**************************************************************************** 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: 1tra_old.pdb Date and time: Tue Feb 11 23:39:39 2025 Number of base-pairs: 29 Number of atoms: 1767 **************************************************************************** HEADER T-RNA 16-MAY-86 1TRA TITLE RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TITLE 2 TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, TITLE 3 AND BASE-PAIR PROPELLER TWIST ANGLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNAPHE; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS T-RNA, SINGLE STRAND, LOOPS EXPDTA X-RAY DIFFRACTION AUTHOR E.WESTHOF,M.SUNDARALINGAM REVDAT 5 14-FEB-24 1TRA 1 REMARK LINK REVDAT 4 27-JUL-11 1TRA 1 REVDAT REVDAT 3 13-JUL-11 1TRA 1 VERSN REVDAT 2 24-FEB-09 1TRA 1 VERSN REVDAT 1 14-JUL-86 1TRA 0 JRNL AUTH E.WESTHOF,M.SUNDARALINGAM JRNL TITL RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST JRNL TITL 2 PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND JRNL TITL 3 DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST JRNL TITL 4 ANGLES. JRNL REF BIOCHEMISTRY V. 25 4868 1986 JRNL REFN ISSN 0006-2960 JRNL PMID 3533142 JRNL DOI 10.1021/BI00365A022 **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.018) ....>A:...1_:[..G]G-----C[..C]:..72_:A<.... (0.020) | 2 (0.020) ....>A:...2_:[..C]C-----G[..G]:..71_:A<.... (0.018) | 3 (0.018) ....>A:...3_:[..G]G-----C[..C]:..70_:A<.... (0.022) | 4 (0.015) ....>A:...4_:[..G]G-*---U[..U]:..69_:A<.... (0.030) | 5 (0.019) ....>A:...5_:[..A]A-----U[..U]:..68_:A<.... (0.032) | 6 (0.030) ....>A:...6_:[..U]U-----A[..A]:..67_:A<.... (0.018) | 7 (0.030) ....>A:...7_:[..U]U-----A[..A]:..66_:A<.... (0.019) | 8 (0.018) ....>A:..49_:[5MC]c-----G[..G]:..65_:A<.... (0.021) | 9 (0.029) ....>A:..50_:[..U]U-----A[..A]:..64_:A<.... (0.019) | 10 (0.016) ....>A:..51_:[..G]G-----C[..C]:..63_:A<.... (0.020) | 11 (0.027) ....>A:..52_:[..U]U-----A[..A]:..62_:A<.... (0.018) | 12 (0.019) ....>A:..53_:[..G]G-----C[..C]:..61_:A<.... (0.023) | 13 (0.031) ....>A:..54_:[5MU]t-**--a[1MA]:..58_:A<.... (0.020) | 14 (0.015) ....>A:..55_:[PSU]P-**+-G[..G]:..18_:A<.... (0.019) x 15 (0.020) ....>A:..36_:[..A]A-**--U[..U]:..33_:A<.... (0.031) | 16 (0.021) ....>A:..38_:[..A]A-**--c[OMC]:..32_:A<.... (0.020) | 17 (0.015) ....>A:..39_:[PSU]P-*---A[..A]:..31_:A<.... (0.022) | 18 (0.023) ....>A:..40_:[5MC]c-----G[..G]:..30_:A<.... (0.017) | 19 (0.028) ....>A:..41_:[..U]U-----A[..A]:..29_:A<.... (0.021) | 20 (0.021) ....>A:..42_:[..G]G-----C[..C]:..28_:A<.... (0.020) | 21 (0.019) ....>A:..43_:[..G]G-----C[..C]:..27_:A<.... (0.021) | 22 (0.020) ....>A:..44_:[..A]A-**--g[M2G]:..26_:A<.... (0.019) | 23 (0.021) ....>A:..10_:[2MG]g-----C[..C]:..25_:A<.... (0.022) | 24 (0.020) ....>A:..11_:[..C]C-----G[..G]:..24_:A<.... (0.018) | 25 (0.032) ....>A:..12_:[..U]U-----A[..A]:..23_:A<.... (0.018) | 26 (0.019) ....>A:..13_:[..C]C-----G[..G]:..22_:A<.... (0.018) | 27 (0.020) ....>A:..14_:[..A]A-**--U[..U]:...8_:A<.... (0.028) | 28 (0.015) ....>A:..15_:[..G]G-**+-C[..C]:..48_:A<.... (0.021) x 29 (0.016) ....>A:..19_:[..G]G-----C[..C]:..56_:A<.... (0.022) + Note: This structure contains 9[7] non-Watson-Crick base-pairs. **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 G-----C [3] O6 - N4 3.04 N1 - N3 3.03 N2 - O2 2.94 2 C-----G [3] O2 - N2 2.80 N3 - N1 2.88 N4 - O6 2.83 3 G-----C [3] O6 - N4 3.09 N1 - N3 3.01 N2 - O2 2.81 4 G-*---U [2] O6 - N3 2.87 N1 - O2 2.81 5 A-----U [2] N6 - O4 2.90 N1 - N3 2.98 6 U-----A [2] N3 - N1 2.79 O4 - N6 2.93 7 U-----A [2] N3 - N1 3.00 O4 - N6 2.84 8 c-----G [3] O2 - N2 3.10 N3 - N1 2.99 N4 - O6 2.80 9 U-----A [2] N3 - N1 2.82 O4 - N6 2.92 10 G-----C [3] O6 - N4 2.73 N1 - N3 2.62 N2 - O2 2.59 11 U-----A [2] N3 - N1 2.92 O4 - N6 2.95 12 G-----C [3] O6 - N4 2.70 N1 - N3 2.74 N2 - O2 2.71 13 t-**--a [2] O2 - N6 3.42 O4 * N7 2.80 14 P-**+-G [2] O4 * N2 2.94 O4'* O6 3.52 15 A-**--U [2] OP2- N3 3.01 N7 * O2 3.46 16 A-**--c [1] N6 - O2 2.94 17 P-*---A [1] O2 * N1 2.49 18 c-----G [3] O2 - N2 3.08 N3 - N1 2.95 N4 - O6 2.83 19 U-----A [2] N3 - N1 2.77 O4 - N6 2.91 20 G-----C [3] O6 - N4 2.71 N1 - N3 2.82 N2 - O2 2.94 21 G-----C [3] O6 - N4 2.62 N1 - N3 2.68 N2 - O2 2.79 22 A-**--g [2] N6 - O6 2.53 N1 - N1 2.90 23 g-----C [3] O6 - N4 3.09 N1 - N3 3.08 N2 - O2 3.06 24 C-----G [3] O2 - N2 2.80 N3 - N1 2.66 N4 - O6 2.72 25 U-----A [2] N3 - N1 3.09 O4 - N6 2.84 26 C-----G [3] O2 - N2 2.86 N3 - N1 2.81 N4 - O6 2.71 27 A-**--U [2] N7 - N3 2.78 N6 - O2 3.48 28 G-**+-C [2] N1 - O2 2.53 N2 - N3 2.99 29 G-----C [3] O6 - N4 2.88 N1 - N3 2.58 N2 - O2 2.49 **************************************************************************** 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 GC/GC 6.15( 3.10) 0.00( 0.00) 0.00( 0.00) 7.36( 4.07) 13.51( 7.17) 2 CG/CG 0.62( 0.05) 0.00( 0.00) 3.06( 0.70) 0.00( 0.00) 3.68( 0.76) 3 GG/UC 1.53( 0.29) 0.00( 0.00) 0.70( 0.00) 0.00( 0.00) 2.22( 0.29) 4 GA/UU 4.26( 2.78) 0.00( 0.00) 0.00( 0.00) 3.34( 1.19) 7.60( 3.97) 5 AU/AU 5.27( 3.81) 0.00( 0.00) 0.00( 0.00) 4.25( 2.75) 9.52( 6.56) 6 UU/AA 1.63( 0.20) 0.00( 0.00) 0.00( 0.00) 2.37( 2.10) 4.01( 2.30) 7 Uc/GA 0.63( 0.00) 0.00( 0.00) 0.00( 0.00) 2.96( 1.41) 3.59( 1.41) 8 cU/AG 0.00( 0.00) 0.00( 0.00) 0.52( 0.00) 2.62( 2.45) 3.14( 2.45) 9 UG/CA 0.00( 0.00) 0.00( 0.00) 3.93( 2.25) 0.03( 0.00) 3.96( 2.25) 10 GU/AC 6.40( 3.40) 0.00( 0.00) 0.00( 0.00) 5.49( 4.01) 11.88( 7.41) 11 UG/CA 0.02( 0.00) 0.00( 0.00) 3.90( 1.57) 0.00( 0.00) 3.92( 1.57) 12 Gt/aC 7.87( 2.83) 0.00( 0.00) 0.00( 0.00) 2.98( 0.53) 10.85( 3.36) 13 tP/Ga 5.92( 1.03) 0.00( 0.00) 0.00( 0.00) 8.10( 3.20) 14.02( 4.23) 14 PA/UG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 15 AA/cU 0.65( 0.00) 0.00( 0.00) 0.00( 0.00) 6.61( 3.70) 7.25( 3.70) 16 AP/Ac 5.37( 2.01) 0.00( 0.00) 0.00( 0.00) 5.86( 2.17) 11.24( 4.18) 17 Pc/GA 3.18( 0.02) 0.00( 0.00) 0.00( 0.00) 5.94( 4.15) 9.12( 4.17) 18 cU/AG 0.07( 0.00) 0.00( 0.00) 0.52( 0.00) 1.35( 1.32) 1.94( 1.32) 19 UG/CA 0.00( 0.00) 0.00( 0.00) 3.60( 2.09) 0.00( 0.00) 3.60( 2.09) 20 GG/CC 4.57( 3.34) 0.00( 0.00) 0.06( 0.00) 0.78( 0.15) 5.41( 3.49) 21 GA/gC 2.14( 0.52) 0.00( 0.00) 0.00( 0.00) 1.90( 0.73) 4.05( 1.24) 22 Ag/Cg 0.00( 0.00) 0.00( 0.00) 2.03( 0.24) 0.01( 0.00) 2.03( 0.24) 23 gC/GC 2.98( 0.40) 0.00( 0.00) 0.00( 0.00) 6.79( 4.38) 9.77( 4.78) 24 CU/AG 0.42( 0.00) 0.00( 0.00) 0.00( 0.00) 3.67( 3.21) 4.09( 3.21) 25 UC/GA 1.46( 0.20) 0.00( 0.00) 0.00( 0.00) 0.23( 0.00) 1.69( 0.20) 26 CA/UG 0.00( 0.00) 2.29( 0.02) 0.82( 0.00) 0.00( 0.00) 3.11( 0.02) 27 AG/CU 1.48( 0.33) 0.00( 0.00) 0.47( 0.00) 0.00( 0.00) 1.95( 0.33) 28 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 26.539 -2.866 53.707 0.763 0.406 -0.503 2 C-G 30.157 -2.653 51.780 0.731 0.543 -0.414 3 G-C 31.844 -2.306 49.241 0.656 0.439 -0.614 4 G-U 32.733 -1.782 46.021 0.552 0.655 -0.516 5 A-U 33.694 0.288 43.169 0.353 0.746 -0.564 6 U-A 33.469 3.444 41.271 0.337 0.798 -0.500 7 U-A 33.745 6.947 40.097 0.425 0.875 -0.231 8 c-G 33.871 10.879 40.970 0.471 0.865 -0.169 9 U-A 35.240 14.938 42.161 0.497 0.838 -0.224 10 G-C 37.573 16.773 43.187 0.666 0.718 -0.203 11 U-A 40.633 18.683 43.472 0.698 0.657 -0.285 12 G-C 44.850 19.690 41.805 0.732 0.591 -0.337 13 t-a 49.182 18.148 40.778 0.772 0.557 -0.307 14 P+G 48.921 22.928 38.184 0.638 0.700 -0.322 15 A-U 42.604 -11.185 -3.392 0.165 0.251 0.954 16 A-c 45.839 -8.909 -0.222 0.266 0.634 0.726 17 P-A 47.481 -5.499 2.127 -0.056 0.721 0.690 18 c-G 47.439 -2.778 3.242 -0.066 0.677 0.733 19 U-A 45.726 0.241 5.305 -0.075 0.649 0.757 20 G-C 43.670 2.204 7.186 -0.140 0.462 0.875 21 G-C 41.840 3.422 11.015 -0.090 0.456 0.885 22 A-g 40.027 3.121 14.556 -0.060 0.161 0.985 23 g-C 39.266 0.240 18.691 0.287 -0.024 0.958 24 C-G 40.663 -1.206 21.209 0.283 0.143 0.949 25 U-A 42.973 -0.797 24.197 0.208 0.321 0.924 26 C-G 43.874 3.014 26.225 0.282 0.347 0.895 27 A-U 47.258 3.897 28.041 0.352 0.330 0.876 28 G+C 46.057 9.231 30.121 0.288 0.414 0.864 29 G-C 57.358 22.614 34.655 0.885 0.328 -0.331 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 G-C -1.16 -0.32 -0.07 8.25 2.68 -0.46 2 C-G 0.12 -0.19 0.57 -2.94 6.70 -0.11 3 G-C 0.65 0.03 -0.11 8.30 -6.86 3.22 4 G-U -2.30 -0.46 0.59 15.88 -2.11 -0.29 5 A-U -0.11 -0.13 -0.76 8.29 -9.12 -2.16 6 U-A 0.21 -0.16 -0.40 9.58 -15.89 1.50 7 U-A 0.11 -0.02 -0.32 2.96 -4.08 -5.95 8 c-G -0.61 -0.03 0.02 8.28 -13.18 -5.90 9 U-A -0.08 -0.18 0.69 -6.01 -7.56 -2.32 10 G-C -0.72 -0.57 0.32 5.89 -15.63 -0.19 11 U-A 0.04 -0.05 0.12 4.92 -10.66 -3.20 12 G-C -0.24 -0.26 -0.09 -21.10 -13.25 -2.27 13 t-a 3.68 -0.77 -0.32 -2.19 -4.63 -112.19 14 P+G 0.29 -6.17 1.02 16.40 9.11 -87.26 15 A-U -6.24 -8.02 1.73 -18.26 9.89 -48.83 16 A-c -6.76 -2.49 1.18 17.08 13.14 -1.07 17 P-A -2.07 -0.32 -0.08 -6.26 -17.86 -7.32 18 c-G -0.15 -0.08 -0.36 8.26 -18.72 -3.28 19 U-A 0.28 -0.21 -0.40 5.34 -6.39 1.89 20 G-C -0.43 -0.32 0.28 4.83 -13.70 -5.76 21 G-C 0.52 -0.36 0.38 -9.99 -18.20 -6.56 22 A-g 0.14 1.27 -1.02 -27.62 -23.99 -21.47 23 g-C -0.93 -0.13 -0.40 -13.48 -11.69 -0.16 24 C-G -0.59 -0.36 0.26 -0.65 -24.77 -3.12 25 U-A -0.27 0.10 0.41 -6.22 -1.92 -10.16 26 C-G -0.67 -0.23 0.36 -0.24 -14.25 -4.89 27 A-U -4.50 -2.10 0.26 8.83 6.69 -108.15 28 G+C 0.29 4.71 -0.04 0.98 3.09 146.92 29 G-C -0.31 -0.50 0.51 -25.22 -29.80 -2.99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.75 -0.63 0.15 -0.21 -8.03 -10.09 s.d. 2.04 2.13 0.58 12.00 11.06 43.82 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 GC/GC -0.28 -1.76 3.70 -8.95 -3.21 33.82 2 CG/CG 0.31 -1.49 2.66 11.95 6.54 31.97 3 GG/UC 0.05 -2.08 2.67 -8.44 12.27 23.16 4 GA/UU -0.37 -1.15 3.45 9.50 8.67 40.72 5 AU/AU 0.29 -1.47 3.37 0.79 4.77 31.97 6 UU/AA -0.19 -1.19 3.50 1.72 16.76 30.63 7 Uc/GA -0.01 -2.30 3.31 0.53 4.43 26.39 8 cU/AG -0.23 -2.14 3.89 -3.61 1.08 36.07 9 UG/CA 0.32 -1.76 2.58 4.28 11.16 29.50 10 GU/AC -0.22 -1.39 3.33 -0.76 6.12 34.05 11 UG/CA 0.85 -1.87 4.17 3.28 4.02 30.85 12 Gt/aC -2.57 -2.88 2.70 0.82 -3.37 86.94 13 tP/Ga 2.77 -2.94 3.65 5.49 9.83 51.17 14 PA/UG ---- ---- ---- ---- ---- ---- 15 AA/cU 0.70 -2.26 4.49 4.16 26.09 70.68 16 AP/Ac -0.54 -1.36 4.21 -6.01 18.36 43.35 17 Pc/GA -0.29 -1.13 2.70 -3.41 1.05 39.05 18 cU/AG 0.35 -1.67 3.66 -1.08 1.94 38.49 19 UG/CA -0.28 -1.82 2.87 1.71 13.08 27.85 20 GG/CC 0.11 -1.52 4.14 -2.43 1.63 33.93 21 GA/gC -0.62 -2.00 3.40 14.48 10.73 37.31 22 Ag/Cg -1.92 -2.79 3.81 14.98 17.09 51.07 23 gC/GC -1.06 -1.36 2.72 -5.04 8.13 40.45 24 CU/AG -0.59 -1.42 3.48 -2.50 10.89 35.39 25 UC/GA 2.12 -1.96 3.34 4.63 -1.40 22.86 26 CA/UG -2.53 -0.50 2.98 0.06 -4.23 59.91 27 AG/CU 2.85 -3.80 3.42 4.23 4.37 -59.21 28 GG/CC ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.04 -1.85 3.39 1.55 7.18 35.71 s.d. 1.28 0.69 0.54 6.26 7.41 24.20 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 GC/GC -2.35 -1.11 3.79 -5.39 15.01 35.10 2 CG/CG -3.29 0.93 2.29 11.26 -20.57 34.69 3 GG/UC -6.38 -1.48 1.32 27.24 18.74 27.48 4 GA/UU -2.46 1.47 3.00 12.10 -13.26 42.62 5 AU/AU -3.48 -0.38 3.13 8.60 -1.43 32.33 6 UU/AA -4.49 0.58 2.52 29.12 -2.99 34.86 7 Uc/GA -6.07 0.15 2.89 9.61 -1.16 26.75 8 cU/AG -3.62 -0.23 3.83 1.75 5.81 36.26 9 UG/CA -4.65 -0.04 1.84 20.88 -7.99 31.78 10 GU/AC -3.26 0.26 3.05 10.34 1.28 34.59 11 UG/CA -4.42 -0.79 3.97 7.49 -6.11 31.27 12 Gt/aC -2.03 1.88 2.77 -2.45 -0.60 86.99 13 tP/Ga -4.03 -2.75 3.33 11.23 -6.27 52.31 14 PA/UG ---- ---- ---- ---- ---- ---- 15 AA/cU -2.89 -0.41 3.62 21.81 -3.48 74.85 16 AP/Ac -3.53 0.08 3.44 23.52 7.70 47.27 17 Pc/GA -1.79 0.09 2.68 1.57 5.09 39.20 18 cU/AG -2.79 -0.67 3.56 2.93 1.63 38.55 19 UG/CA -5.37 0.78 1.83 25.44 -3.32 30.76 20 GG/CC -2.93 -0.68 4.05 2.79 4.16 34.05 21 GA/gC -3.91 2.33 2.37 15.71 -21.19 41.29 22 Ag/Cg -3.96 2.91 2.24 18.79 -16.47 55.59 23 gC/GC -2.63 1.06 2.52 11.56 7.16 41.52 24 CU/AG -3.70 0.59 2.96 17.38 3.99 37.06 25 UC/GA -4.30 -3.48 3.80 -3.48 -11.52 23.36 26 CA/UG -0.31 2.53 3.00 -4.23 -0.06 60.05 27 AG/CU 3.59 3.10 3.47 -4.41 4.27 -59.50 28 GG/CC ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -3.27 0.26 2.97 10.43 -1.60 37.35 s.d. 1.91 1.58 0.72 10.48 9.73 24.55 **************************************************************************** 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 9 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 -1.19 -0.18 -0.07 8.50 1.73 -0.46 2 C-G 0.12 -0.19 0.57 -2.99 6.68 -0.11 3 G-C 0.65 0.07 -0.11 8.74 -6.29 3.22 * 4 G-U -2.34 0.09 0.59 14.94 -5.78 -0.29 5 A-U -0.11 -0.13 -0.76 8.20 -9.20 -2.16 6 U-A 0.21 -0.16 -0.40 9.77 -15.77 1.49 7 U-A 0.11 -0.02 -0.32 2.99 -4.06 -5.95 8 c-G -0.61 0.01 0.02 7.37 -13.71 -5.87 9 U-A -0.08 -0.18 0.69 -6.09 -7.49 -2.31 10 G-C -0.76 -0.51 0.32 4.73 -16.02 -0.19 11 U-A 0.04 -0.05 0.12 4.91 -10.66 -3.19 12 G-C -0.24 -0.26 -0.09 -21.17 -13.14 -2.30 * 13 t-a 3.36 1.69 -0.32 1.15 -4.99 -112.16 * 14 P+G 4.52 4.22 1.02 -17.54 6.65 -87.67 * 15 A-U -8.85 4.99 1.73 7.15 19.50 -49.22 * 16 A-c -6.69 2.68 1.18 21.48 -1.68 -1.08 * 17 P-A -2.09 0.13 -0.08 -9.95 -16.10 -7.25 18 c-G -0.15 -0.07 -0.36 7.82 -18.90 -3.25 19 U-A 0.29 -0.20 -0.40 5.48 -6.27 1.89 20 G-C -0.44 -0.30 0.28 4.26 -13.89 -5.73 21 G-C 0.54 -0.33 0.38 -8.82 -18.80 -6.50 * 22 A-g 0.10 1.27 -1.02 -26.74 -24.98 -21.59 23 g-C -0.94 -0.05 -0.40 -14.40 -10.54 -0.16 24 C-G -0.61 -0.32 0.26 -2.29 -24.67 -3.05 25 U-A -0.27 0.10 0.41 -6.27 -1.74 -10.18 26 C-G -0.69 -0.18 0.36 -1.29 -14.19 -4.85 * 27 A-U -4.47 2.17 0.26 10.76 -2.64 -108.22 * 28 G+C 4.34 1.86 -0.04 3.20 0.51 146.91 29 G-C -0.31 -0.50 0.51 -25.25 -29.78 -2.96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.57 0.54 0.15 -0.39 -8.84 -10.11 s.d. 2.67 1.40 0.58 11.91 10.50 43.87 ---------------------------------------------------------------------------- Simple base-pair step parameters based on consecutive C1'-C1' vectors step Shift Slide Rise Tilt Roll Twist 1 GC/GC -0.36 -1.74 3.70 -9.10 -2.76 26.85 2 CG/CG 0.36 -1.48 2.66 11.72 6.95 29.34 * 3 GG/UC -0.12 -2.08 2.67 -7.39 12.93 39.26 * 4 GA/UU -0.50 -1.10 3.45 10.46 7.48 28.67 5 AU/AU 0.29 -1.47 3.37 0.79 4.77 30.38 6 UU/AA -0.18 -1.19 3.50 1.52 16.78 30.89 7 Uc/GA -0.07 -2.30 3.31 0.65 4.41 30.55 8 cU/AG -0.30 -2.13 3.89 -3.57 1.21 32.71 9 UG/CA 0.25 -1.77 2.58 4.72 10.98 33.57 10 GU/AC -0.27 -1.38 3.33 -0.53 6.14 29.68 11 UG/CA 0.83 -1.87 4.17 3.31 4.00 31.73 * 12 Gt/aC -2.01 -3.29 2.70 1.42 -3.17 64.57 * 13 tP/Ga 3.82 1.30 3.65 -6.65 9.08 -36.54 * 14 PA/UG ---- ---- ---- ---- ---- ---- * 15 AA/cU -1.27 -1.99 4.49 22.59 13.70 49.58 * 16 AP/Ac -1.07 -1.00 4.21 2.29 19.19 14.91 * 17 Pc/GA -0.40 -1.09 2.70 -3.28 1.40 29.54 18 cU/AG 0.35 -1.67 3.66 -1.08 1.93 35.88 19 UG/CA -0.30 -1.82 2.87 1.83 13.06 31.75 20 GG/CC 0.12 -1.52 4.14 -2.45 1.62 28.16 * 21 GA/gC -0.53 -2.02 3.40 13.98 11.38 38.63 * 22 Ag/Cg -1.99 -2.74 3.81 15.39 16.71 57.77 23 gC/GC -1.15 -1.29 2.72 -4.47 8.45 38.77 24 CU/AG -0.64 -1.39 3.48 -2.10 10.97 33.45 25 UC/GA 2.03 -2.04 3.34 4.57 -1.59 25.48 * 26 CA/UG -2.57 0.23 2.98 -1.13 -4.07 84.99 * 27 AG/CU -1.83 -4.38 3.42 5.90 -1.44 2.37 * 28 GG/CC ---- ---- ---- ---- ---- ---- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.29 -1.66 3.39 2.28 6.54 32.42 s.d. 1.28 1.03 0.54 7.47 6.68 20.96 **************************************************************************** Structure classification: This structure contains more than one helical regions 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 49.9 61.4 10.5 8.9 9.7 2 C-G 55.5 54.3 10.6 8.9 9.8 3 G-C 62.2 53.4 10.6 9.1 10.0 4 G-U 42.4 69.6 10.5 8.9 9.8 5 A-U 53.6 55.8 10.6 8.9 9.8 6 U-A 56.8 53.8 10.5 8.8 9.8 7 U-A 54.6 52.4 10.9 9.1 9.9 8 c-G 50.5 55.6 11.0 9.2 10.0 9 U-A 55.6 55.2 10.5 8.9 9.8 10 G-C 51.5 59.2 10.2 8.6 9.5 11 U-A 54.7 53.0 10.7 9.0 9.9 12 G-C 55.0 53.9 10.5 8.7 9.6 13 t-a 22.8 21.4 10.0 7.4 6.1 14 P+G 115.2 32.2 8.5 8.2 9.6 15 A-U 34.0 89.8 7.5 6.6 6.6 16 A-c 14.9 93.5 10.7 9.4 10.0 17 P-A 40.6 62.9 10.9 9.1 9.8 18 c-G 51.2 53.5 10.9 9.1 9.9 19 U-A 58.5 53.9 10.4 8.8 9.8 20 G-C 49.4 52.9 10.8 8.9 9.7 21 G-C 54.0 47.2 10.7 8.9 9.6 22 A-g 46.6 43.5 12.5 10.4 10.7 23 g-C 50.5 58.9 10.7 9.0 9.9 24 C-G 48.1 55.2 10.7 8.8 9.7 25 U-A 48.3 50.9 11.2 9.3 10.0 26 C-G 49.0 53.8 10.8 9.0 9.8 27 A-U 27.8 30.3 9.3 6.9 5.9 28 G+C 38.0 69.7 10.1 8.7 10.4 29 G-C 54.4 52.7 10.2 8.5 9.3 **************************************************************************** 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 GC/GC -1.58 7.82 3.40 -3.64 8.09 2.67 A 2 CG/CG -1.77 8.24 2.91 -4.81 7.56 4.24 A 3 GG/UC -1.66 7.89 2.94 -7.55 5.77 5.97 A 4 GA/UU -1.62 8.27 2.58 -3.98 7.62 3.94 A 5 AU/AU -1.54 8.41 1.97 -4.89 8.04 3.16 A 6 UU/AA -1.52 8.27 2.13 -5.81 6.31 5.76 A 7 Uc/GA -1.29 7.66 3.23 -7.22 7.03 4.43 A 8 cU/AG -1.76 8.10 2.73 -5.18 8.02 2.98 A 9 UG/CA -1.48 8.15 2.77 -5.95 6.71 5.34 A 10 GU/AC -1.39 8.21 2.45 -4.50 7.67 3.82 A 11 UG/CA -1.72 8.12 2.71 -5.93 7.72 3.69 A 12 Gt/aC -0.69 7.12 3.05 -2.16 7.21 2.85 13 tP/Ga 3.81 4.66 0.59 -0.05 4.45 1.70 14 PA/UG --- --- --- --- --- --- --- 15 AA/cU -0.53 5.19 4.56 -2.91 3.60 5.70 16 AP/Ac -1.09 7.92 2.79 -4.19 6.27 5.76 17 Pc/GA -1.78 8.77 1.81 -3.42 8.72 2.13 A 18 cU/AG -2.04 8.34 2.11 -4.67 8.23 2.52 A 19 UG/CA -1.35 8.33 2.63 -6.53 6.47 5.86 A 20 GG/CC -0.84 8.20 2.57 -3.64 8.07 2.93 A 21 GA/gC -1.16 8.46 2.38 -4.23 7.57 4.45 22 Ag/Cg -2.43 6.67 4.11 -5.94 5.28 5.23 23 gC/GC -1.81 8.16 2.18 -4.26 7.59 3.74 A 24 CU/AG -1.13 8.47 2.64 -4.67 7.36 4.96 A 25 UC/GA -1.49 8.71 2.44 -5.56 8.84 1.75 A 26 CA/UG -1.39 8.50 2.14 -1.67 8.62 1.60 27 AG/CU 2.87 1.73 2.56 6.01 1.91 2.82 28 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 GC/GC --- --- --- --- 2 CG/CG --- --- --- --- 3 GG/UC 17.4 --- 15.8 --- 4 GA/UU 17.1 15.3 15.8 12.8 5 AU/AU 17.7 15.7 15.3 12.6 6 UU/AA 17.9 16.1 17.2 14.5 7 Uc/GA 16.9 15.3 17.7 15.3 8 cU/AG 16.7 15.1 18.1 17.2 9 UG/CA 17.0 15.6 15.2 12.0 10 GU/AC 16.9 15.5 15.8 12.7 11 UG/CA 16.4 --- 13.9 --- 12 Gt/aC --- --- --- --- 13 tP/Ga --- --- --- --- 14 PA/UG --- --- --- --- 15 AA/cU --- --- --- --- 16 AP/Ac --- --- --- --- 17 Pc/GA 17.2 --- 14.1 --- 18 cU/AG 16.4 15.1 14.3 10.7 19 UG/CA 16.2 15.3 16.2 9.3 20 GG/CC 18.3 15.4 14.7 9.6 21 GA/gC 19.0 14.6 13.5 10.9 22 Ag/Cg 17.3 14.0 11.9 9.9 23 gC/GC 17.4 15.4 11.8 11.7 24 CU/AG 17.3 16.2 15.5 10.6 25 UC/GA 16.8 --- 8.7 --- 26 CA/UG --- --- --- --- 27 AG/CU --- --- --- --- 28 GG/CC --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 0.13(3.18) **************************************************************************** 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 --- 155.6 62.4 80.7 -138.1 -102.8 -174.3 2 C -30.0 140.6 35.2 79.4 -110.8 -119.3 172.7 3 G -28.5 131.8 34.4 79.3 -163.7 -120.2 -157.8 4 G 19.6 136.0 4.7 81.2 178.6 -46.3 -157.9 5 A -105.1 -158.7 64.9 81.6 175.8 -48.6 -148.9 6 U -89.9 -163.3 63.6 81.0 -168.9 -67.6 -146.5 7 U -98.8 -178.1 95.0 141.8 -86.3 -59.7 -136.4 8 c -68.6 -114.5 102.6 79.4 -148.4 -76.4 -175.8 9 U -83.0 -170.4 65.3 79.8 -151.0 -71.9 -168.2 10 G -51.0 -176.8 37.4 84.7 -170.8 -70.3 -149.5 11 U -98.2 -175.1 78.3 83.4 -151.2 -63.7 -165.4 12 G -94.9 159.6 90.8 79.8 -123.7 -100.9 170.5 13 t -43.5 156.1 44.1 78.4 -120.4 -80.5 -159.1 14 P -43.4 167.2 46.6 81.4 -143.6 -68.5 -161.1 15 A -69.2 102.6 99.9 75.9 -114.6 -85.8 173.9 16 A -33.7 167.2 21.3 79.4 -147.8 -70.9 -155.4 17 P -58.0 151.2 75.7 81.3 -121.5 -66.3 172.5 18 c -104.5 142.7 98.1 79.9 -120.8 -85.8 -178.9 19 U -43.9 167.5 27.0 79.6 -157.5 -71.7 -153.0 20 G -55.8 -177.5 41.6 80.5 -171.6 -64.1 -150.8 21 G -63.9 177.3 68.2 82.0 -157.5 -66.4 -164.8 22 A -63.8 -171.4 44.8 82.0 179.7 -27.8 -144.4 23 g -146.8 112.9 45.7 80.4 -122.1 -101.0 163.8 24 C -76.5 163.7 67.0 82.7 -126.7 -94.4 -165.3 25 U -21.2 162.9 10.1 83.2 174.5 -7.3 -152.1 26 C -166.0 141.0 154.9 81.1 -161.1 -66.6 -172.4 27 A -174.8 164.4 164.3 78.6 -106.6 -77.7 177.5 28 G -12.5 155.1 16.9 80.7 -163.2 176.3 -156.1 29 G -137.1 -170.3 117.0 143.9 -76.2 -74.6 -99.5 Strand II base alpha beta gamma delta epsilon zeta chi 1 C -85.3 162.1 84.9 81.7 -166.0 -62.9 -178.4 2 G -94.2 -171.9 60.0 80.2 -152.0 -72.2 -172.1 3 C -29.8 151.4 17.3 81.7 172.3 -46.2 -153.6 4 U -98.8 177.8 73.4 82.9 -128.6 -112.1 177.9 5 U -29.3 159.0 30.1 80.3 -169.6 -53.6 -158.9 6 A -90.0 -168.4 66.5 83.1 -147.7 -89.6 -167.2 7 A -37.0 176.3 30.6 78.6 -177.2 -60.9 -158.7 8 G -102.9 -169.7 84.3 81.3 -143.4 -85.8 -171.2 9 A -62.2 171.4 54.9 83.4 -168.7 -60.0 -161.7 10 C -58.4 173.9 54.0 82.3 -153.0 -84.0 -161.7 11 A -102.1 -165.5 65.3 80.0 -149.2 -74.2 -166.1 12 C -71.0 179.9 24.5 80.4 175.3 -51.1 -154.5 13 a -14.1 -177.3 33.8 145.7 -60.9 -175.1 -83.9 14 G -157.1 138.5 -29.0 148.5 -112.0 -167.2 -100.5 15 U -135.0 -144.8 66.7 82.7 177.0 -38.8 -145.3 16 c -79.6 -155.7 50.7 80.6 160.1 -29.2 -144.1 17 A -85.5 -167.5 52.6 79.5 -165.1 -41.9 -137.2 18 G -96.0 -155.6 58.2 81.4 178.5 -41.1 -149.7 19 A -51.4 177.6 36.6 81.4 169.0 -42.0 -166.9 20 C -58.0 162.1 61.9 80.6 -153.0 -71.4 -164.5 21 C -97.5 -144.4 42.7 82.7 -139.2 -84.3 -162.9 22 g -93.5 -161.6 70.5 82.8 173.3 -31.6 -159.4 23 C -62.4 178.9 44.7 83.5 -171.2 -61.7 -143.3 24 G -55.7 166.1 53.3 82.8 -142.0 -73.0 -161.7 25 A -72.5 179.6 53.3 83.0 -153.6 -76.4 -162.8 26 G 108.3 -159.4 -157.3 82.4 -147.4 -85.6 -172.8 27 U -73.9 -150.5 64.0 81.7 -137.8 -134.7 -164.4 28 C -37.8 173.6 134.3 143.1 -115.5 110.0 -134.4 29 C -177.1 155.1 42.9 81.9 -120.1 -74.5 -169.4 **************************************************************************** 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 0.1 -23.0 35.2 -36.7 23.1 37.2 18.7 C3'-endo 2 C -0.1 -23.3 36.1 -37.2 23.5 38.1 18.7 C3'-endo 3 G 0.1 -23.3 35.7 -36.8 23.3 37.7 18.5 C3'-endo 4 G -0.0 -23.1 35.7 -36.9 23.3 37.7 18.7 C3'-endo 5 A 0.5 -23.1 35.3 -36.2 22.7 37.1 18.0 C3'-endo 6 U 0.1 -22.8 35.4 -36.3 23.1 37.3 18.5 C3'-endo 7 U -23.0 36.5 -35.6 23.0 -0.1 37.5 161.6 C2'-endo 8 c -0.2 -22.9 35.9 -36.9 23.4 37.9 18.8 C3'-endo 9 U -0.0 -22.9 35.4 -36.6 23.2 37.4 18.7 C3'-endo 10 G 0.5 -23.3 35.6 -36.9 23.1 37.5 18.3 C3'-endo 11 U 0.5 -23.1 35.3 -36.7 23.1 37.2 18.4 C3'-endo 12 G 0.7 -24.2 36.4 -37.6 23.3 38.2 17.8 C3'-endo 13 t -0.0 -23.3 35.8 -37.1 23.3 37.7 18.6 C3'-endo 14 P 0.7 -24.0 36.3 -37.6 23.6 38.1 18.1 C3'-endo 15 A 0.5 -23.9 36.3 -37.1 23.1 38.1 17.8 C3'-endo 16 A 0.6 -23.4 35.6 -36.7 22.8 37.4 18.0 C3'-endo 17 P -0.1 -22.6 35.2 -36.5 23.0 37.2 18.8 C3'-endo 18 c 0.2 -23.1 35.4 -36.0 22.7 37.2 18.0 C3'-endo 19 U 0.6 -23.6 36.2 -36.6 22.8 37.9 17.6 C3'-endo 20 G 0.2 -23.2 35.9 -36.8 23.2 37.8 18.4 C3'-endo 21 G 0.5 -23.2 35.6 -36.7 22.9 37.4 18.1 C3'-endo 22 A 0.1 -23.1 35.7 -36.8 23.3 37.7 18.6 C3'-endo 23 g 0.0 -23.4 35.8 -36.8 23.5 37.8 18.5 C3'-endo 24 C 0.3 -23.1 35.6 -36.4 22.9 37.5 18.1 C3'-endo 25 U 0.3 -23.1 35.7 -36.2 22.8 37.5 18.0 C3'-endo 26 C 0.0 -23.2 35.9 -37.1 23.5 37.9 18.7 C3'-endo 27 A 0.0 -22.9 35.5 -37.0 23.0 37.5 18.7 C3'-endo 28 G 0.4 -23.5 35.8 -36.8 23.1 37.7 18.0 C3'-endo 29 G -23.1 36.2 -36.1 22.6 -0.5 38.0 162.0 C2'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 C 0.3 -23.1 35.3 -36.2 22.8 37.2 18.2 C3'-endo 2 G -0.3 -22.9 35.7 -36.8 23.6 37.8 19.0 C3'-endo 3 C 0.2 -23.0 35.4 -36.3 23.0 37.3 18.3 C3'-endo 4 U 0.4 -23.0 35.2 -36.4 23.0 37.1 18.4 C3'-endo 5 U 0.0 -22.7 35.1 -36.3 23.0 37.0 18.7 C3'-endo 6 A 0.7 -23.6 35.8 -36.6 23.1 37.6 17.8 C3'-endo 7 A 0.1 -23.3 35.5 -36.9 23.4 37.5 18.7 C3'-endo 8 G 0.3 -23.9 36.6 -37.0 23.5 38.5 17.9 C3'-endo 9 A 0.2 -22.8 35.5 -37.0 23.3 37.5 18.8 C3'-endo 10 C 0.3 -23.2 35.4 -36.6 23.1 37.3 18.3 C3'-endo 11 A 0.5 -23.4 35.8 -36.7 22.8 37.6 17.9 C3'-endo 12 C -0.2 -22.6 34.9 -36.2 23.1 36.9 19.0 C3'-endo 13 a -23.3 36.8 -35.5 22.9 -0.0 37.5 161.2 C2'-endo 14 G -23.2 36.8 -35.9 22.9 -0.3 37.8 161.6 C2'-endo 15 U 0.2 -23.2 35.7 -36.6 23.4 37.6 18.4 C3'-endo 16 c 0.3 -23.2 35.2 -36.3 22.8 37.1 18.2 C3'-endo 17 A 0.4 -23.2 35.6 -36.7 22.9 37.4 18.2 C3'-endo 18 G 0.3 -23.2 35.7 -36.8 23.1 37.6 18.3 C3'-endo 19 A -0.0 -23.0 35.5 -36.6 23.2 37.5 18.6 C3'-endo 20 C 0.3 -23.4 36.0 -37.0 23.4 37.9 18.3 C3'-endo 21 C 0.4 -23.4 35.8 -36.9 23.2 37.7 18.3 C3'-endo 22 g 0.3 -23.2 35.5 -36.6 23.1 37.4 18.3 C3'-endo 23 C 0.2 -22.9 35.5 -36.8 23.3 37.5 18.7 C3'-endo 24 G 0.4 -23.2 35.9 -37.1 23.2 37.9 18.3 C3'-endo 25 A 0.6 -23.6 35.9 -36.7 23.1 37.7 17.8 C3'-endo 26 G 0.4 -23.5 35.9 -36.7 23.1 37.8 18.0 C3'-endo 27 U 0.5 -23.4 36.1 -37.0 23.2 38.0 18.1 C3'-endo 28 C -22.9 36.4 -35.6 22.9 -0.6 37.5 161.9 C2'-endo 29 C 0.1 -23.2 35.4 -36.5 23.2 37.3 18.5 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/C 6.00 5.00 1 C/G 5.64 5.15 2 C/G 4.94 5.44 2 G/C 5.96 5.12 3 G/G 5.84 5.70 3 C/U 5.88 5.95 4 G/A 5.55 5.54 4 U/U 5.78 4.94 5 A/U 5.96 5.38 5 U/A 5.65 5.39 6 U/U 5.85 5.59 6 A/A 5.70 5.35 7 U/c 7.98 5.81 7 A/G 5.95 5.75 8 c/U 5.48 6.17 8 G/A 5.98 5.24 9 U/G 5.63 5.59 9 A/C 5.77 5.49 10 G/U 5.84 5.20 10 C/A 5.50 5.34 11 U/G 6.13 5.08 11 A/C 5.61 5.61 12 G/t 6.10 5.90 12 C/a 14.27 8.18 13 t/P 5.10 5.69 13 a/G 14.28 6.27 14 P/A --- --- 14 G/U --- --- 15 A/A 11.86 10.88 15 U/c 5.85 5.56 16 A/P 5.00 4.60 16 c/A 5.59 5.54 17 P/c 6.00 5.26 17 A/G 5.83 5.11 18 c/U 6.42 6.03 18 G/A 6.11 5.73 19 U/G 5.48 5.46 19 A/C 6.03 5.30 20 G/G 5.72 4.94 20 C/C 4.41 5.43 21 G/A 6.05 5.65 21 C/g 6.36 5.91 22 A/g 15.53 12.10 22 g/C 5.88 5.38 23 g/C 5.61 6.49 23 C/G 5.57 5.51 24 C/U 5.81 5.87 24 G/A 5.72 5.14 25 U/C 5.85 4.89 25 A/G 6.81 6.06 26 C/A 7.00 6.21 26 G/U 17.09 9.20 27 A/G 5.94 5.13 27 U/C 10.77 4.53 28 G/G --- --- 28 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 GC/GC 7.47 7.32 6.52 10.28 8.75 7.76 2 CG/CG 10.23 9.41 8.47 7.72 7.87 7.07 3 GG/UC 7.06 9.42 9.06 12.04 11.47 10.82 4 GA/UU 10.36 9.58 8.69 6.87 6.48 5.65 5 AU/AU 9.01 8.38 7.67 9.81 9.03 8.25 6 UU/AA 9.39 9.45 8.69 7.76 8.73 8.17 7 Uc/GA 9.77 10.72 10.10 10.44 10.32 9.74 8 cU/AG 9.23 8.74 7.96 9.88 8.81 8.04 9 UG/CA 9.65 9.46 8.86 8.31 8.93 8.28 10 GU/AC 9.12 8.76 7.96 8.66 8.15 7.40 11 UG/CA 9.45 8.77 8.14 10.07 9.73 9.00 12 Gt/aC 10.07 8.79 7.71 7.33 4.81 4.20 13 tP/Ga 3.03 2.12 2.08 8.74 9.48 8.89 14 PA/UG ---- ---- ---- ---- ---- ---- 15 AA/cU 7.85 7.68 7.75 6.04 4.38 3.06 16 AP/Ac 7.95 9.27 8.89 7.61 6.64 5.70 17 Pc/GA 9.61 8.03 7.16 9.22 7.15 6.30 18 cU/AG 8.97 7.76 6.99 9.97 8.76 7.97 19 UG/CA 9.94 10.30 9.65 8.48 9.12 8.72 20 GG/CC 8.15 7.60 6.90 9.55 8.72 7.93 21 GA/gC 12.00 10.50 9.79 5.47 6.59 6.20 22 Ag/Cg 11.17 11.49 10.69 4.92 6.25 5.87 23 gC/GC 9.44 9.18 8.33 7.97 7.00 6.29 24 CU/AG 9.76 9.08 8.38 7.70 7.93 7.33 25 UC/GA 8.89 6.86 6.84 12.56 11.77 10.91 26 CA/UG 10.19 8.48 7.51 8.08 5.42 4.32 27 AG/CU 10.41 7.85 6.71 13.52 10.09 8.98 28 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 GC/GC 27.28 -1.52 50.88 0.89 0.38 -0.26 2 CG/CG 28.27 -2.30 48.72 0.40 0.74 -0.54 3 GG/UC 29.32 3.59 47.73 0.88 0.47 -0.09 4 GA/UU 30.89 0.57 44.77 0.46 0.84 -0.29 5 AU/AU 33.73 3.61 45.10 0.48 0.74 -0.47 6 UU/AA 34.84 6.42 44.64 0.75 0.53 -0.40 7 Uc/GA 37.66 7.83 44.88 0.55 0.78 -0.29 8 cU/AG 37.70 11.65 42.22 0.40 0.88 -0.25 9 UG/CA 39.36 12.62 41.74 0.53 0.64 -0.56 10 GU/AC 40.50 15.78 41.32 0.56 0.76 -0.34 11 UG/CA 41.54 17.77 38.74 0.61 0.66 -0.43 12 Gt/aC 46.43 18.53 39.41 0.76 0.56 -0.35 13 tP/Ga 47.86 22.50 43.21 0.73 0.67 -0.12 14 PA/UG ---- ---- ---- ---- ---- ---- 15 AA/cU 44.05 -8.09 -3.04 -0.08 0.52 0.85 16 AP/Ac 44.03 -5.45 0.25 -0.00 0.37 0.93 17 Pc/GA 45.78 -4.22 2.82 0.03 0.69 0.72 18 cU/AG 45.25 -3.07 5.80 -0.02 0.65 0.76 19 UG/CA 43.15 -2.99 8.94 0.30 0.43 0.85 20 GG/CC 44.40 0.92 10.49 -0.10 0.53 0.84 21 GA/gC 42.84 -0.48 13.45 0.35 0.33 0.88 22 Ag/Cg 43.60 -0.06 16.14 0.28 0.40 0.87 23 gC/GC 42.05 1.13 19.72 0.07 0.06 1.00 24 CU/AG 41.77 2.52 22.25 -0.02 0.13 0.99 25 UC/GA 38.12 2.17 25.56 0.16 0.51 0.85 26 CA/UG 45.53 5.46 26.22 0.32 0.40 0.86 27 AG/CU 49.74 8.13 26.84 0.39 0.42 0.82 28 GG/CC ---- ---- ---- ---- ---- ----