (0.006) | 20 (0.006) ....>C:.943_:[..A]A-**--G[..G]:.925_:C<.... (0.007) | 21 (0.007) ....>C:.910_:[..G]G-----C[..C]:.924_:C<.... (0.011) | 22 (0.012) ....>C:.911_:[..C]C-----G[..G]:.923_:C<.... (0.007) | 23 (0.006) ....>C:.912_:[..U]U-----A[..A]:.922_:C<.... (0.011) | 24 (0.005) ....>C:.913_:[..C]C-----G[..G]:.921_:C<.... (0.005) | 25 (0.007) ....>C:.914_:[..A]A-**--U[..U]:.908_:C<.... (0.006) | 26 (0.010) ....>C:.915_:[..G]G-**+-C[..C]:.947_:C<.... (0.004) | 27 (0.006) ....>C:.916_:[..C]C-**--G[..G]:.958_:C<.... (0.006) x 28 (0.017) ....>C:.918_:[..G]G-----C[..C]:.955_:C<.... (0.003) + 29 (0.003) ....>D:.901_:[..G]G-----C[..C]:.971_:D<.... (0.003) | 30 (0.004) ....>D:.902_:[..G]G-*---C[..C]:.970_:D<.... (0.006) | 31 (0.009) ....>D:.903_:[..G]G-----C[..C]:.969_:D<.... (0.010) | 32 (0.006) ....>D:.904_:[..C]C-----G[..G]:.968_:D<.... (0.007) | 33 (0.007) ....>D:.905_:[..G]G-----C[..C]:.967_:D<.... (0.007) | 34 (0.005) ....>D:.906_:[..G]G-----C[..C]:.966_:D<.... (0.003) | 35 (0.003) ....>D:.907_:[..C]C-*---G[..G]:.965_:D<.... (0.006) | 36 (0.005) ....>D:.948_:[..G]G-----C[..C]:.964_:D<.... (0.006) | 37 (0.002) ....>D:.949_:[..U]U-----A[..A]:.963_:D<.... (0.004) | 38 (0.004) ....>D:.950_:[..A]A-----U[..U]:.962_:D<.... (0.004) | 39 (0.006) ....>D:.951_:[..G]G-----C[..C]:.961_:D<.... (0.002) | 40 (0.003) ....>D:.952_:[..G]G-----C[..C]:.960_:D<.... (0.003) | 41 (0.003) ....>D:.953_:[..U]U-**--A[..A]:.957_:D<.... (0.006) | 42 (0.004) ....>D:.954_:[..U]U-**+-G[..G]:.917_:D<.... (0.007) x 43 (0.005) ....>D:.938_:[..G]G-----C[..C]:.930_:D<.... (0.005) | 44 (0.001) ....>D:.939_:[..C]C-----G[..G]:.929_:D<.... (0.014) | 45 (0.008) ....>D:.940_:[..G]G-----C[..C]:.928_:D<.... (0.006) | 46 (0.003) ....>D:.941_:[..A]A-----U[..U]:.927_:D<.... (0.005) | 47 (0.004) ....>D:.942_:[..G]G-----C[..C]:.926_:D<.... (0.004) | 48 (0.004) ....>D:.943_:[..A]A-**--G[..G]:.925_:D<.... (0.007) | 49 (0.012) ....>D:.910_:[..G]G-----C[..C]:.924_:D<.... (0.007) | 50 (0.012) ....>D:.911_:[..C]C-----G[..G]:.923_:D<.... (0.006) | 51 (0.008) ....>D:.912_:[..U]U-----A[..A]:.922_:D<.... (0.010) | 52 (0.004) ....>D:.913_:[..C]C-----G[..G]:.921_:D<.... (0.006) | 53 (0.005) ....>D:.914_:[..A]A-**--U[..U]:.908_:D<.... (0.005) | 54 (0.012) ....>D:.915_:[..G]G-**+-C[..C]:.947_:D<.... (0.014) x 55 (0.012) ....>D:.918_:[..G]G-----C[..C]:.955_:D<.... (0.002) + Note: This structure contains 13[11] non-Watson-Crick base-pairs. **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 G-----C [3] O6 - N4 3.60 N1 - N3 3.53 N2 - O2 3.44 2 G-----C [2] O6 * N3 2.57 N1 - O2 2.94 3 G-----C [3] O6 - N4 2.83 N1 - N3 2.97 N2 - O2 3.12 4 C-----G [3] O2 - N2 2.95 N3 - N1 2.84 N4 - O6 2.83 5 G-----C [3] O6 - N4 2.98 N1 - N3 2.87 N2 - O2 2.65 6 G-----C [2] O6 - N4 2.86 N1 - N3 3.19 7 C-----G [2] O2 - N2 3.38 N3 - N1 3.42 8 G-----C [3] O6 - N4 3.33 N1 - N3 2.97 N2 - O2 2.49 9 U-----A [2] N3 - N1 2.82 O4 - N6 2.94 10 A-----U [2] N6 - O4 3.22 N1 - N3 2.82 11 G-----C [3] O6 - N4 2.64 N1 - N3 2.73 N2 - O2 2.72 12 G-----C [3] O6 - N4 3.08 N1 - N3 3.29 N2 - O2 3.37 13 U-**--A [2] O2 - N6 3.12 N3 - N7 3.18 14 U-**+-G [2] O2'- O6 3.26 O2 - N1 2.76 15 G-----C [3] O6 - N4 3.08 N1 - N3 2.90 N2 - O2 2.63 16 C-----G [3] O2 - N2 2.45 N3 - N1 2.74 N4 - O6 2.97 17 G-----C [3] O6 - N4 2.83 N1 - N3 2.85 N2 - O2 2.79 18 A-----U [2] N6 - O4 2.74 N1 - N3 2.66 19 G-----C [3] O6 - N4 2.77 N1 - N3 2.74 N2 - O2 2.82 20 A-**--G [2] N6 - O6 2.75 N1 - N1 2.72 21 G-----C [3] O6 - N4 3.05 N1 - N3 3.25 N2 - O2 3.35 22 C-----G [3] O2 - N2 2.64 N3 - N1 2.90 N4 - O6 3.15 23 U-----A [2] N3 - N1 2.90 O4 - N6 2.76 24 C-----G [3] O2 - N2 2.82 N3 - N1 2.72 N4 - O6 2.48 25 A-**--U [2] N7 - N3 2.85 N6 - O2 3.04 26 G-**+-C [2] N1 - O2 2.77 N2 - N3 2.98 27 C-**--G [2] O4'* O6 3.17 O2 * N7 2.79 28 G-----C [3] O6 - N4 3.20 N1 - N3 2.84 N2 - O2 2.92 29 G-----C [3] O6 - N4 3.33 N1 - N3 3.24 N2 - O2 3.34 30 G-*---C [2] O6 * N3 2.71 N1 - O2 2.93 31 G-----C [3] O6 - N4 2.38 N1 - N3 2.88 N2 - O2 3.43 32 C-----G [3] O2 - N2 2.79 N3 - N1 2.83 N4 - O6 2.85 33 G-----C [3] O6 - N4 2.75 N1 - N3 2.76 N2 - O2 2.67 34 G-----C [3] O6 - N4 2.76 N1 - N3 2.96 N2 - O2 3.28 35 C-*---G [2] O2 - N1 3.39 N3 * O6 3.40 36 G-----C [3] O6 - N4 3.22 N1 - N3 2.87 N2 - O2 2.58 37 U-----A [2] N3 - N1 3.01 O4 - N6 3.05 38 A-----U [2] N6 - O4 3.22 N1 - N3 2.91 39 G-----C [3] O6 - N4 2.91 N1 - N3 2.84 N2 - O2 2.67 40 G-----C [3] O6 - N4 2.68 N1 - N3 3.15 N2 - O2 3.51 41 U-**--A [2] O2 - N6 3.23 N3 - N7 2.92 42 U-**+-G [2] O2'- O6 3.50 O2 - N1 2.81 43 G-----C [3] O6 - N4 3.13 N1 - N3 3.12 N2 - O2 2.97 44 C-----G [3] O2 - N2 2.58 N3 - N1 3.00 N4 - O6 3.33 45 G-----C [3] O6 - N4 3.01 N1 - N3 2.92 N2 - O2 2.74 46 A-----U [2] N6 - O4 2.80 N1 - N3 2.67 47 G-----C [3] O6 - N4 2.99 N1 - N3 2.98 N2 - O2 3.11 48 A-**--G [2] N6 - O6 3.22 N1 - N1 2.92 49 G-----C [3] O6 - N4 3.08 N1 - N3 3.19 N2 - O2 3.23 50 C-----G [3] O2 - N2 2.74 N3 - N1 2.96 N4 - O6 3.18 51 U-----A [2] N3 - N1 2.88 O4 - N6 2.74 52 C-----G [3] O2 - N2 2.85 N3 - N1 2.77 N4 - O6 2.54 53 A-**--U [2] N7 - N3 2.69 N6 - O2 2.90 54 G-**+-C [2] N1 - O2 2.69 N2 - N3 2.69 55 G-----C [2] N1 - N3 3.30 N2 - O2 2.81 **************************************************************************** Overlap area in Angstrom^2 between polygons defined by atoms on successive bases. Polygons projected in the mean plane of the designed base-pair step. Values in parentheses measure the overlap of base ring atoms only. Those outside parentheses include exocyclic atoms on the ring. Intra- and inter-strand overlap is designated according to the following diagram: i2 3' 5' j2 /|\ | | | Strand I | | II | | | | | \|/ i1 5' 3' j1 step i1-i2 i1-j2 j1-i2 j1-j2 sum 1 GG/CC 3.17( 1.64) 0.00( 0.00) 0.00( 0.00) 1.96( 0.25) 5.13( 1.88) 2 GG/CC 4.61( 3.14) 0.00( 0.00) 0.09( 0.00) 0.86( 0.00) 5.57( 3.14) 3 GC/GC 7.27( 4.32) 0.00( 0.00) 0.00( 0.00) 5.73( 2.63) 13.00( 6.95) 4 CG/CG 0.04( 0.00) 0.00( 0.00) 4.27( 1.57) 0.00( 0.00) 4.31( 1.57) 5 GG/CC 3.55( 2.15) 0.00( 0.00) 0.49( 0.00) 0.00( 0.00) 4.04( 2.15) 6 GC/GC 5.14( 2.91) 0.00( 0.00) 0.00( 0.00) 3.12( 1.19) 8.26( 4.10) 7 CG/CG 0.01( 0.00) 0.00( 0.00) 3.91( 1.44) 0.00( 0.00) 3.92( 1.44) 8 GU/AC 3.69( 1.24) 0.00( 0.00) 0.00( 0.00) 5.37( 3.67) 9.06( 4.91) 9 UA/UA 0.03( 0.00) 0.00( 0.00) 2.26( 1.74) 0.03( 0.00) 2.33( 1.74) 10 AG/CU 2.73( 2.34) 0.00( 0.00) 0.91( 0.00) 0.00( 0.00) 3.63( 2.34) 11 GG/CC 3.83( 2.47) 0.00( 0.00) 0.51( 0.00) 0.00( 0.00) 4.34( 2.47) 12 GU/AC 5.39( 2.42) 0.00( 0.00) 0.00( 0.00) 5.93( 2.70) 11.32( 5.13) 13 UU/GA 5.29( 2.71) 0.00( 0.00) 0.00( 0.00) 4.97( 2.85) 10.26( 5.56) 14 UG/CG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 15 GC/GC 3.16( 1.09) 0.00( 0.00) 0.00( 0.00) 6.16( 2.73) 9.33( 3.82) 16 CG/CG 0.00( 0.00) 0.00( 0.00) 5.72( 2.88) 0.00( 0.00) 5.72( 2.88) 17 GA/UC 3.33( 1.89) 0.00( 0.00) 0.00( 0.00) 0.25( 0.00) 3.58( 1.89) 18 AG/CU 2.71( 2.36) 0.00( 0.00) 0.99( 0.00) 0.00( 0.00) 3.70( 2.36) 19 GA/GC 1.80( 0.28) 0.00( 0.00) 0.00( 0.00) 4.22( 1.83) 6.02( 2.11) 20 AG/CG 0.00( 0.00) 0.00( 0.00) 1.06( 0.00) 0.01( 0.00) 1.07( 0.00) 21 GC/GC 5.34( 2.18) 0.00( 0.00) 0.00( 0.00) 7.22( 4.62) 12.56( 6.81) 22 CU/AG 0.45( 0.00) 0.00( 0.00) 0.17( 0.00) 1.17( 1.12) 1.80( 1.12) 23 UC/GA 0.29( 0.02) 0.00( 0.00) 0.00( 0.00) 2.05( 0.63) 2.34( 0.64) 24 CA/UG 0.00( 0.00) 1.15( 0.00) 3.86( 1.10) 0.00( 0.00) 5.01( 1.10) 25 AG/CU 3.52( 1.31) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 3.52( 1.31) 26 GC/GC 4.86( 1.90) 0.39( 0.00) 0.00( 0.00) 0.04( 0.00) 5.29( 1.90) 27 CG/CG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 28 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 29 GG/CC 2.05( 0.73) 0.00( 0.00) 0.02( 0.00) 0.93( 0.00) 3.00( 0.73) 30 GG/CC 4.00( 2.61) 0.00( 0.00) 0.00( 0.00) 2.12( 0.47) 6.11( 3.08) 31 GC/GC 7.37( 3.82) 0.00( 0.00) 0.00( 0.00) 4.60( 1.81) 11.97( 5.63) 32 CG/CG 0.19( 0.00) 0.00( 0.00) 4.10( 1.37) 0.02( 0.00) 4.30( 1.37) 33 GG/CC 4.43( 3.20) 0.00( 0.00) 0.21( 0.00) 0.00( 0.00) 4.64( 3.20) 34 GC/GC 5.33( 3.13) 0.00( 0.00) 0.00( 0.00) 3.86( 1.66) 9.19( 4.79) 35 CG/CG 0.00( 0.00) 0.00( 0.00) 4.69( 1.92) 0.00( 0.00) 4.69( 1.92) 36 GU/AC 4.00( 1.55) 0.00( 0.00) 0.00( 0.00) 4.35( 2.69) 8.35( 4.23) 37 UA/UA 0.01( 0.00) 0.00( 0.00) 1.49( 1.22) 0.17( 0.00) 1.66( 1.22) 38 AG/CU 3.42( 3.04) 0.00( 0.00) 0.23( 0.00) 0.00( 0.00) 3.65( 3.04) 39 GG/CC 3.47( 1.84) 0.00( 0.00) 1.07( 0.00) 0.00( 0.00) 4.54( 1.84) 40 GU/AC 6.66( 3.95) 0.00( 0.00) 0.00( 0.00) 6.86( 3.36) 13.52( 7.31) 41 UU/GA 5.29( 2.01) 0.00( 0.00) 0.00( 0.00) 4.17( 2.43) 9.46( 4.44) 42 UG/CG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 43 GC/GC 3.07( 0.91) 0.00( 0.00) 0.00( 0.00) 5.47( 2.70) 8.54( 3.61) 44 CG/CG 0.00( 0.00) 0.00( 0.00) 4.84( 2.09) 0.00( 0.00) 4.84( 2.09) 45 GA/UC 3.85( 2.56) 0.00( 0.00) 0.00( 0.00) 0.65( 0.04) 4.50( 2.59) 46 AG/CU 2.58( 2.28) 0.00( 0.00) 0.98( 0.00) 0.00( 0.00) 3.57( 2.28) 47 GA/GC 2.48( 0.42) 0.00( 0.00) 0.00( 0.00) 4.58( 2.04) 7.06( 2.46) 48 AG/CG 0.00( 0.00) 0.00( 0.00) 1.29( 0.01) 0.03( 0.00) 1.32( 0.02) 49 GC/GC 5.82( 2.66) 0.00( 0.00) 0.00( 0.00) 6.56( 3.60) 12.38( 6.26) 50 CU/AG 0.29( 0.00) 0.00( 0.00) 0.22( 0.00) 0.65( 0.65) 1.16( 0.65) 51 UC/GA 0.06( 0.00) 0.00( 0.00) 0.01( 0.00) 2.11( 0.66) 2.17( 0.66) 52 CA/UG 0.00( 0.00) 1.08( 0.00) 4.31( 1.43) 0.00( 0.00) 5.40( 1.43) 53 AG/CU 3.96( 1.69) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 3.96( 1.69) 54 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) **************************************************************************** Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure bp Ox Oy Oz Nx Ny Nz 1 G-C 99.678 42.213 45.778 0.401 0.691 -0.602 2 G-C 100.870 44.241 42.595 0.515 0.760 -0.397 3 G-C 101.161 47.315 40.753 0.424 0.788 -0.446 4 C-G 101.082 50.662 39.973 0.292 0.859 -0.421 5 G-C 101.284 54.098 39.424 0.563 0.682 -0.466 6 G-C 103.271 58.052 40.033 0.653 0.755 -0.064 7 C-G 105.827 59.024 40.243 0.688 0.702 0.184 8 G-C 109.358 60.521 41.743 0.865 0.483 -0.135 9 U-A 112.763 61.102 43.047 0.872 0.474 -0.125 10 A-U 115.777 60.915 42.014 0.858 0.461 -0.226 11 G-C 119.057 60.650 39.627 0.782 0.429 -0.452 12 G-C 120.903 61.246 36.082 0.718 0.463 -0.520 13 U-A 122.170 60.877 31.710 0.701 0.470 -0.537 14 U+G 124.351 64.388 31.516 0.667 0.562 -0.489 15 G-C 89.109 81.003 9.032 0.898 -0.169 0.407 16 C-G 92.418 82.755 10.245 0.899 -0.185 0.398 17 G-C 94.984 83.788 12.898 0.796 -0.348 0.495 18 A-U 96.786 82.848 16.394 0.638 -0.478 0.604 19 G-C 96.996 80.145 19.435 0.558 -0.646 0.521 20 A-G 97.350 77.565 22.655 0.525 -0.709 0.471 21 G-C 95.388 73.301 24.329 0.405 -0.870 0.283 22 C-G 96.462 70.005 24.059 0.439 -0.873 0.213 23 U-A 98.882 66.976 23.939 0.586 -0.687 0.430 24 C-G 102.472 66.941 24.437 0.663 -0.690 0.290 25 A-U 106.008 65.171 23.656 0.704 -0.624 0.339 26 G+C 109.456 66.427 26.767 0.631 -0.714 0.304 27 C-G 110.747 62.329 26.424 0.467 -0.697 0.545 28 G-C 128.108 65.298 23.220 0.644 0.418 -0.641 29 G-C 173.047 110.282 -3.255 -0.662 -0.354 0.661 30 G-C 170.992 109.166 0.056 -0.841 -0.411 0.352 31 G-C 167.978 109.050 2.471 -0.831 -0.313 0.461 32 C-G 164.310 109.523 2.922 -0.851 -0.253 0.460 33 G-C 160.637 109.505 3.497 -0.845 -0.414 0.339 34 G-C 157.136 107.893 2.508 -0.821 -0.562 0.102 35 C-G 155.971 105.625 2.309 -0.748 -0.647 -0.149 36 G-C 154.151 102.255 0.692 -0.522 -0.840 0.148 37 U-A 153.225 98.599 -0.515 -0.587 -0.793 0.163 38 A-U 153.124 95.503 0.222 -0.460 -0.820 0.341 39 G-C 153.167 92.910 2.670 -0.512 -0.762 0.397 40 G-C 152.593 90.599 6.586 -0.505 -0.685 0.526 41 U-A 152.563 89.249 10.784 -0.523 -0.707 0.476 42 U+G 149.147 86.968 11.419 -0.760 -0.506 0.407 43 G-C 134.999 123.613 33.862 0.092 -0.900 -0.426 44 C-G 133.160 120.624 32.166 0.166 -0.860 -0.482 45 G-C 132.013 118.071 29.323 0.336 -0.725 -0.600 46 A-U 132.774 116.439 26.138 0.395 -0.701 -0.593 47 G-C 135.672 116.135 22.807 0.601 -0.548 -0.581 48 A-G 138.246 115.455 19.913 0.659 -0.555 -0.508 49 G-C 142.512 117.154 18.170 0.860 -0.415 -0.298 50 C-G 145.633 115.658 18.433 0.840 -0.498 -0.214 51 U-A 148.282 112.814 18.622 0.683 -0.621 -0.386 52 C-G 148.154 109.228 18.220 0.653 -0.680 -0.332 53 A-U 149.409 105.891 18.919 0.510 -0.819 -0.262 54 G+C 148.194 102.288 15.882 0.634 -0.668 -0.390 55 G-C 148.240 83.025 19.631 -0.497 -0.571 0.654 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 G-C -1.35 -0.10 -1.36 -3.83 -13.62 6.71 2 G-C -1.64 -0.64 -0.10 -11.09 -7.04 -8.14 3 G-C -0.64 -0.24 -0.28 -1.14 -17.69 -2.99 4 C-G 0.23 -0.31 -0.91 9.59 -22.00 4.41 5 G-C -0.00 -0.19 0.99 15.87 9.85 4.89 6 G-C 0.57 -0.03 -1.07 -12.25 -25.60 -3.64 7 C-G 1.64 -0.07 -1.41 26.03 -28.59 15.80 8 G-C -0.56 -0.01 0.07 -9.38 -7.27 9.00 9 U-A 0.19 -0.15 0.16 -2.86 -0.47 0.77 10 A-U -0.41 -0.12 0.37 7.40 -4.67 7.57 11 G-C 0.17 -0.31 -0.45 -5.93 -9.01 -1.40 12 G-C -0.96 -0.01 -0.39 -15.93 -2.78 -5.84 13 U-A 4.32 -1.75 0.01 -7.47 8.68 -96.16 14 U+G 0.96 -5.26 0.23 10.39 13.14 -98.33 15 G-C -0.49 -0.17 0.31 0.55 -8.44 2.87 16 C-G 0.36 -0.24 0.03 5.11 -9.99 5.46 17 G-C -0.10 -0.18 0.19 2.64 -7.38 -1.34 18 A-U 0.06 -0.32 -0.62 -10.59 -11.79 0.80 19 G-C -0.58 -0.37 -0.05 -16.82 -23.48 -2.69 20 A-G 0.16 1.38 -0.17 -34.19 -27.24 -16.92 21 G-C -1.26 -0.24 0.08 -5.81 -1.86 -5.89 22 C-G 0.79 -0.23 -0.14 -3.51 -14.26 6.48 23 U-A -0.38 -0.09 1.05 -25.37 -2.85 -7.80 24 C-G 0.29 -0.43 0.34 1.06 -0.48 -6.06 25 A-U -4.18 -2.09 -0.11 -0.28 17.38 -102.17 26 G+C 0.12 3.62 0.87 3.11 15.34 151.86 27 C-G 4.96 -6.70 2.14 39.09 32.26 -15.75 28 G-C 0.06 0.02 -0.10 -32.35 -41.07 3.33 29 G-C -0.85 -0.38 -1.58 2.80 -20.37 13.22 30 G-C -2.12 -0.55 -0.01 -7.92 -7.77 -4.07 31 G-C -0.62 -0.52 -0.66 -3.52 -19.43 -11.14 32 C-G -0.18 -0.22 -0.65 8.08 -14.81 1.82 33 G-C 0.06 -0.25 0.01 3.95 -5.19 -0.15 34 G-C 0.19 -0.12 -0.57 -9.38 -24.49 -3.51 35 C-G 1.96 -0.06 -1.42 31.66 -24.96 10.57 36 G-C -1.27 -0.44 0.07 -1.92 -17.36 8.16 37 U-A 0.13 0.02 0.59 -10.05 -0.75 -0.91 38 A-U 0.52 0.02 -0.25 -3.57 -1.18 5.66 39 G-C 0.30 -0.13 0.08 2.34 -7.30 1.15 40 G-C -0.76 -0.18 -0.63 -18.46 -7.28 -12.23 41 U-A 4.70 -2.99 0.60 -2.90 16.77 -96.45 42 U+G 0.12 -5.65 0.85 4.82 32.34 -117.67 43 G-C -0.02 0.11 -0.04 0.09 2.21 0.05 44 C-G 0.36 0.04 -0.06 0.18 -9.04 8.43 45 G-C -0.40 -0.12 -0.40 -10.65 -9.67 2.87 46 A-U 0.56 -0.25 -0.20 -9.43 -10.08 1.23 47 G-C -0.63 -0.10 -0.38 -21.60 -26.63 -1.19 48 A-G 0.07 1.67 -0.18 -37.46 -24.11 -9.95 49 G-C -0.96 -0.12 0.03 -3.35 -7.72 -3.49 50 C-G 0.34 -0.05 -0.18 -3.36 -15.40 6.20 51 U-A -0.43 -0.10 1.02 -24.44 0.17 -7.19 52 C-G 0.15 -0.44 0.78 -1.36 1.13 -5.67 53 A-U -4.15 -2.21 0.42 -1.59 17.98 -100.18 54 G+C 0.26 3.89 0.37 10.25 15.66 157.54 55 G-C 0.53 0.55 0.04 -37.45 -28.00 11.88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.00 -0.43 -0.05 -4.04 -7.02 -5.46 s.d. 1.54 1.68 0.67 14.81 15.35 45.40 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 GG/CC -0.36 -1.53 3.63 -14.02 0.40 27.97 2 GG/CC 0.49 -1.35 3.30 6.06 1.06 39.51 3 GC/GC 0.63 -1.40 3.08 8.53 1.66 32.86 4 CG/CG 0.08 -1.74 3.02 -17.71 6.33 30.09 5 GG/CC 0.06 -2.03 3.98 19.71 13.93 38.40 6 GC/GC 1.22 -0.11 2.45 14.39 3.01 30.76 7 CG/CG 0.11 -1.69 3.75 -7.69 23.36 23.31 8 GU/AC -0.92 -1.84 3.07 0.82 -0.17 37.39 9 UA/UA 0.48 -1.62 2.70 0.54 5.82 28.35 10 AG/CU 0.15 -2.22 3.40 6.93 12.00 29.61 11 GG/CC 0.67 -2.12 3.38 2.16 5.24 26.75 12 GU/AC -2.59 -2.22 3.04 1.43 0.10 92.77 13 UU/GA 1.46 -1.84 3.41 5.93 2.00 43.25 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GC/GC -0.72 -2.25 3.15 -0.99 -0.30 33.08 16 CG/CG -0.43 -2.21 3.10 -2.16 12.20 28.68 17 GA/UC 0.04 -1.79 3.63 6.74 11.46 31.30 18 AG/CU 0.74 -2.16 3.37 0.93 11.71 29.10 19 GA/GC -1.21 -1.78 3.54 2.55 4.23 39.49 20 AG/CG -2.42 -3.04 3.11 15.13 4.65 49.43 21 GC/GC -0.28 -1.18 3.26 3.77 2.32 46.73 22 CU/AG -0.31 -1.38 3.61 -5.75 17.58 31.13 23 UC/GA 1.24 -2.36 2.45 7.68 -5.01 27.48 24 CA/UG -2.00 -1.05 3.34 4.54 2.68 55.40 25 AG/CU 2.29 -3.44 2.47 -6.76 -1.79 -57.65 26 GC/GC -0.23 2.52 3.49 6.98 15.27 144.46 27 CG/CG ---- ---- ---- ---- ---- ---- 28 GG/CC ---- ---- ---- ---- ---- ---- 29 GG/CC -0.51 -1.55 3.71 -19.48 7.38 26.87 30 GG/CC -0.13 -1.52 3.55 8.11 -2.15 39.91 31 GC/GC 1.19 -1.57 3.16 3.65 0.19 30.04 32 CG/CG 0.14 -1.57 3.37 -4.26 10.73 31.72 33 GG/CC 0.65 -1.74 3.52 7.48 14.31 34.58 34 GC/GC 1.08 -0.18 2.31 14.69 5.88 35.91 35 CG/CG -0.07 -1.80 3.75 -6.85 23.29 15.34 36 GU/AC -0.78 -2.02 3.31 -4.33 -1.73 42.71 37 UA/UA -0.08 -1.60 2.75 7.66 10.01 31.70 38 AG/CU 0.48 -1.97 2.94 -1.75 5.19 25.57 39 GG/CC 0.48 -2.55 3.78 6.12 6.07 26.39 40 GU/AC -2.26 -2.23 3.06 -2.78 1.74 94.70 41 UU/GA 0.96 -1.04 3.91 18.30 -1.33 50.01 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GC/GC -0.43 -2.23 3.17 -3.19 4.86 33.11 44 CG/CG -0.72 -2.12 3.30 -0.66 14.19 25.96 45 GA/UC -0.03 -1.48 3.35 -0.59 3.62 35.36 46 AG/CU 0.82 -2.41 3.62 7.90 12.46 25.33 47 GA/GC -0.76 -1.45 3.58 0.45 5.34 39.27 48 AG/CG -2.47 -2.84 3.16 18.13 3.87 51.38 49 GC/GC 0.01 -1.15 3.27 4.25 5.42 41.21 50 CU/AG 0.06 -1.52 3.58 -4.42 14.48 32.50 51 UC/GA 1.18 -2.43 2.39 4.88 -0.53 27.90 52 CA/UG -1.74 -0.96 3.04 11.12 -4.84 56.21 53 AG/CU 2.09 -3.22 2.99 -10.72 8.08 -59.44 54 GG/CC ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.05 -1.73 3.25 2.31 6.05 35.39 s.d. 1.11 0.89 0.40 8.62 6.68 28.79 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 GG/CC -2.93 -2.37 3.40 0.77 26.96 31.23 2 GG/CC -2.10 -0.01 3.30 1.56 -8.89 39.97 3 GC/GC -2.65 0.22 3.07 2.86 -14.75 33.95 4 CG/CG -3.68 -2.42 2.23 10.95 30.64 35.37 5 GG/CC -4.07 1.93 2.83 19.06 -26.97 45.11 6 GC/GC -0.58 -0.17 2.72 5.30 -25.39 34.02 7 CG/CG -6.51 -1.38 1.43 44.80 14.76 33.76 8 GU/AC -2.85 1.54 3.05 -0.26 -1.28 37.40 9 UA/UA -4.26 -0.88 2.34 11.73 -1.09 28.93 10 AG/CU -5.87 0.84 2.33 22.02 -12.72 32.63 11 GG/CC -5.75 -0.89 2.96 11.17 -4.61 27.33 12 GU/AC -1.54 1.81 3.00 0.07 -0.99 92.78 13 UU/GA -2.68 -1.36 3.48 2.70 -7.99 43.68 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GC/GC -3.89 1.10 3.19 -0.52 1.73 33.10 16 CG/CG -6.02 0.47 2.04 23.30 4.12 31.18 17 GA/UC -4.94 1.04 2.77 20.13 -11.85 33.94 18 AG/CU -6.01 -1.22 2.37 22.20 -1.77 31.34 19 GA/GC -3.12 2.09 3.26 6.22 -3.76 39.78 20 AG/CG -3.74 3.61 2.06 5.41 -17.57 51.75 21 GC/GC -1.66 0.66 3.17 2.91 -4.74 46.93 22 CU/AG -4.75 -0.32 2.52 29.70 9.72 36.09 23 UC/GA -3.76 -1.02 3.06 -10.19 -15.61 28.94 24 CA/UG -1.28 2.40 3.13 2.87 -4.87 55.63 25 AG/CU 3.62 2.08 2.60 1.85 -6.98 -58.03 26 GC/GC 1.24 0.15 3.59 8.01 -3.66 144.85 27 CG/CG ---- ---- ---- ---- ---- ---- 28 GG/CC ---- ---- ---- ---- ---- ---- 29 GG/CC -4.02 -2.70 2.91 13.58 35.87 33.88 30 GG/CC -1.92 1.16 3.53 -3.11 -11.72 40.75 31 GC/GC -3.05 -1.56 3.27 0.37 -7.00 30.25 32 CG/CG -4.37 -0.91 2.67 18.87 7.49 33.70 33 GG/CC -4.48 -0.05 2.70 22.61 -11.82 38.07 34 GC/GC -0.82 -0.25 2.49 9.02 -22.53 39.13 35 CG/CG -8.23 -1.21 0.58 55.80 16.42 28.65 36 GU/AC -2.59 0.62 3.45 -2.37 5.92 42.95 37 UA/UA -3.96 1.07 2.09 17.48 -13.39 34.05 38 AG/CU -5.52 -1.47 2.46 11.56 3.90 26.14 39 GG/CC -6.90 0.61 3.16 12.87 -12.97 27.74 40 GU/AC -1.55 1.49 3.08 1.18 1.89 94.74 41 UU/GA -1.06 0.39 4.03 -1.52 -20.86 53.07 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GC/GC -4.60 0.26 2.85 8.45 5.55 33.61 44 CG/CG -6.74 1.29 1.92 28.99 1.35 29.54 45 GA/UC -2.96 -0.03 3.18 5.95 0.97 35.54 46 AG/CU -7.42 0.05 2.35 25.80 -16.36 29.25 47 GA/GC -2.80 1.17 3.35 7.90 -0.66 39.62 48 AG/CG -3.30 3.60 2.04 4.30 -20.17 54.41 49 GC/GC -2.18 0.42 3.09 7.64 -5.98 41.76 50 CU/AG -4.57 -0.73 2.66 24.29 7.41 35.77 51 UC/GA -4.88 -1.54 2.60 -1.08 -10.01 28.32 52 CA/UG -0.76 2.35 2.75 -5.07 -11.65 57.40 53 AG/CU 2.78 1.53 3.66 -8.04 -10.66 -60.80 54 GG/CC ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -3.38 0.28 2.79 10.21 -3.60 37.53 s.d. 2.39 1.47 0.61 12.96 13.33 28.67 **************************************************************************** The 'simple' parameters are intuitive for non-Watson-Crick base pairs and associated base-pair steps (where the above corresponding 3DNA parameters often appear cryptic). Note that they are for structural *description* only, not to be fed into the 'rebuild' program. See URL http://x3dna.org/highlights/details-on-the-simple-base-pair-parameters and related blogposts on the 3DNA home page for details. This structure contains 13 non-Watson-Crick (with leading *) base pair(s) ---------------------------------------------------------------------------- Simple base-pair parameters based on RC8--YC6 vectors bp Shear Stretch Stagger Buckle Propeller Opening 1 G-C -1.35 0.08 -1.36 -5.55 -13.01 6.66 2 G-C -1.72 -0.36 -0.10 -12.10 -5.11 -8.16 3 G-C -0.66 -0.20 -0.28 -2.23 -17.59 -2.95 4 C-G 0.23 -0.31 -0.91 9.91 -21.85 4.34 5 G-C -0.00 -0.19 0.99 15.74 10.04 4.92 6 G-C 0.57 0.01 -1.07 -10.48 -26.38 -3.57 7 C-G 1.64 0.15 -1.41 29.55 -24.93 15.69 8 G-C -0.56 0.02 0.07 -9.71 -6.81 9.01 9 U-A 0.19 -0.15 0.16 -2.85 -0.51 0.77 10 A-U -0.41 -0.10 0.37 7.22 -4.95 7.58 11 G-C 0.18 -0.30 -0.45 -5.71 -9.14 -1.40 12 G-C -0.96 0.07 -0.39 -16.11 -1.34 -5.90 * 13 U-A 4.38 1.59 0.01 -11.36 1.46 -96.11 * 14 U+G 3.99 3.56 0.23 -16.63 2.04 -98.19 15 G-C -0.50 -0.14 0.31 0.17 -8.46 2.86 16 C-G 0.37 -0.23 0.03 5.42 -9.83 5.45 17 G-C -0.10 -0.18 0.19 2.60 -7.40 -1.34 18 A-U 0.06 -0.32 -0.62 -10.41 -11.95 0.80 19 G-C -0.60 -0.35 -0.05 -17.82 -22.73 -2.66 * 20 A-G 0.10 1.39 -0.17 -32.80 -28.90 -17.16 21 G-C -1.28 -0.08 0.08 -5.99 -1.13 -5.89 22 C-G 0.81 -0.17 -0.14 -2.41 -14.49 6.43 23 U-A -0.38 -0.07 1.05 -25.46 -1.86 -7.99 24 C-G 0.30 -0.42 0.34 1.08 -0.45 -6.06 * 25 A-U -4.42 1.53 -0.11 12.25 12.33 -101.52 * 26 G+C 3.43 1.16 0.87 15.45 2.50 151.63 * 27 C-G 8.21 1.48 2.14 -12.30 49.17 -15.97 28 G-C 0.06 0.02 -0.10 -30.25 -42.64 3.23 29 G-C -0.88 -0.31 -1.58 1.06 -20.54 13.01 * 30 G-C -2.19 -0.08 -0.01 -9.39 -5.91 -4.07 31 G-C -0.65 -0.48 -0.66 -4.70 -19.18 -10.99 32 C-G -0.19 -0.21 -0.65 7.69 -15.02 1.81 33 G-C 0.06 -0.25 0.01 4.00 -5.15 -0.15 34 G-C 0.19 -0.11 -0.57 -8.70 -24.74 -3.44 * 35 C-G 1.94 0.26 -1.42 35.16 -19.73 10.70 36 G-C -1.32 -0.28 0.07 -4.11 -16.98 8.06 37 U-A 0.13 0.02 0.59 -10.04 -0.85 -0.91 38 A-U 0.51 0.05 -0.25 -3.50 -1.38 5.66 39 G-C 0.30 -0.12 0.08 2.59 -7.21 1.15 40 G-C -0.77 -0.12 -0.63 -18.90 -6.03 -12.36 * 41 U-A 5.23 1.92 0.60 -15.08 7.89 -95.86 * 42 U+G 4.63 3.23 0.85 -29.49 -14.11 -115.65 43 G-C -0.02 0.11 -0.04 0.09 2.21 0.05 44 C-G 0.35 0.05 -0.06 0.45 -9.03 8.40 45 G-C -0.40 -0.11 -0.40 -10.95 -9.33 2.88 46 A-U 0.57 -0.22 -0.20 -8.75 -10.67 1.23 47 G-C -0.63 -0.08 -0.38 -22.65 -25.75 -1.18 * 48 A-G 0.01 1.67 -0.18 -36.36 -25.74 -10.24 49 G-C -0.96 -0.04 0.03 -4.04 -7.38 -3.49 50 C-G 0.34 -0.04 -0.18 -2.90 -15.49 6.15 51 U-A -0.43 -0.08 1.02 -24.40 1.39 -7.36 52 C-G 0.16 -0.44 0.78 -1.38 1.11 -5.67 * 53 A-U -4.49 1.41 0.42 11.71 13.73 -99.49 * 54 G+C 3.70 1.21 0.37 18.34 -3.70 157.42 55 G-C 0.48 0.60 0.04 -34.47 -31.59 12.13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.31 0.27 -0.05 -5.45 -8.60 -5.41 s.d. 2.10 0.88 0.67 14.80 14.04 45.21 ---------------------------------------------------------------------------- Simple base-pair step parameters based on consecutive C1'-C1' vectors step Shift Slide Rise Tilt Roll Twist 1 GG/CC -0.57 -1.46 3.63 -13.82 2.36 29.41 2 GG/CC 0.34 -1.39 3.30 6.14 0.41 34.20 3 GC/GC 0.60 -1.41 3.08 8.56 1.46 28.54 4 CG/CG 0.10 -1.74 3.02 -17.77 6.17 30.72 5 GG/CC 0.13 -2.03 3.98 19.24 14.56 35.09 6 GC/GC 1.22 0.01 2.45 14.02 4.42 26.39 7 CG/CG 0.19 -1.69 3.75 -8.69 23.00 34.15 8 GU/AC -0.95 -1.82 3.07 0.82 -0.18 33.33 9 UA/UA 0.47 -1.63 2.70 0.60 5.82 31.85 10 AG/CU 0.12 -2.22 3.40 7.08 11.91 26.28 11 GG/CC 0.60 -2.14 3.38 2.34 5.16 32.58 * 12 GU/AC -2.15 -2.65 3.04 1.39 0.36 62.19 * 13 UU/GA 2.30 0.44 3.41 0.96 6.18 -30.38 * 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GC/GC -0.74 -2.24 3.15 -0.99 -0.29 28.23 16 CG/CG -0.41 -2.21 3.10 -2.31 12.17 31.31 17 GA/UC 0.04 -1.79 3.63 6.75 11.45 30.12 18 AG/CU 0.71 -2.17 3.37 1.10 11.70 31.84 * 19 GA/GC -1.20 -1.78 3.54 2.53 4.24 34.69 * 20 AG/CG -2.53 -2.96 3.11 15.28 4.13 58.61 21 GC/GC -0.30 -1.17 3.26 3.81 2.25 35.49 22 CU/AG -0.28 -1.39 3.61 -6.17 17.44 37.79 23 UC/GA 1.24 -2.36 2.45 7.66 -5.03 23.88 * 24 CA/UG -2.18 -0.60 3.34 5.01 1.64 83.49 * 25 AG/CU -1.93 -3.65 2.47 -4.80 5.09 12.44 * 26 GC/GC 0.71 2.43 3.49 12.10 11.64 -5.55 * 27 CG/CG ---- ---- ---- ---- ---- ---- 28 GG/CC ---- ---- ---- ---- ---- ---- * 29 GG/CC -0.73 -1.46 3.71 -18.21 10.12 33.18 * 30 GG/CC -0.32 -1.49 3.55 7.77 -3.17 31.69 31 GC/GC 1.13 -1.62 3.16 3.65 0.05 27.91 32 CG/CG 0.13 -1.57 3.37 -4.16 10.77 30.51 33 GG/CC 0.67 -1.73 3.52 7.32 14.40 33.39 * 34 GC/GC 1.09 -0.08 2.31 14.08 7.22 27.75 * 35 CG/CG -0.04 -1.80 3.75 -7.30 23.15 31.99 36 GU/AC -0.89 -1.98 3.31 -4.42 -1.48 34.77 37 UA/UA -0.03 -1.60 2.75 7.35 10.24 29.56 38 AG/CU 0.56 -1.95 2.94 -1.95 5.12 26.92 39 GG/CC 0.43 -2.56 3.78 6.24 5.95 31.59 * 40 GU/AC -1.66 -2.71 3.06 -3.12 1.03 59.59 * 41 UU/GA 1.35 0.43 3.91 8.94 16.02 -17.21 * 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GC/GC -0.39 -2.24 3.17 -3.27 4.81 30.75 44 CG/CG -0.72 -2.12 3.30 -0.67 14.19 30.12 45 GA/UC -0.02 -1.48 3.35 -0.63 3.62 30.10 46 AG/CU 0.85 -2.40 3.62 7.79 12.52 30.79 * 47 GA/GC -0.76 -1.45 3.58 0.46 5.34 35.03 * 48 AG/CG -2.54 -2.77 3.16 18.22 3.39 58.41 49 GC/GC -0.02 -1.15 3.27 4.38 5.31 34.09 50 CU/AG 0.05 -1.52 3.58 -4.37 14.49 37.11 51 UC/GA 1.15 -2.45 2.39 4.87 -0.60 24.52 * 52 CA/UG -1.91 -0.55 3.04 9.77 -7.19 83.59 * 53 AG/CU -1.80 -3.39 2.99 1.86 13.29 9.42 * 54 GG/CC ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.18 -1.66 3.25 2.36 6.67 31.88 s.d. 1.10 1.03 0.40 8.09 6.73 19.06 **************************************************************************** Structure classification: This is a right-handed nucleic acid structure **************************************************************************** lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the base-pair C1'-C1' line C1'-C1': distance between C1' atoms for each base-pair RN9-YN1: distance between RN9-YN1 atoms for each base-pair RC8-YC6: distance between RC8-YC6 atoms for each base-pair bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6 1 G-C 50.3 63.4 10.7 9.1 10.1 2 G-C 41.7 58.1 10.6 8.7 9.4 3 G-C 48.8 54.1 10.8 9.0 9.8 4 C-G 56.4 55.1 10.4 8.8 9.7 5 G-C 57.5 56.2 10.4 8.8 9.8 6 G-C 55.3 46.9 11.1 9.2 10.0 7 C-G 68.8 52.6 10.2 8.8 9.9 8 G-C 56.1 61.6 10.4 8.8 10.0 9 U-A 55.8 54.1 10.5 8.8 9.8 10 A-U 56.0 60.9 10.2 8.7 9.8 11 G-C 55.0 51.6 10.6 8.8 9.7 12 G-C 45.5 55.3 11.0 9.2 10.0 13 U-A 32.7 18.2 10.1 7.5 6.6 14 U+G 103.7 25.0 9.2 8.5 9.9 15 G-C 53.5 56.6 10.6 8.9 9.9 16 C-G 58.7 55.1 10.3 8.7 9.8 17 G-C 53.9 53.7 10.7 8.9 9.8 18 A-U 56.1 54.2 10.3 8.7 9.6 19 G-C 49.7 53.9 10.5 8.7 9.6 20 A-G 52.4 45.9 12.2 10.3 10.7 21 G-C 43.4 57.1 10.9 9.1 9.8 22 C-G 60.1 53.1 10.4 8.7 9.8 23 U-A 51.6 52.3 10.7 8.9 9.7 24 C-G 52.5 50.4 10.6 8.8 9.6 25 A-U 22.5 30.0 9.5 7.0 6.1 26 G+C 33.6 61.6 10.4 8.8 10.2 27 C-G 88.1 27.2 7.5 6.3 6.3 28 G-C 59.2 49.9 10.4 8.7 9.7 29 G-C 55.0 63.5 10.2 8.7 9.8 30 G-C 40.6 62.2 10.7 8.9 9.7 31 G-C 44.3 49.5 10.8 8.8 9.5 32 C-G 52.1 56.0 10.6 8.9 9.8 33 G-C 56.0 54.0 10.5 8.8 9.8 34 G-C 54.2 49.0 10.9 9.1 9.9 35 C-G 68.8 49.6 10.3 8.9 9.8 36 G-C 51.5 64.9 10.1 8.5 9.6 37 U-A 55.6 53.3 10.7 9.0 9.9 38 A-U 60.5 55.0 10.5 8.9 10.0 39 G-C 56.3 52.1 10.7 8.9 9.9 40 G-C 44.3 51.7 11.0 9.1 9.7 41 U-A 38.5 21.5 9.1 6.8 6.0 42 U+G 94.4 33.3 9.2 8.4 10.1 43 G-C 55.1 53.2 10.9 9.2 10.1 44 C-G 59.5 57.4 10.5 8.9 10.0 45 G-C 54.3 57.0 10.5 8.9 9.9 46 A-U 58.9 51.7 10.4 8.7 9.7 47 G-C 50.9 54.2 10.7 8.9 9.8 48 A-G 54.7 48.6 12.2 10.4 11.0 49 G-C 47.2 57.0 10.9 9.1 9.9 50 C-G 57.8 54.8 10.5 8.9 10.0 51 U-A 51.6 52.7 10.7 8.9 9.7 52 C-G 51.6 51.4 10.6 8.8 9.6 53 A-U 20.6 30.4 9.5 6.9 6.0 54 G+C 37.3 58.9 10.4 8.7 10.2 55 G-C 68.4 54.1 10.3 8.9 10.1 **************************************************************************** Classification of each dinucleotide step in a right-handed nucleic acid structure: A-like; B-like; TA-like, or other cases. step Xp Yp Zp XpH YpH ZpH Form 1 GG/CC -1.55 8.45 1.93 -4.31 8.43 2.42 A 2 GG/CC -1.61 8.44 2.07 -3.47 8.39 2.09 A 3 GC/GC -1.63 8.68 1.57 -4.19 8.60 1.95 A 4 CG/CG -1.73 8.47 2.47 -4.64 7.92 3.32 A 5 GG/CC -1.81 8.02 3.01 -5.38 6.70 5.20 A 6 GC/GC -2.02 8.70 0.39 -2.34 8.62 1.45 7 CG/CG -2.26 7.74 2.80 -8.24 3.81 6.98 A 8 GU/AC -1.92 7.86 2.94 -4.61 7.87 2.91 A 9 UA/UA -1.60 8.15 2.83 -5.72 7.43 4.39 A 10 AG/CU -1.80 8.12 2.86 -7.38 6.54 5.53 A 11 GG/CC -1.66 8.00 2.77 -7.19 7.34 4.17 A 12 GU/AC -0.23 7.37 3.16 -1.27 7.37 3.20 13 UU/GA 3.83 4.28 -0.31 1.04 4.28 0.35 14 UG/CG --- --- --- --- --- --- --- 15 GC/GC -1.87 8.15 2.66 -5.59 8.17 2.59 A 16 CG/CG -1.72 8.48 2.81 -7.50 6.76 5.83 A 17 GA/UC -1.51 8.29 2.52 -6.16 7.00 5.04 A 18 AG/CU -2.24 8.52 1.94 -8.00 7.22 4.91 A 19 GA/GC -1.28 8.41 2.48 -4.10 8.11 3.31 20 AG/CG -2.15 6.66 4.42 -5.51 6.28 4.37 21 GC/GC -1.68 8.20 2.48 -3.18 8.08 2.82 A 22 CU/AG -1.50 8.14 2.85 -6.14 5.82 6.29 A 23 UC/GA -1.24 8.45 2.88 -4.56 8.80 1.20 24 CA/UG -1.77 8.37 2.18 -2.93 8.26 2.75 25 AG/CU 2.79 1.58 2.18 5.82 1.53 1.54 26 GC/GC -0.40 8.14 2.08 -0.05 8.04 2.38 27 CG/CG --- --- --- --- --- --- --- 28 GG/CC --- --- --- --- --- --- --- 29 GG/CC -1.93 8.30 1.73 -5.48 7.63 3.90 A 30 GG/CC -1.38 8.61 2.02 -3.02 8.69 1.29 A 31 GC/GC -1.18 8.77 1.48 -4.10 8.76 1.49 32 CG/CG -1.64 8.62 2.17 -5.75 7.52 4.69 A 33 GG/CC -1.70 8.32 2.37 -5.90 6.85 5.30 A 34 GC/GC -2.05 8.70 0.66 -2.73 8.49 2.18 35 CG/CG -2.05 7.91 2.77 -9.67 2.40 7.72 A 36 GU/AC -2.14 7.72 3.15 -4.58 7.84 2.85 A 37 UA/UA -1.47 8.26 2.87 -5.10 7.09 5.07 A 38 AG/CU -1.67 8.38 2.57 -7.04 7.72 4.14 A 39 GG/CC -1.73 7.89 2.94 -8.29 7.09 4.36 A 40 GU/AC 0.02 7.32 3.06 -1.06 7.28 3.10 41 UU/GA 3.77 3.99 -0.35 2.01 4.00 0.82 42 UG/CG --- --- --- --- --- --- --- 43 GC/GC -1.70 7.99 2.77 -6.07 7.52 3.87 A 44 CG/CG -1.71 8.27 2.56 -8.23 6.08 6.16 A 45 GA/UC -1.43 8.31 2.30 -4.25 8.04 3.11 A 46 AG/CU -2.21 8.61 1.98 -9.02 6.99 5.23 A 47 GA/GC -1.52 8.56 2.21 -4.13 8.20 3.30 48 AG/CG -2.31 6.76 4.35 -5.23 6.47 4.13 49 GC/GC -1.56 8.23 2.49 -3.57 7.86 3.46 A 50 CU/AG -1.69 8.18 2.88 -6.14 6.39 5.83 A 51 UC/GA -1.26 8.27 3.22 -5.79 8.33 2.94 52 CA/UG -1.62 8.38 2.02 -2.38 8.53 1.79 53 AG/CU 2.66 1.62 2.00 4.90 1.79 0.73 54 GG/CC --- --- --- --- --- --- --- **************************************************************************** Minor and major groove widths: direct P-P distances and refined P-P distances which take into account the directions of the sugar-phosphate backbones (Subtract 5.8 Angstrom from the values to take account of the vdw radii of the phosphate groups, and for comparison with FreeHelix and Curves.) Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343. Minor Groove Major Groove P-P Refined P-P Refined 1 GG/CC --- --- --- --- 2 GG/CC --- --- --- --- 3 GC/GC 16.5 --- 18.2 --- 4 CG/CG 16.7 15.3 18.2 15.8 5 GG/CC 17.9 16.0 16.1 12.3 6 GC/GC 17.9 16.2 16.0 12.4 7 CG/CG 16.6 15.0 17.0 14.3 8 GU/AC 16.4 14.9 17.7 16.0 9 UA/UA 17.0 15.6 15.2 11.1 10 AG/CU 16.6 15.2 15.4 12.9 11 GG/CC 15.9 --- 15.7 --- 12 GU/AC --- --- --- --- 13 UU/GA --- --- --- --- 14 UG/CG --- --- --- --- 15 GC/GC --- --- --- --- 16 CG/CG --- --- --- --- 17 GA/UC 16.6 --- 16.3 --- 18 AG/CU 18.0 14.7 15.7 10.0 19 GA/GC 18.3 14.1 14.8 12.0 20 AG/CG 16.8 14.3 15.0 13.9 21 GC/GC 16.8 15.2 11.8 11.8 22 CU/AG 17.2 16.1 15.3 10.9 23 UC/GA 16.8 15.5 8.8 8.7 24 CA/UG 16.2 --- 18.8 --- 25 AG/CU --- --- --- --- 26 GC/GC --- --- --- --- 27 CG/CG --- --- --- --- 28 GG/CC --- --- --- --- 29 GG/CC --- --- --- --- 30 GG/CC --- --- --- --- 31 GC/GC 16.7 --- 18.5 --- 32 CG/CG 16.9 15.4 18.3 15.6 33 GG/CC 18.0 16.2 16.3 12.5 34 GC/GC 18.1 16.4 16.3 11.8 35 CG/CG 16.3 14.8 16.6 13.5 36 GU/AC 15.9 14.5 17.7 16.2 37 UA/UA 16.7 15.6 15.2 10.9 38 AG/CU 16.7 15.5 15.6 12.9 39 GG/CC 16.0 --- 15.9 --- 40 GU/AC --- --- --- --- 41 UU/GA --- --- --- --- 42 UG/CG --- --- --- --- 43 GC/GC --- --- --- --- 44 CG/CG --- --- --- --- 45 GA/UC 16.6 --- 16.3 --- 46 AG/CU 18.0 14.7 15.6 10.2 47 GA/GC 18.5 14.3 14.8 12.0 48 AG/CG 17.0 14.5 14.8 13.6 49 GC/GC 16.9 15.3 11.8 11.8 50 CU/AG 17.2 16.0 15.6 11.1 51 UC/GA 16.8 --- 8.9 --- 52 CA/UG --- --- --- --- 53 AG/CU --- --- --- --- 54 GG/CC --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 0.07(5.90) **************************************************************************** Main chain and chi torsion angles: Note: alpha: O3'(i-1)-P-O5'-C5' beta: P-O5'-C5'-C4' gamma: O5'-C5'-C4'-C3' delta: C5'-C4'-C3'-O3' epsilon: C4'-C3'-O3'-P(i+1) zeta: C3'-O3'-P(i+1)-O5'(i+1) chi for pyrimidines(Y): O4'-C1'-N1-C2 chi for purines(R): O4'-C1'-N9-C4 Strand I base alpha beta gamma delta epsilon zeta chi 1 G --- -113.4 70.2 82.9 174.9 -72.3 -149.4 2 G 158.9 -156.4 176.3 86.6 -110.7 -100.5 166.0 3 G 116.7 -141.9 -168.9 84.7 -134.4 -72.2 -168.8 4 C -50.4 167.5 48.1 78.6 -155.4 -74.4 -144.5 5 G -60.4 175.3 44.3 81.0 -152.6 -71.3 -166.6 6 G -64.7 174.0 57.2 84.1 -138.9 -86.6 -161.0 7 C -44.8 160.3 62.6 110.9 -80.1 -62.9 -109.5 8 G 91.9 174.6 51.2 81.6 -136.1 -84.4 175.1 9 U -58.1 176.1 47.7 81.7 -156.1 -67.6 -163.1 10 A -61.2 -179.5 42.2 79.7 -161.9 -89.3 -158.6 11 G 153.5 -142.8 173.0 85.1 -101.0 -66.7 173.9 12 G -101.3 100.8 133.3 84.2 -129.0 -72.6 160.9 13 U -65.5 -172.4 39.6 82.3 -139.3 -70.2 -157.8 14 U -52.4 167.4 48.7 81.6 -131.3 -71.3 -157.3 15 G -47.0 125.9 41.7 73.7 -152.7 -79.1 179.3 16 C -62.8 -177.1 48.9 81.1 -149.4 -72.8 -161.6 17 G -66.5 174.3 50.6 76.3 -157.6 -70.1 -167.2 18 A -61.2 177.1 55.8 83.6 -169.3 -35.7 -160.5 19 G -178.5 151.5 165.4 84.6 -145.6 -79.4 -176.4 20 A -54.2 169.7 51.0 82.2 -141.7 -64.2 -160.5 21 G 57.9 -145.7 127.3 87.5 -130.9 -71.4 164.6 22 C -71.1 -175.2 49.0 84.7 -154.0 -64.5 -153.2 23 U -69.2 -176.6 44.9 78.2 -170.1 -53.6 -168.9 24 C 159.4 -170.7 -180.0 83.1 -169.9 -69.1 -169.9 25 A 157.3 -178.2 -178.9 80.3 -123.9 -69.9 166.9 26 G -54.1 160.4 54.6 88.7 -136.9 -60.9 -163.2 27 C -108.7 -137.8 68.2 105.2 -60.3 91.4 -98.3 28 G -73.4 -85.5 -130.8 96.8 157.9 -86.2 -127.7 29 G --- -115.8 67.8 83.6 177.9 -74.8 -140.9 30 G 164.8 -162.7 169.3 87.5 -101.9 -80.1 169.2 31 G 45.1 -129.0 -98.8 93.6 -163.2 -53.0 -153.3 32 C 156.7 -173.6 172.1 83.8 -132.8 -71.7 -159.1 33 G -54.6 170.2 39.6 77.6 -150.4 -71.7 -160.3 34 G -62.7 166.9 60.9 80.9 -130.0 -89.6 -165.1 35 C -43.1 158.5 57.9 109.4 -64.5 -78.7 -109.8 36 G 48.4 168.0 48.8 81.0 -140.9 -78.0 178.0 37 U -58.3 179.0 44.0 81.8 -158.0 -64.7 -170.6 38 A -75.1 -169.7 46.5 82.5 -169.2 -88.5 -154.5 39 G 149.0 -139.7 173.5 84.5 -104.2 -56.3 173.7 40 G -104.1 94.2 148.7 86.6 -113.3 -74.8 159.5 41 U -65.4 172.7 48.3 84.7 -139.8 -75.6 -165.0 42 U -72.5 169.7 55.3 86.8 -142.9 -55.5 -161.0 43 G -53.1 130.1 39.7 75.4 -169.4 -64.8 -178.5 44 C -79.1 -158.1 48.9 83.5 -165.5 -64.2 -162.6 45 G -82.6 -166.8 54.0 80.8 -163.5 -66.1 -167.4 46 A -63.3 -178.5 54.4 86.1 -169.6 -60.1 -160.1 47 G 157.2 -172.3 -179.9 82.5 -146.6 -78.8 -175.2 48 A -60.6 169.7 54.2 82.4 -136.6 -68.7 -163.5 49 G 88.9 -142.7 90.7 88.1 -141.8 -75.1 179.5 50 C -68.0 179.0 52.3 84.2 -148.8 -63.3 -156.8 51 U -69.1 -176.7 47.0 76.7 -173.2 -50.3 -168.4 52 C 154.7 -178.7 -176.8 83.9 -174.0 -48.8 -174.2 53 A 176.7 160.6 167.7 85.3 -126.7 -67.0 175.4 54 G -57.4 164.3 54.8 91.2 -149.6 -62.3 -154.0 55 G -173.0 -115.2 171.1 87.0 -136.0 -162.5 -142.3 Strand II base alpha beta gamma delta epsilon zeta chi 1 C -59.4 168.1 50.0 80.9 -139.3 -77.2 -150.0 2 C -48.1 155.1 46.0 80.9 -148.4 -77.2 -161.5 3 C 158.9 -162.8 170.4 86.5 -122.8 -88.5 -173.6 4 G -57.1 171.9 48.9 80.4 178.8 -77.9 -149.6 5 C -56.1 170.8 39.7 81.8 -151.4 -69.7 178.4 6 C 88.6 -101.7 -174.4 89.7 -110.8 -84.0 -178.5 7 G -61.1 168.2 48.8 82.9 -104.4 -137.5 -171.4 8 C -50.8 154.9 52.2 82.8 -150.5 -84.3 -168.0 9 A 155.8 -145.0 162.1 86.1 -125.9 -81.8 178.0 10 U -61.8 -169.2 40.8 82.8 -164.1 -97.1 -164.5 11 C -58.6 -176.1 41.7 82.9 -155.8 -60.4 -163.9 12 C -69.4 177.3 41.6 85.9 -155.4 -73.0 -168.6 13 A -77.1 -139.0 62.7 97.7 21.1 65.1 -84.2 14 G 64.2 177.0 -73.0 92.4 61.9 140.1 -110.5 15 C 165.2 -174.7 169.2 85.4 -132.6 -71.8 -173.9 16 G 41.2 -159.9 -76.9 96.2 -169.7 -50.6 -159.4 17 C -59.3 165.8 53.4 77.6 -134.1 -83.5 -171.0 18 U -61.6 -176.2 40.2 81.0 -145.1 -75.0 -153.6 19 C -56.0 172.9 49.7 81.0 -144.5 -76.2 -164.4 20 G -63.6 174.1 50.9 81.3 -142.8 -67.1 -160.4 21 C -57.1 156.7 55.0 79.9 -147.1 -67.3 -169.0 22 G -84.8 -179.6 61.5 84.0 -133.7 -78.0 -164.8 23 A -59.7 177.6 52.5 83.2 -156.4 -70.9 -158.8 24 G 108.4 -173.7 -164.6 82.9 -163.5 -77.0 -171.1 25 U -78.9 -139.4 56.2 85.7 -147.4 -159.3 -154.1 26 C -123.0 -144.8 67.3 89.1 76.5 -148.1 -129.0 27 G 173.6 -120.0 -65.8 84.6 -166.6 30.8 -5.9 28 C 163.0 167.4 52.5 81.4 -141.9 -55.5 -164.2 29 C -57.6 177.0 45.3 81.5 -151.1 -64.7 -144.2 30 C -55.6 155.3 53.3 79.5 -143.9 -77.9 -168.2 31 C 163.4 -165.3 170.2 88.4 -123.3 -81.7 -171.8 32 G -63.5 -178.4 42.6 79.3 178.0 -77.7 -153.7 33 C -70.0 173.6 48.0 82.5 -156.8 -66.4 -164.4 34 C 112.3 -112.9 178.7 88.4 -121.2 -80.4 -176.0 35 G -44.9 148.2 51.9 81.7 -117.0 -132.0 -178.3 36 C -48.3 173.5 36.3 79.4 -141.2 -93.7 -162.5 37 A 150.1 -141.2 168.3 85.9 -133.7 -67.5 171.8 38 U -72.1 -164.6 43.0 79.9 -167.1 -92.4 -152.2 39 C -64.7 -163.1 44.1 85.1 -159.6 -61.0 -166.6 40 C -62.0 154.8 39.8 83.3 -159.3 -66.6 -168.8 41 A 27.6 101.9 55.5 97.9 -62.9 -162.2 -113.7 42 G 61.9 -166.0 -65.5 86.6 -179.4 -100.3 -119.1 43 C 174.6 -167.7 163.7 87.9 -112.3 -84.7 -178.0 44 G -63.0 -175.1 39.9 75.8 -171.0 -74.5 -159.9 45 C -59.7 -178.9 40.4 79.9 -153.8 -62.6 -151.8 46 U -62.5 -166.3 36.4 80.6 -156.4 -66.4 -155.7 47 C -61.3 179.0 46.8 82.1 -152.6 -68.1 -155.8 48 G -68.3 178.7 52.9 84.4 -148.5 -63.8 -158.3 49 C -59.3 160.1 53.4 81.5 -149.3 -65.5 -167.9 50 G -78.5 -173.6 50.7 85.5 -139.4 -77.7 -161.4 51 A -43.9 162.4 48.1 83.8 -161.0 -68.1 -162.9 52 G 97.8 -165.4 -166.4 83.9 -150.2 -91.6 -176.4 53 U -67.0 -146.5 51.7 85.3 -162.6 -170.0 -156.8 54 C -95.9 -152.1 72.2 103.0 174.7 135.8 -136.5 55 C 153.8 152.6 55.7 87.4 -131.1 -71.6 -169.1 **************************************************************************** Sugar conformational parameters: Note: v0: C4'-O4'-C1'-C2' v1: O4'-C1'-C2'-C3' v2: C1'-C2'-C3'-C4' v3: C2'-C3'-C4'-O4' v4: C3'-C4'-O4'-C1' tm: the amplitude of pucker P: the phase angle of pseudorotation Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 G -1.6 -22.9 37.3 -39.2 25.7 39.9 20.8 C3'-endo 2 G 0.9 -22.8 34.7 -35.4 21.8 36.4 17.4 C3'-endo 3 G 10.6 -32.4 40.9 -35.9 15.9 41.0 4.0 C3'-endo 4 C -2.2 -23.7 39.1 -41.4 27.4 42.0 21.5 C3'-endo 5 G 3.7 -26.9 38.7 -37.7 21.3 39.7 13.4 C3'-endo 6 G 3.9 -27.8 39.6 -38.5 21.8 40.7 13.2 C3'-endo 7 C -7.9 -5.8 16.1 -21.3 18.4 21.1 40.2 C4'-exo 8 G 10.5 -32.6 41.2 -36.1 16.3 41.3 4.2 C3'-endo 9 U 8.3 -30.5 40.0 -36.3 17.7 40.4 7.0 C3'-endo 10 A 6.1 -30.1 41.6 -39.1 20.8 42.3 10.4 C3'-endo 11 G 6.3 -27.9 37.8 -35.4 18.2 38.3 9.5 C3'-endo 12 G 6.5 -26.8 36.0 -33.3 16.9 36.4 8.7 C3'-endo 13 U 7.6 -30.5 40.6 -37.4 18.7 41.0 8.2 C3'-endo 14 U 3.7 -27.7 40.1 -38.9 22.2 41.2 13.5 C3'-endo 15 G -5.5 -21.7 39.3 -43.4 30.8 43.6 25.6 C3'-endo 16 C 2.0 -26.2 39.1 -39.0 23.5 40.7 15.9 C3'-endo 17 G -1.1 -26.2 42.1 -43.7 28.3 44.8 19.9 C3'-endo 18 A -0.5 -22.3 35.5 -36.8 23.5 37.7 19.4 C3'-endo 19 G 2.7 -24.9 36.4 -35.9 20.9 37.6 14.6 C3'-endo 20 A 0.1 -23.1 36.1 -37.3 23.4 38.1 18.6 C3'-endo 21 G 8.6 -28.7 36.7 -33.0 15.4 36.9 5.6 C3'-endo 22 C 12.5 -34.1 41.6 -35.3 14.5 41.6 1.4 C3'-endo 23 U 2.8 -27.8 40.9 -40.2 23.7 42.3 14.8 C3'-endo 24 C -1.9 -20.9 34.5 -36.7 24.3 37.1 21.6 C3'-endo 25 A -4.8 -20.7 37.4 -40.9 28.5 41.2 24.9 C3'-endo 26 G 2.1 -22.6 33.2 -33.1 19.7 34.4 15.4 C3'-endo 27 C 8.0 -20.9 25.1 -21.4 8.5 25.1 0.7 C3'-endo 28 G 19.2 -33.6 34.4 -24.4 3.5 35.3 346.8 C2'-exo 29 G -2.5 -20.6 34.3 -36.8 24.8 37.1 22.4 C3'-endo 30 G 0.6 -21.8 33.3 -34.1 21.3 35.0 17.9 C3'-endo 31 G 19.8 -36.0 37.5 -27.3 4.8 38.2 348.3 C2'-exo 32 C 8.7 -28.7 37.0 -33.2 15.5 37.2 5.7 C3'-endo 33 G 0.3 -25.9 40.3 -41.3 25.7 42.4 18.3 C3'-endo 34 G 1.8 -26.5 39.7 -39.9 24.0 41.3 16.2 C3'-endo 35 C -5.8 -8.9 18.9 -23.1 18.3 22.7 33.4 C3'-endo 36 G 4.3 -27.7 39.2 -37.7 21.2 40.1 12.6 C3'-endo 37 U 6.6 -28.9 38.9 -36.1 18.6 39.4 9.1 C3'-endo 38 A 4.2 -26.7 37.8 -36.4 20.3 38.8 12.5 C3'-endo 39 G 6.4 -28.6 38.9 -36.3 18.8 39.4 9.5 C3'-endo 40 G 8.9 -27.9 35.2 -31.3 14.2 35.3 4.6 C3'-endo 41 U 2.1 -24.4 36.2 -36.2 21.5 37.6 15.6 C3'-endo 42 U 4.0 -26.4 37.4 -36.2 20.3 38.4 12.7 C3'-endo 43 G -4.3 -21.9 38.4 -41.9 29.1 42.1 24.3 C3'-endo 44 C 5.5 -29.8 41.4 -39.2 21.2 42.2 11.1 C3'-endo 45 G -0.8 -25.6 40.9 -42.2 27.1 43.4 19.4 C3'-endo 46 A 1.3 -23.6 35.6 -36.0 21.8 37.2 16.7 C3'-endo 47 G -2.9 -20.9 35.5 -38.1 25.8 38.5 22.7 C3'-endo 48 A 1.7 -25.0 37.5 -37.7 22.7 39.1 16.3 C3'-endo 49 G 6.2 -28.2 38.3 -35.8 18.7 38.9 9.7 C3'-endo 50 C 11.6 -33.9 42.1 -36.2 15.6 42.2 2.8 C3'-endo 51 U -2.4 -23.6 39.0 -41.3 27.7 42.0 21.7 C3'-endo 52 C 2.0 -24.8 36.8 -36.8 22.0 38.2 15.7 C3'-endo 53 A -3.1 -19.3 33.3 -36.0 24.4 36.3 23.3 C3'-endo 54 G -0.5 -19.3 30.3 -31.9 20.5 32.2 19.7 C3'-endo 55 G -17.5 -5.6 25.0 -36.0 33.5 36.4 46.6 C4'-exo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 C 7.7 -31.2 41.6 -38.1 19.3 42.0 8.2 C3'-endo 2 C 4.2 -27.0 38.3 -37.1 20.8 39.3 12.7 C3'-endo 3 C 10.6 -29.6 36.6 -31.7 13.3 36.7 2.5 C3'-endo 4 G -5.3 -19.6 35.7 -39.7 28.3 39.7 26.1 C3'-endo 5 C -1.3 -22.6 36.6 -38.5 25.1 39.1 20.5 C3'-endo 6 C 8.6 -28.0 35.9 -32.0 14.6 36.0 5.2 C3'-endo 7 G 0.5 -25.1 38.9 -39.7 24.6 40.9 17.9 C3'-endo 8 C -3.3 -20.6 35.2 -38.3 26.3 38.5 23.6 C3'-endo 9 A 6.7 -26.7 35.6 -33.0 16.5 36.0 8.4 C3'-endo 10 U 1.3 -23.1 35.0 -35.4 21.5 36.6 16.8 C3'-endo 11 C 5.5 -27.2 37.5 -35.4 18.9 38.1 10.5 C3'-endo 12 C 8.4 -28.8 37.0 -33.3 15.8 37.2 6.0 C3'-endo 13 A -4.0 -12.9 23.6 -26.8 19.4 26.5 27.2 C3'-endo 14 G -13.0 -2.1 15.1 -23.2 22.5 23.8 50.5 C4'-exo 15 C 10.1 -30.6 38.8 -34.0 15.1 38.9 4.0 C3'-endo 16 G 22.9 -39.7 40.7 -28.5 3.5 41.9 346.3 C2'-exo 17 C 0.1 -25.6 39.8 -40.7 25.9 42.0 18.5 C3'-endo 18 U 2.3 -25.7 37.9 -37.7 22.4 39.3 15.4 C3'-endo 19 C -0.6 -23.1 36.8 -38.2 24.5 39.1 19.6 C3'-endo 20 G 1.5 -26.1 39.4 -39.6 23.9 41.1 16.5 C3'-endo 21 C 2.3 -28.6 42.6 -42.2 25.2 44.3 15.5 C3'-endo 22 G 1.7 -25.4 38.4 -38.5 23.1 40.0 16.3 C3'-endo 23 A 2.2 -25.2 37.4 -37.1 21.9 38.8 15.3 C3'-endo 24 G -2.8 -22.0 37.3 -39.7 26.6 40.3 22.4 C3'-endo 25 U 9.0 -31.5 40.6 -36.3 17.3 40.8 6.0 C3'-endo 26 C -0.0 -16.0 24.9 -26.0 16.3 26.3 19.0 C3'-endo 27 G 13.2 -35.6 43.1 -36.4 14.8 43.1 1.0 C3'-endo 28 C 0.8 -24.3 37.2 -37.7 23.3 39.0 17.5 C3'-endo 29 C 9.1 -31.8 41.3 -37.0 17.7 41.6 6.2 C3'-endo 30 C 8.0 -30.8 40.9 -37.4 18.6 41.3 7.8 C3'-endo 31 C 12.8 -31.7 37.6 -31.5 11.8 37.6 359.4 C2'-exo 32 G -1.6 -23.4 38.2 -40.1 26.4 40.8 20.9 C3'-endo 33 C -4.4 -20.7 36.5 -40.1 27.9 40.2 24.7 C3'-endo 34 C 5.4 -26.2 36.1 -34.1 18.0 36.7 10.5 C3'-endo 35 G -4.1 -20.9 36.7 -40.2 27.8 40.3 24.4 C3'-endo 36 C 2.4 -26.2 38.6 -38.5 22.8 40.1 15.4 C3'-endo 37 A 8.0 -27.6 35.7 -32.3 15.3 36.0 6.3 C3'-endo 38 U 3.0 -26.2 38.2 -37.5 21.8 39.4 14.4 C3'-endo 39 C 8.5 -29.5 38.2 -34.4 16.3 38.4 6.1 C3'-endo 40 C 6.4 -27.9 37.4 -34.8 17.9 37.9 9.1 C3'-endo 41 A -26.9 7.1 13.8 -29.7 35.4 35.0 66.9 C4'-exo 42 G -1.4 -21.3 34.6 -36.5 23.8 37.0 20.8 C3'-endo 43 C 13.6 -33.3 39.3 -32.7 12.1 39.4 359.0 C2'-exo 44 G 3.4 -29.4 42.9 -41.9 24.4 44.3 14.3 C3'-endo 45 C 6.1 -29.4 40.3 -37.8 20.0 40.9 10.2 C3'-endo 46 U 1.9 -25.5 37.9 -38.0 22.8 39.4 16.0 C3'-endo 47 C -0.1 -23.3 36.4 -37.6 23.8 38.4 18.9 C3'-endo 48 G 5.0 -27.2 37.8 -36.0 19.7 38.6 11.4 C3'-endo 49 C 1.9 -26.4 39.8 -39.5 23.7 41.3 15.9 C3'-endo 50 G 3.8 -26.1 37.2 -36.2 20.4 38.2 13.2 C3'-endo 51 A 1.8 -25.0 37.4 -37.4 22.5 38.9 16.1 C3'-endo 52 G 1.4 -25.8 39.0 -39.3 23.7 40.7 16.6 C3'-endo 53 U 10.0 -32.0 40.7 -35.8 16.4 40.8 4.7 C3'-endo 54 C -5.9 -6.1 14.8 -19.0 15.7 18.6 37.2 C4'-exo 55 C 4.0 -24.9 34.8 -33.6 18.7 35.6 12.3 C3'-endo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II step P--P C1'--C1' step P--P C1'--C1' 1 G/G 5.46 4.95 1 C/C 5.80 5.28 2 G/G 6.20 5.78 2 C/C 6.31 5.57 3 G/C 6.65 5.48 3 C/G 6.26 5.08 4 C/G 5.78 5.43 4 G/C 5.45 5.40 5 G/G 5.65 5.33 5 C/C 6.41 6.40 6 G/C 5.79 5.62 6 C/G 4.98 4.79 7 C/G 7.71 5.51 7 G/C 5.98 5.61 8 G/U 5.48 6.22 8 C/A 6.44 5.34 9 U/A 5.78 5.41 9 A/U 5.46 5.29 10 A/G 5.64 5.16 10 U/C 5.46 5.72 11 G/G 6.11 5.11 11 C/C 5.61 5.79 12 G/U 6.59 6.33 12 C/A 12.74 7.26 13 U/U 4.96 5.27 13 A/G 14.16 6.50 14 U/G --- --- 14 G/C --- --- 15 G/C 5.86 6.00 15 C/G 5.99 5.35 16 C/G 5.47 5.60 16 G/C 5.65 5.80 17 G/A 5.79 5.55 17 C/U 5.27 5.29 18 A/G 6.12 5.40 18 U/C 5.62 6.07 19 G/A 6.83 5.59 19 C/G 5.53 5.43 20 A/G 14.44 11.81 20 G/C 5.97 5.35 21 G/C 6.30 6.25 21 C/G 5.46 5.06 22 C/U 5.62 5.60 22 G/A 5.85 5.50 23 U/C 5.80 5.24 23 A/G 6.84 5.59 24 C/A 7.13 5.89 24 G/U 17.32 9.44 25 A/G 6.30 5.31 25 U/C 10.57 3.59 26 G/C 5.83 6.84 26 C/G 7.29 4.10 27 C/G --- --- 27 G/C --- --- 28 G/G --- --- 28 C/C --- --- 29 G/G 5.42 5.23 29 C/C 5.86 5.74 30 G/G 6.12 5.61 30 C/C 6.37 5.40 31 G/C 6.37 5.35 31 C/G 6.00 5.19 32 C/G 6.38 5.54 32 G/C 5.71 5.48 33 G/G 5.51 5.09 33 C/C 6.54 6.25 34 G/C 5.70 5.67 34 C/G 5.45 5.22 35 C/G 7.72 5.37 35 G/C 5.13 5.17 36 G/U 5.68 6.05 36 C/A 6.56 5.56 37 U/A 5.73 5.74 37 A/U 5.54 4.90 38 A/G 5.73 4.76 38 U/C 5.42 5.85 39 G/G 6.19 5.04 39 C/C 5.86 6.10 40 G/U 6.26 6.17 40 C/A 12.17 7.05 41 U/U 5.52 5.52 41 A/G 13.99 5.35 42 U/G --- --- 42 G/C --- --- 43 G/C 6.07 6.03 43 C/G 5.75 5.57 44 C/G 5.43 5.76 44 G/C 5.55 5.56 45 G/A 5.71 5.42 45 C/U 5.29 5.44 46 A/G 6.03 5.38 46 U/C 5.58 6.14 47 G/A 6.85 5.57 47 C/G 5.67 5.46 48 A/G 14.61 11.88 48 G/C 5.98 5.49 49 G/C 5.81 5.87 49 C/G 5.28 5.10 50 C/U 5.76 5.67 50 G/A 5.98 5.56 51 U/C 5.83 5.26 51 A/G 6.81 5.59 52 C/A 7.13 5.89 52 G/U 17.17 9.44 53 A/G 6.40 5.36 53 U/C 10.84 3.73 54 G/G --- --- 54 C/C --- --- **************************************************************************** Helix radius (radial displacement of P, O4', and C1' atoms in local helix frame of each dimer) Strand I Strand II step P O4' C1' P O4' C1' 1 GG/CC 7.86 7.20 6.79 11.23 9.62 8.75 2 GG/CC 10.01 7.84 7.09 8.32 7.35 6.47 3 GC/GC 9.76 8.17 7.47 9.38 7.92 7.19 4 CG/CG 5.81 6.50 5.93 12.58 10.54 9.73 5 GG/CC 11.05 10.45 9.68 6.15 7.06 6.81 6 GC/GC 8.52 6.46 5.59 9.35 7.70 6.74 7 CG/CG 6.01 9.34 9.13 12.29 11.98 11.53 8 GU/AC 10.37 9.67 8.80 7.95 7.18 6.58 9 UA/UA 8.42 8.67 8.15 10.35 9.77 9.08 10 AG/CU 11.19 10.97 10.44 8.52 9.45 9.08 11 GG/CC 10.72 9.72 9.38 9.91 10.44 9.92 12 GU/AC 10.01 8.69 7.70 6.26 4.68 3.98 13 UU/GA 5.45 3.61 2.50 6.33 8.26 7.74 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GC/GC 10.47 9.87 9.12 9.34 8.13 7.69 16 CG/CG 9.80 10.38 9.91 10.40 10.13 9.79 17 GA/UC 10.62 10.28 9.67 8.02 8.56 8.16 18 AG/CU 11.06 9.63 9.39 10.54 10.72 10.24 19 GA/GC 11.74 10.08 9.31 6.52 6.60 6.15 20 AG/CG 11.86 11.72 10.94 4.90 5.69 5.51 21 GC/GC 9.23 8.12 7.30 8.15 6.98 6.14 22 CU/AG 8.09 8.74 8.23 8.96 9.31 8.91 23 UC/GA 9.86 7.35 7.00 10.09 9.40 8.63 24 CA/UG 9.89 8.36 7.55 8.59 5.14 4.23 25 AG/CU 8.49 6.82 5.55 13.46 9.88 8.78 26 GC/GC 6.75 4.51 3.64 10.14 5.88 4.91 27 CG/CG ---- ---- ---- ---- ---- ---- 28 GG/CC ---- ---- ---- ---- ---- ---- 29 GG/CC 7.28 7.56 7.26 11.63 10.46 9.66 30 GG/CC 11.43 8.55 7.78 7.09 6.08 5.31 31 GC/GC 8.67 6.89 6.55 10.78 9.35 8.57 32 CG/CG 8.18 8.38 7.90 10.76 9.82 9.17 33 GG/CC 9.22 9.14 8.56 8.87 8.87 8.39 34 GC/GC 8.46 6.61 5.70 9.38 7.84 6.88 35 CG/CG 7.38 10.40 10.40 12.99 12.93 12.67 36 GU/AC 9.65 8.82 8.01 8.52 7.44 6.73 37 UA/UA 10.21 9.74 9.00 7.26 7.84 7.38 38 AG/CU 9.14 9.10 8.75 11.79 11.34 10.71 39 GG/CC 12.82 11.42 10.98 8.99 10.18 9.91 40 GU/AC 9.84 8.13 7.09 6.29 4.59 3.99 41 UU/GA 7.10 5.60 4.35 4.26 5.54 5.22 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GC/GC 9.51 9.67 9.03 9.82 9.48 8.93 44 CG/CG 11.14 11.75 11.25 9.42 10.31 10.06 45 GA/UC 9.05 8.30 7.56 9.14 8.37 7.65 46 AG/CU 13.19 11.44 11.11 9.63 10.71 10.43 47 GA/GC 11.02 9.37 8.59 7.38 7.25 6.64 48 AG/CG 11.80 11.57 10.71 4.92 5.60 5.32 49 GC/GC 9.02 8.30 7.51 8.27 7.47 6.65 50 CU/AG 8.47 8.65 8.15 9.28 9.48 8.97 51 UC/GA 10.17 8.27 8.00 10.27 10.36 9.66 52 CA/UG 10.17 8.25 7.37 8.30 5.06 4.14 53 AG/CU 8.60 6.28 5.06 12.54 8.91 7.84 54 GG/CC ---- ---- ---- ---- ---- ---- **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz 1 GG/CC 100.07 46.31 46.08 0.75 0.38 -0.55 2 GG/CC 100.14 46.74 43.15 0.43 0.85 -0.30 3 GC/GC 101.10 49.57 42.84 0.43 0.88 -0.20 4 CG/CG 105.29 52.28 40.56 0.19 0.50 -0.84 5 GG/CC 103.72 54.78 43.41 0.92 0.29 -0.26 6 GC/GC 104.76 58.03 39.95 0.92 0.39 -0.05 7 CG/CG 110.84 56.52 36.59 0.24 0.86 -0.46 8 GU/AC 112.08 58.39 40.81 0.87 0.46 -0.15 9 UA/UA 112.94 61.47 38.56 0.75 0.63 -0.18 10 AG/CU 114.12 61.39 36.23 0.56 0.78 -0.30 11 GG/CC 116.01 64.72 36.42 0.71 0.61 -0.36 12 GU/AC 120.45 62.22 33.48 0.71 0.48 -0.52 13 UU/GA 124.93 61.71 33.64 0.77 0.49 -0.41 14 UG/CG ---- ---- ---- ---- ---- ---- 15 GC/GC 89.31 82.13 13.23 0.91 -0.16 0.38 16 CG/CG 91.22 79.65 15.38 0.87 -0.48 0.11 17 GA/UC 92.50 79.98 15.49 0.71 -0.66 0.25 18 AG/CU 95.35 77.18 14.18 0.81 -0.52 0.26 19 GA/GC 95.72 76.27 19.13 0.63 -0.66 0.42 20 AG/CG 95.95 73.90 19.09 0.67 -0.72 0.19 21 GC/GC 97.24 72.15 23.35 0.49 -0.82 0.28 22 CU/AG 100.67 70.79 26.50 0.09 -0.78 0.61 23 UC/GA 100.29 69.28 27.14 0.79 -0.43 0.44 24 CA/UG 105.38 67.80 25.25 0.63 -0.67 0.38 25 AG/CU 110.07 66.23 22.44 0.62 -0.67 0.42 26 GC/GC 110.41 64.49 26.41 0.53 -0.75 0.41 27 CG/CG ---- ---- ---- ---- ---- ---- 28 GG/CC ---- ---- ---- ---- ---- ---- 29 GG/CC 168.03 110.44 -3.83 -0.36 -0.86 0.37 30 GG/CC 168.79 110.93 0.49 -0.93 -0.23 0.29 31 GC/GC 165.59 107.63 -0.11 -0.89 -0.30 0.35 32 CG/CG 162.04 106.41 0.31 -0.63 -0.48 0.61 33 GG/CC 160.88 105.86 0.56 -0.55 -0.73 0.40 34 GC/GC 157.23 106.39 2.66 -0.51 -0.85 0.14 35 CG/CG 159.06 99.28 6.72 -0.80 -0.02 0.59 36 GU/AC 155.19 99.48 1.81 -0.58 -0.82 0.05 37 UA/UA 154.67 97.84 3.39 -0.72 -0.55 0.43 38 AG/CU 150.34 97.48 4.97 -0.62 -0.76 0.21 39 GG/CC 150.26 97.25 7.49 -0.75 -0.55 0.37 40 GU/AC 151.51 90.87 8.98 -0.49 -0.71 0.50 41 UU/GA 150.71 88.04 10.10 -0.66 -0.74 0.14 42 UG/CG ---- ---- ---- ---- ---- ---- 43 GC/GC 135.01 123.80 29.05 0.24 -0.91 -0.33 44 CG/CG 136.28 122.62 26.31 0.55 -0.82 -0.16 45 GA/UC 134.90 118.53 27.68 0.38 -0.77 -0.51 46 AG/CU 139.23 119.45 28.54 0.60 -0.79 -0.12 47 GA/GC 139.12 116.27 23.17 0.56 -0.66 -0.50 48 AG/CG 141.88 116.70 23.10 0.68 -0.71 -0.18 49 GC/GC 143.18 114.68 19.01 0.76 -0.54 -0.36 50 CU/AG 144.41 111.70 15.99 0.79 -0.23 -0.56 51 UC/GA 145.42 111.58 14.36 0.55 -0.69 -0.47 52 CA/UG 146.89 106.71 17.93 0.49 -0.74 -0.47 53 AG/CU 148.29 102.46 19.54 0.44 -0.76 -0.48 54 GG/CC ---- ---- ---- ---- ---- ----