**************************************************************************** This structure has broken O3'[i] to P[i+1] linkages **************************************************************************** 3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab. **************************************************************************** 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: 1BY4-DNA_no_prot_old.pdb Date and time: Sun Sep 29 02:16:56 2013 Number of base-pairs: 30 Number of atoms: 1237 **************************************************************************** HEADER GENE REGULATION/DNA 22-OCT-98 1BY4 TITLE STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THE TITLE 2 RXR ON DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RETINOIC ACID RECEPTOR RXR-ALPHA); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'- COMPND 7 D(*C*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*AP*G)-3'); COMPND 8 CHAIN: E, G; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'- COMPND 12 D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*A)-3'); COMPND 13 CHAIN: F, H; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES KEYWDS RXR, NUCLEAR RECEPTOR, HORMONE RESPONSE ELEMENT, PROTEIN- KEYWDS 2 DNA INTERATIONS, CRYSTAL STRUCTURE, GENE REGULATION/DNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.ZHAO,S.A.CHASSE,S.DEVARAKONDA,M.L.SIERK,B.AHVAZI, AUTHOR 2 P.B.SIGLER,F.RASTINEJAD REVDAT 4 24-FEB-09 1BY4 1 VERSN REVDAT 3 26-SEP-01 1BY4 3 ATOM REVDAT 2 07-MAY-00 1BY4 1 JRNL DBREF SEQADV REVDAT 1 12-JAN-00 1BY4 0 JRNL AUTH Q.ZHAO,S.A.CHASSE,S.DEVARAKONDA,M.L.SIERK,B.AHVAZI, JRNL AUTH 2 F.RASTINEJAD JRNL TITL STRUCTURAL BASIS OF RXR-DNA INTERACTIONS. JRNL REF J.MOL.BIOL. V. 296 509 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10669605 JRNL DOI 10.1006/JMBI.1999.3457 HELIX 5 5 GLU B 1253 ARG B 1264 1 12 HELIX 6 6 GLN B 1288 ALA B 1297 1 10 HELIX 7 7 ARG B 1302 ALA B 1304 5 3 SHEET 1 A 2 HIS B1233 ILE B1234 0 SHEET 2 A 2 ARG B1241 SER B1242 -1 O SER B1242 N HIS B1233 SHEET 1 B 2 GLY B1244 LYS B1245 0 SHEET 2 B 2 TYR B1250 SER B1251 -1 N SER B1251 O GLY B1244 **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.016) E:1495_:[..T]T-----A[..A]:1545_:F (0.020) | 2 (0.016) E:1496_:[..A]A-----T[..T]:1544_:F (0.017) | 3 (0.017) E:1497_:[..G]G-----C[..C]:1543_:F (0.021) | 4 (0.019) E:1498_:[..G]G-----C[..C]:1542_:F (0.014) | 5 (0.018) E:1499_:[..T]T-----A[..A]:1541_:F (0.012) | 6 (0.008) E:1500_:[..C]C-----G[..G]:1540_:F (0.026) | 7 (0.022) E:1501_:[..A]A-----T[..T]:1539_:F (0.009) | 8 (0.026) E:1502_:[..A]A-----T[..T]:1538_:F (0.017) | 9 (0.037) E:1503_:[..A]A-----T[..T]:1537_:F (0.027) | 10 (0.014) E:1504_:[..G]G-----C[..C]:1536_:F (0.023) | 11 (0.025) E:1505_:[..G]G-----C[..C]:1535_:F (0.020) | 12 (0.011) E:1506_:[..T]T-----A[..A]:1534_:F (0.009) | 13 (0.027) E:1507_:[..C]C-----G[..G]:1533_:F (0.013) | 14 (0.032) E:1508_:[..A]A-----T[..T]:1532_:F (0.018) | 15 (0.020) E:1509_:[..G]Gx---xC[..C]:1531_:F (0.011) | 16 (0.019) G:2495_:[..T]T-----A[..A]:2545_:H (0.012) | 17 (0.011) G:2496_:[..A]A-----T[..T]:2544_:H (0.013) | 18 (0.038) G:2497_:[..G]G-----C[..C]:2543_:H (0.014) | 19 (0.015) G:2498_:[..G]G-----C[..C]:2542_:H (0.021) | 20 (0.023) G:2499_:[..T]T-----A[..A]:2541_:H (0.019) | 21 (0.010) G:2500_:[..C]C-----G[..G]:2540_:H (0.026) | 22 (0.018) G:2501_:[..A]A-----T[..T]:2539_:H (0.010) | 23 (0.027) G:2502_:[..A]A-----T[..T]:2538_:H (0.009) | 24 (0.042) G:2503_:[..A]A-----T[..T]:2537_:H (0.021) | 25 (0.019) G:2504_:[..G]G-----C[..C]:2536_:H (0.012) | 26 (0.030) G:2505_:[..G]G-----C[..C]:2535_:H (0.014) | 27 (0.010) G:2506_:[..T]T-----A[..A]:2534_:H (0.022) | 28 (0.012) G:2507_:[..C]C-----G[..G]:2533_:H (0.014) | 29 (0.019) G:2508_:[..A]A-----T[..T]:2532_:H (0.015) | 30 (0.031) G:2509_:[..G]G-----C[..C]:2531_:H (0.017) | **************************************************************************** Detailed H-bond information: atom-name pair and length [ON] 1 T-----A [2] N3 - N1 2.85 O4 - N6 3.29 2 A-----T [2] N6 - O4 2.70 N1 - N3 2.83 3 G-----C [3] O6 - N4 2.52 N1 - N3 2.59 N2 - O2 2.69 4 G-----C [3] O6 - N4 2.99 N1 - N3 2.79 N2 - O2 2.50 5 T-----A [2] N3 - N1 2.96 O4 - N6 2.83 6 C-----G [3] O2 - N2 2.86 N3 - N1 3.13 N4 - O6 3.35 7 A-----T [2] N6 - O4 2.79 N1 - N3 2.84 8 A-----T [2] N6 - O4 2.96 N1 - N3 2.92 9 A-----T [2] N6 - O4 2.72 N1 - N3 3.03 10 G-----C [3] O6 - N4 2.99 N1 - N3 2.84 N2 - O2 2.67 11 G-----C [3] O6 - N4 3.21 N1 - N3 3.19 N2 - O2 3.15 12 T-----A [2] N3 - N1 3.16 O4 - N6 3.25 13 C-----G [3] O2 - N2 2.62 N3 - N1 2.91 N4 - O6 3.13 14 A-----T [2] N6 - O4 2.68 N1 - N3 2.76 15 G-----C [3] O6 - N4 2.73 N1 - N3 2.59 N2 - O2 2.48 16 T-----A [2] N3 - N1 2.99 O4 - N6 2.91 17 A-----T [2] N6 - O4 2.31 N1 - N3 2.27 18 G-----C [3] O6 - N4 2.62 N1 - N3 2.88 N2 - O2 3.10 19 G-----C [3] O6 - N4 3.23 N1 - N3 3.01 N2 - O2 2.83 20 T-----A [2] N3 - N1 3.14 O4 - N6 3.24 21 C-----G [3] O2 - N2 2.94 N3 - N1 3.10 N4 - O6 3.25 22 A-----T [2] N6 - O4 2.94 N1 - N3 3.11 23 A-----T [2] N6 - O4 3.22 N1 - N3 2.99 24 A-----T [2] N6 - O4 2.68 N1 - N3 2.91 25 G-----C [3] O6 - N4 3.03 N1 - N3 2.81 N2 - O2 2.60 26 G-----C [3] O6 - N4 3.19 N1 - N3 3.21 N2 - O2 3.05 27 T-----A [2] N3 - N1 2.47 O4 - N6 2.60 28 C-----G [3] O2 - N2 3.00 N3 - N1 3.04 N4 - O6 2.94 29 A-----T [2] N6 - O4 3.44 N1 - N3 3.17 30 G-----C [3] O6 - N4 3.03 N1 - N3 2.92 N2 - O2 2.84 **************************************************************************** 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 TA/TA 0.36( 0.00) 0.00( 0.00) 0.00( 0.00) 6.13( 1.43) 6.49( 1.43) 2 AG/CT 7.33( 5.49) 0.00( 0.00) 0.00( 0.00) 4.53( 0.00) 11.87( 5.49) 3 GG/CC 6.01( 3.19) 0.00( 0.00) 0.00( 0.00) 1.74( 0.00) 7.75( 3.19) 4 GT/AC 6.37( 1.94) 0.00( 0.00) 0.00( 0.00) 5.38( 4.12) 11.76( 6.06) 5 TC/GA 5.38( 1.00) 0.00( 0.00) 0.00( 0.00) 1.99( 0.12) 7.37( 1.12) 6 CA/TG 1.00( 0.00) 0.00( 0.00) 0.00( 0.00) 4.43( 0.54) 5.42( 0.54) 7 AA/TT 5.33( 3.51) 0.00( 0.00) 0.00( 0.00) 4.52( 0.00) 9.85( 3.51) 8 AA/TT 2.02( 1.36) 0.00( 0.00) 0.00( 0.00) 4.89( 0.02) 6.91( 1.38) 9 AG/CT 4.44( 3.24) 0.00( 0.00) 0.03( 0.00) 3.27( 0.00) 7.74( 3.24) 10 GG/CC 4.92( 3.46) 0.00( 0.00) 0.00( 0.00) 0.57( 0.00) 5.49( 3.46) 11 GT/AC 5.71( 1.48) 0.00( 0.00) 0.00( 0.00) 3.58( 1.96) 9.29( 3.44) 12 TC/GA 7.20( 2.02) 0.00( 0.00) 0.00( 0.00) 2.15( 0.49) 9.35( 2.52) 13 CA/TG 0.63( 0.00) 0.00( 0.00) 0.00( 0.00) 7.03( 2.15) 7.66( 2.15) 14 AG/CT 1.65( 0.79) 0.00( 0.00) 0.03( 0.00) 5.60( 0.65) 7.27( 1.44) 15 GT/AC 0.33( 0.00) 0.00( 0.00) 0.00( 0.00) 6.06( 4.00) 6.38( 4.00) 16 TA/TA 1.63( 0.16) 0.00( 0.00) 0.00( 0.00) 3.90( 0.71) 5.53( 0.88) 17 AG/CT 3.01( 1.37) 0.00( 0.00) 0.00( 0.00) 4.17( 0.00) 7.18( 1.37) 18 GG/CC 4.68( 2.70) 0.00( 0.00) 0.00( 0.00) 0.61( 0.00) 5.28( 2.70) 19 GT/AC 6.16( 1.80) 0.00( 0.00) 0.00( 0.00) 4.93( 3.38) 11.10( 5.18) 20 TC/GA 6.12( 1.17) 0.00( 0.00) 0.00( 0.00) 1.72( 0.04) 7.84( 1.21) 21 CA/TG 0.73( 0.00) 0.00( 0.00) 0.00( 0.00) 3.35( 0.06) 4.08( 0.06) 22 AA/TT 6.38( 4.64) 0.00( 0.00) 0.00( 0.00) 4.20( 0.00) 10.58( 4.64) 23 AA/TT 2.18( 0.88) 0.00( 0.00) 0.00( 0.00) 6.15( 0.63) 8.33( 1.51) 24 AG/CT 4.06( 2.97) 0.00( 0.00) 0.00( 0.00) 1.95( 0.00) 6.01( 2.97) 25 GG/CC 4.99( 2.61) 0.00( 0.00) 0.00( 0.00) 2.05( 0.34) 7.04( 2.95) 26 GT/AC 6.69( 1.90) 0.00( 0.00) 0.00( 0.00) 4.26( 2.59) 10.95( 4.49) 27 TC/GA 4.00( 0.48) 0.00( 0.00) 0.00( 0.00) 1.86( 0.27) 5.86( 0.75) 28 CA/TG 0.23( 0.00) 0.00( 0.00) 0.00( 0.00) 4.84( 0.55) 5.07( 0.55) 29 AG/CT 2.42( 1.17) 0.00( 0.00) 0.00( 0.00) 6.49( 0.84) 8.91( 2.01) **************************************************************************** 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 T-A 18.14 5.55 21.62 0.07 0.08 0.99 2 A-T 20.04 5.81 24.55 0.00 0.28 0.96 3 G-C 19.53 5.80 27.57 0.08 0.19 0.98 4 G-C 19.79 5.26 31.37 0.03 -0.07 1.00 5 T-A 18.97 5.24 34.62 0.18 0.02 0.98 6 C-G 21.02 5.90 37.08 -0.04 -0.29 0.96 7 A-T 19.59 5.73 41.07 0.06 -0.19 0.98 8 A-T 20.10 5.52 44.56 0.07 -0.15 0.99 9 A-T 20.72 4.80 47.50 0.02 -0.20 0.98 10 G-C 20.76 5.24 51.36 -0.02 -0.25 0.97 11 G-C 20.19 5.91 55.43 -0.15 -0.02 0.99 12 T-A 20.01 6.36 58.40 -0.10 -0.15 0.98 13 C-G 19.50 4.25 61.43 -0.27 -0.12 0.96 14 A-T 20.44 4.96 65.63 -0.19 -0.24 0.95 15 G-C 19.23 4.11 69.05 -0.07 -0.19 0.98 16 T-A 17.01 3.63 72.00 0.05 -0.10 0.99 17 A-T 16.36 2.90 75.20 -0.13 -0.13 0.98 18 G-C 15.28 3.29 78.73 -0.03 -0.25 0.97 19 G-C 15.91 3.92 81.88 -0.08 0.08 0.99 20 T-A 16.30 4.31 84.84 -0.06 0.17 0.98 21 C-G 14.72 3.89 88.16 0.11 0.15 0.98 22 A-T 16.02 3.70 91.60 -0.01 0.20 0.98 23 A-T 15.36 3.65 95.05 -0.06 0.20 0.98 24 A-T 15.06 4.79 98.11 0.02 0.08 1.00 25 G-C 15.31 3.95 102.35 0.03 0.20 0.98 26 G-C 15.35 3.66 105.89 0.16 0.07 0.99 27 T-A 15.73 2.96 108.66 0.19 0.08 0.98 28 C-G 15.89 5.04 112.25 0.25 -0.02 0.97 29 A-T 15.31 4.27 115.96 0.13 0.11 0.99 30 G-C 16.17 4.92 119.84 0.13 0.28 0.95 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 T-A 0.12 -0.02 0.85 -22.24 -12.77 5.42 2 A-T 0.33 -0.38 -1.20 -6.85 -14.90 -1.98 3 G-C -0.12 -0.47 -0.00 7.81 -12.27 -2.93 4 G-C -0.58 -0.24 -0.13 -15.80 -14.03 4.57 5 T-A -0.01 -0.24 1.15 -6.20 -1.93 -4.28 6 C-G 0.66 0.12 -0.90 28.98 -5.29 6.33 7 A-T 0.60 -0.22 -0.57 7.07 -28.65 -0.48 8 A-T 0.05 -0.04 -0.09 -3.37 -21.41 -2.07 9 A-T -0.95 -0.40 -0.37 -0.00 3.87 -10.90 10 G-C -0.67 -0.24 -0.21 -8.04 -10.50 3.81 11 G-C -0.38 0.27 -0.84 -30.70 -19.22 4.62 12 T-A -0.92 0.10 0.75 -4.75 0.80 0.62 13 C-G 0.03 -0.06 0.07 6.74 7.24 5.13 14 A-T -0.18 -0.28 -0.10 -4.18 -17.52 -2.29 15 G-C -0.08 -0.36 0.01 -20.14 -19.17 1.77 16 T-A -0.34 0.04 0.53 -12.53 -0.37 -4.58 17 A-T 0.67 -0.95 0.85 -6.41 -24.38 -16.20 18 G-C 0.09 -0.18 -0.34 -6.63 -19.86 -7.59 19 G-C -0.41 -0.01 0.28 -7.22 -16.32 2.05 20 T-A 0.11 0.22 -0.17 6.67 -8.73 0.80 21 C-G 0.63 0.07 0.05 21.40 -14.37 2.03 22 A-T 0.19 0.02 -0.58 15.88 -22.76 -0.93 23 A-T -0.02 0.03 -0.38 3.80 -19.07 3.26 24 A-T 0.53 -0.17 -0.68 -0.20 -5.54 -7.34 25 G-C -0.39 -0.16 -0.32 -14.28 -11.20 6.42 26 G-C -0.05 0.23 -0.72 -21.20 -6.53 0.98 27 T-A -0.29 -0.44 -0.10 6.54 -7.64 2.20 28 C-G 0.21 -0.01 -0.08 5.16 0.34 -2.21 29 A-T -0.38 0.14 0.65 5.15 -24.67 0.78 30 G-C 0.13 0.03 -0.60 -23.16 -22.07 3.69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.05 -0.12 -0.11 -3.29 -12.30 -0.31 s.d. 0.43 0.26 0.57 13.54 9.29 5.23 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 TA/TA -1.36 1.22 2.99 12.08 -3.29 42.20 2 AG/CT 0.92 -0.28 2.91 -6.01 2.98 24.33 3 GG/CC 0.77 -0.03 3.77 4.14 15.18 36.49 4 GT/AC -0.80 -0.82 3.15 -9.65 1.54 33.26 5 TC/GA 1.60 1.40 2.47 19.93 -8.25 39.88 6 CA/TG -0.97 1.34 3.91 -2.85 7.69 38.76 7 AA/TT 0.47 -0.08 3.50 -0.59 2.16 29.47 8 AA/TT -0.19 -0.49 3.04 -2.78 -2.87 31.41 9 AG/CT 1.00 -0.83 3.67 -3.60 -0.95 42.51 10 GG/CC 0.55 -1.11 3.97 10.84 10.40 32.66 11 GT/AC -0.36 -0.62 2.92 -7.78 -0.79 29.92 12 TC/GA 1.23 1.15 3.32 8.68 5.23 38.92 13 CA/TG -1.52 1.78 3.68 -5.00 6.87 35.96 14 AG/CT -0.36 -0.64 3.65 -7.15 1.25 40.09 15 GT/AC -2.14 -0.45 3.02 -6.20 6.23 44.66 16 TA/TA -0.63 -0.06 3.28 -3.99 -9.97 35.40 17 AG/CT 0.62 1.15 3.47 8.11 -4.05 36.82 18 GG/CC 0.74 -0.95 3.05 0.70 19.27 32.59 19 GT/AC -0.39 -0.46 2.95 4.35 2.99 30.24 20 TC/GA 1.39 1.31 3.17 0.95 -9.63 40.80 21 CA/TG -0.70 1.20 3.41 5.83 5.04 36.59 22 AA/TT 0.91 -0.07 3.39 2.26 1.67 30.73 23 AA/TT -0.72 -0.19 3.19 -4.29 7.19 40.74 24 AG/CT 1.13 -0.88 4.09 -5.16 -4.60 36.45 25 GG/CC -0.10 -0.82 3.46 5.52 8.70 30.29 26 GT/AC -0.36 -0.84 2.73 -0.19 2.17 31.03 27 TC/GA 1.11 1.73 3.60 5.99 -2.43 38.39 28 CA/TG -0.98 1.24 3.50 -6.91 7.15 37.15 29 AG/CT -0.32 -0.18 4.02 6.35 7.71 40.11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. 0.02 0.13 3.35 0.81 2.57 35.79 s.d. 0.97 0.96 0.40 7.09 6.84 4.85 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 TA/TA 1.89 2.78 2.44 -4.45 -16.36 43.94 2 AG/CT -1.38 -3.60 2.56 6.91 13.93 25.22 3 GG/CC -2.11 -0.57 3.55 22.98 -6.27 39.63 4 GT/AC -1.61 -0.12 3.21 2.62 16.43 34.62 5 TC/GA 2.44 -0.60 2.63 -11.16 -26.97 45.13 6 CA/TG 0.86 1.02 4.15 11.44 4.24 39.59 7 AA/TT -0.64 -1.06 3.47 4.23 1.15 29.55 8 AA/TT -0.40 -0.13 3.08 -5.28 5.11 31.66 9 AG/CT -1.03 -1.78 3.59 -1.31 4.96 42.67 10 GG/CC -3.59 0.96 3.48 17.39 -18.13 35.86 11 GT/AC -1.03 -0.69 2.94 -1.50 14.75 30.90 12 TC/GA 1.03 -0.73 3.62 7.69 -12.77 40.16 13 CA/TG 1.70 1.59 4.10 10.93 7.96 36.92 14 AG/CT -1.08 -0.37 3.64 1.81 10.33 40.72 15 GT/AC -1.11 2.24 3.19 8.10 8.06 45.47 16 TA/TA 1.28 0.44 3.23 -15.94 6.38 36.95 17 AG/CT 2.33 0.15 3.39 -6.30 -12.61 37.88 18 GG/CC -3.63 -1.06 2.18 31.17 -1.13 37.73 19 GT/AC -1.39 1.49 2.81 5.67 -8.26 30.69 20 TC/GA 2.77 -1.85 2.83 -13.58 -1.34 41.88 21 CA/TG 1.17 1.89 3.39 7.93 -9.17 37.37 22 AA/TT -0.47 -1.25 3.44 3.14 -4.26 30.85 23 AA/TT -1.01 0.57 3.18 10.19 6.09 41.55 24 AG/CT -0.61 -2.64 3.97 -7.28 8.15 37.08 25 GG/CC -3.10 1.20 3.05 16.07 -10.19 31.96 26 GT/AC -1.90 0.64 2.67 4.05 0.35 31.11 27 TC/GA 2.93 -0.85 3.61 -3.67 -9.04 38.91 28 CA/TG 0.88 0.51 3.78 10.98 10.62 38.41 29 AG/CT -1.27 1.28 3.83 11.04 -9.08 41.28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.28 -0.02 3.28 4.27 -0.93 37.09 s.d. 1.85 1.47 0.50 10.64 10.93 5.11 **************************************************************************** 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 T-A 59.6 57.3 10.2 8.7 9.8 2 A-T 54.7 49.4 10.6 8.8 9.6 3 G-C 53.5 52.5 10.4 8.7 9.5 4 G-C 54.1 57.5 10.4 8.7 9.7 5 T-A 56.1 54.0 10.6 8.9 9.8 6 C-G 62.2 57.8 10.3 8.8 9.9 7 A-T 54.3 49.7 10.7 8.9 9.8 8 A-T 54.4 53.5 10.8 9.0 9.9 9 A-T 48.5 53.1 10.7 8.9 9.6 10 G-C 55.5 59.6 10.3 8.8 9.8 11 G-C 61.7 60.8 10.4 9.0 10.0 12 T-A 51.0 61.3 10.8 9.1 10.1 13 C-G 56.3 55.5 10.5 8.9 9.9 14 A-T 54.5 55.1 10.4 8.8 9.7 15 G-C 54.9 54.7 10.2 8.6 9.5 16 T-A 51.6 55.8 10.9 9.1 10.0 17 A-T 52.3 42.4 10.3 8.3 9.0 18 G-C 50.9 47.1 11.0 9.1 9.8 19 G-C 54.3 55.9 10.7 9.0 10.0 20 T-A 55.6 54.3 10.9 9.2 10.2 21 C-G 59.2 55.1 10.6 9.0 10.0 22 A-T 56.4 54.0 10.7 9.0 9.9 23 A-T 57.0 54.7 10.6 9.0 10.0 24 A-T 52.7 46.1 10.9 9.0 9.8 25 G-C 57.5 59.3 10.3 8.7 9.8 26 G-C 57.2 57.0 10.8 9.2 10.1 27 T-A 55.3 60.3 10.1 8.5 9.5 28 C-G 55.0 55.0 10.8 9.1 10.0 29 A-T 49.6 55.4 10.9 9.1 10.1 30 G-C 56.8 50.6 10.7 9.0 9.9 **************************************************************************** Classification of each dinucleotide step in a right-handed nucleic acid structure: A-like; B-like; TA-like; intermediate of A and B, or other cases step Xp Yp Zp XpH YpH ZpH Form 1 TA/TA -2.62 8.79 -0.80 -0.61 8.71 -1.31 B 2 AG/CT -3.04 9.00 -0.65 -4.36 9.00 0.62 B 3 GG/CC -2.66 9.07 0.20 -4.61 8.36 3.49 B 4 GT/AC -3.40 9.13 0.31 -4.73 9.10 0.63 B 5 TC/GA -3.28 8.52 -0.95 -0.67 8.20 -2.51 6 CA/TG -3.19 8.58 -1.90 -2.28 8.78 -0.30 B 7 AA/TT -3.19 9.11 -1.10 -3.80 9.17 -0.45 B 8 AA/TT -2.70 9.03 -0.35 -3.02 8.96 -1.09 B 9 AG/CT -1.83 8.21 1.19 -2.74 8.23 1.03 10 GG/CC -2.88 8.45 0.87 -6.10 7.84 3.27 11 GT/AC -3.08 8.96 0.12 -3.96 8.96 -0.13 B 12 TC/GA -3.15 8.70 -0.03 -2.06 8.65 0.91 B 13 CA/TG -2.77 8.71 -0.70 -1.08 8.70 0.83 B 14 AG/CT -3.47 9.04 -0.86 -4.57 9.06 -0.62 B 15 GT/AC --- --- --- --- --- --- --- 16 TA/TA -2.73 9.05 0.03 -1.53 8.75 -2.29 17 AG/CT -1.65 8.83 -0.52 0.80 8.72 -1.46 18 GG/CC -2.50 9.16 0.66 -5.92 7.62 5.13 19 GT/AC -3.71 9.17 -0.50 -5.02 9.17 0.37 20 TC/GA -3.37 8.66 -1.43 -0.78 8.13 -3.31 21 CA/TG -2.84 8.72 -1.07 -1.87 8.78 0.18 B 22 AA/TT -3.24 9.11 -0.88 -3.70 9.15 -0.43 B 23 AA/TT -2.75 9.10 -0.15 -3.62 9.00 1.35 B 24 AG/CT -2.31 8.62 0.52 -2.77 8.62 -0.58 25 GG/CC -3.24 8.86 0.65 -6.15 8.35 3.10 26 GT/AC -3.20 9.04 -0.26 -5.03 9.04 0.35 B 27 TC/GA -2.87 8.62 -0.74 -0.07 8.56 -1.31 B 28 CA/TG -2.72 8.76 -0.49 -1.71 8.71 1.01 B 29 AG/CT -3.16 9.23 -0.55 -4.22 9.17 1.16 B **************************************************************************** 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 TA/TA --- --- --- --- 2 AG/CT --- --- --- --- 3 GG/CC 13.2 --- 17.1 --- 4 GT/AC 12.7 12.6 19.9 19.8 5 TC/GA 11.6 11.6 17.7 17.6 6 CA/TG 11.0 11.0 17.4 17.4 7 AA/TT 11.3 11.2 17.9 17.9 8 AA/TT 11.5 11.4 17.9 17.9 9 AG/CT 12.3 12.2 20.3 20.1 10 GG/CC 12.8 12.6 18.0 17.9 11 GT/AC 13.4 13.2 17.3 17.3 12 TC/GA 12.8 12.7 17.4 --- 13 CA/TG 10.9 10.4 --- --- 14 AG/CT 10.3 9.5 17.1 --- 15 GT/AC 10.6 --- 14.3 14.3 16 TA/TA --- --- 15.3 15.2 17 AG/CT --- --- 19.1 18.9 18 GG/CC 13.0 --- 17.0 16.9 19 GT/AC 12.9 12.9 18.9 18.9 20 TC/GA 12.0 12.0 17.1 17.1 21 CA/TG 11.2 11.2 18.1 18.1 22 AA/TT 11.5 11.5 18.9 18.8 23 AA/TT 11.8 11.8 18.4 18.4 24 AG/CT 12.3 12.2 20.3 19.9 25 GG/CC 12.3 12.1 17.7 17.6 26 GT/AC 12.7 12.6 17.5 17.4 27 TC/GA 12.6 --- 17.0 --- 28 CA/TG --- --- --- --- 29 AG/CT --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 3.39(0.69) **************************************************************************** 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 T --- --- -166.7 151.8 -137.3 -85.5 179.9 2 A 148.2 -164.4 162.9 148.2 -164.2 -113.3 -118.2 3 G 25.7 133.5 -31.9 152.8 -142.1 -172.2 -75.1 4 G 80.5 -135.8 -148.8 137.9 -165.7 -88.6 -146.3 5 T -44.5 -171.2 34.5 148.3 -165.8 -129.9 -113.1 6 C 24.8 139.3 -15.6 152.2 -91.4 117.7 -45.4 7 A 104.0 -126.2 159.2 131.8 -145.8 -113.5 -115.3 8 A -26.9 137.5 37.5 124.0 -149.6 -170.8 -108.7 9 A 10.1 124.9 -10.9 149.0 159.9 -120.2 -101.4 10 G -68.2 172.1 61.9 90.3 -152.8 -70.2 -165.6 11 G -78.2 163.8 79.2 89.1 -151.3 -103.6 -168.2 12 T -5.3 154.5 34.9 143.0 -154.6 -121.3 -113.6 13 C -5.0 151.7 2.1 144.9 -98.9 124.4 -77.9 14 A 109.5 -124.5 157.4 152.6 -155.2 -93.6 -126.8 15 G -3.9 -133.5 -62.9 150.2 --- --- -125.6 16 T --- -178.0 171.1 141.8 -132.3 -64.3 -122.8 17 A -33.6 -37.4 -104.2 145.1 -133.8 -115.2 -147.2 18 G 128.8 -128.9 157.1 145.1 -179.7 -136.5 -106.9 19 G 154.4 -161.4 -177.6 147.2 -152.1 -128.5 -142.1 20 T 35.4 133.9 -32.8 157.4 -49.5 130.3 -72.8 21 C -45.1 131.8 -7.6 148.0 -134.7 149.7 -61.0 22 A 108.5 -125.8 175.9 141.9 -144.2 -103.1 -114.9 23 A -32.6 144.8 32.1 116.9 -155.4 -148.9 -106.0 24 A -16.9 141.3 11.1 146.1 176.8 -130.9 -116.0 25 G -24.5 155.5 30.5 87.4 -168.3 -62.8 -158.1 26 G -61.5 -172.3 52.5 148.4 -167.9 -137.2 -124.1 27 T 51.5 -179.2 -55.8 153.3 -164.1 -125.6 -101.0 28 C 17.0 126.0 8.1 151.0 -117.9 133.5 -64.9 29 A 108.7 -132.5 170.3 145.9 -175.7 -113.6 -128.0 30 G 61.3 171.2 -69.2 151.4 --- --- -109.1 Strand II base alpha beta gamma delta epsilon zeta chi 1 A -60.8 161.2 63.1 144.6 --- --- -98.5 2 T -49.8 -162.8 36.9 145.1 -167.1 -112.2 -92.3 3 C 2.9 -170.3 -32.1 148.9 168.7 -83.4 -113.6 4 C 21.7 -153.9 -68.7 144.3 -164.8 -115.6 -102.2 5 A -61.4 141.0 49.6 142.4 -161.9 -99.7 -109.6 6 G 32.5 -162.1 -86.9 178.3 -127.4 -170.4 -99.1 7 T -48.1 177.7 41.4 148.1 -138.1 -134.2 -99.5 8 T 48.9 177.1 -57.4 159.4 170.3 -102.4 -90.8 9 T -46.4 -166.3 54.2 144.3 -178.9 -123.0 -108.9 10 C -115.4 -122.1 62.4 140.4 169.8 -115.1 -106.0 11 C 51.4 -167.3 -93.5 150.1 143.9 -78.2 -91.3 12 A -79.5 152.9 54.6 152.3 -159.1 -126.6 -101.7 13 G -56.1 153.7 49.2 149.6 -119.9 179.6 -89.9 14 T 28.6 170.8 -61.1 151.7 -146.8 -111.2 -96.5 15 C --- --- -34.2 153.0 -155.1 -95.1 -132.3 16 A 30.4 129.4 2.8 152.6 --- --- -84.8 17 T -27.4 153.2 39.4 143.3 176.6 -139.5 -102.0 18 C 12.8 176.8 -25.9 144.8 -165.6 -129.6 -108.6 19 C -52.9 156.3 47.1 90.0 -179.3 -102.7 -123.1 20 A -65.8 152.4 51.8 143.1 -167.4 -101.9 -99.5 21 G -63.5 160.7 55.1 143.8 -125.4 -170.2 -109.1 22 T -48.3 -175.8 47.9 141.9 -159.9 -107.9 -109.8 23 T 53.5 161.1 -58.7 155.1 162.2 -100.5 -97.5 24 T 143.0 -177.9 -176.5 146.4 -173.2 -115.6 -126.4 25 C -39.5 -61.2 -107.7 155.7 -160.4 -105.2 -137.2 26 C 73.3 -150.6 -124.9 160.8 -141.3 -52.2 -111.8 27 A -83.0 150.9 47.5 152.3 -153.2 -130.1 -106.6 28 G -60.8 174.2 42.4 153.2 -106.4 166.6 -81.4 29 T -63.4 174.0 43.6 129.5 -154.1 -103.9 -119.1 30 C --- --- 65.2 137.4 -159.7 -81.3 -118.3 **************************************************************************** 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: amplitude of pseudorotation of the sugar ring P: phase angle of pseudorotation of the sugar ring Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 T 24.3 -0.6 -21.4 35.5 -37.9 38.5 236.2 C4'-endo 2 A -11.0 28.4 -34.2 28.4 -11.2 34.2 180.1 C3'-exo 3 G -28.8 43.3 -39.9 25.2 2.0 42.9 158.3 C2'-endo 4 G -13.9 25.1 -26.6 18.8 -3.1 27.2 168.1 C2'-endo 5 T -18.1 35.1 -37.7 28.4 -6.7 38.2 171.1 C2'-endo 6 C -16.5 33.6 -37.1 28.5 -7.6 37.4 173.0 C2'-endo 7 A -25.4 34.6 -31.1 16.6 5.4 34.9 152.9 C2'-endo 8 A -41.8 46.2 -31.9 9.3 20.0 45.2 134.8 C1'-exo 9 A -25.7 40.1 -37.7 24.2 0.6 40.1 160.0 C2'-endo 10 G 3.7 -26.1 37.6 -36.2 20.4 38.6 13.1 C3'-endo 11 G -3.2 -21.6 36.7 -39.3 26.5 39.8 22.8 C3'-endo 12 T -22.3 35.4 -34.8 22.6 -0.4 36.6 162.0 C2'-endo 13 C -22.7 36.0 -35.1 23.1 -0.4 36.9 161.9 C2'-endo 14 A -18.6 35.2 -37.3 27.8 -5.9 37.9 170.1 C2'-endo 15 G 4.8 16.2 -29.6 32.6 -23.9 33.0 206.3 C3'-exo 16 T -23.7 37.3 -36.1 23.2 0.2 38.2 161.1 C2'-endo 17 A 0.2 19.8 -30.7 31.3 -20.2 32.4 198.7 C3'-exo 18 G -29.7 42.2 -37.6 21.4 5.1 41.7 154.3 C2'-endo 19 G -19.1 32.8 -33.6 23.2 -2.7 34.6 165.9 C2'-endo 20 T -14.4 32.4 -36.6 29.3 -9.5 36.7 175.9 C2'-endo 21 C -24.9 39.4 -38.8 25.6 -0.6 40.7 162.3 C2'-endo 22 A -14.2 28.1 -31.1 23.2 -5.9 31.4 172.1 C2'-endo 23 A -37.8 41.6 -28.5 7.8 18.7 40.9 134.1 C1'-exo 24 A -24.9 39.9 -38.0 24.8 -0.0 40.2 161.2 C2'-endo 25 G 5.0 -25.4 34.9 -32.8 17.6 35.5 10.5 C3'-endo 26 G -23.3 35.9 -34.2 21.8 0.9 36.4 160.0 C2'-endo 27 T 3.5 17.4 -30.2 32.9 -23.1 33.1 204.4 C3'-exo 28 C -22.8 38.7 -39.1 27.2 -3.1 40.4 165.5 C2'-endo 29 A -17.3 32.9 -34.9 25.5 -5.3 35.5 169.8 C2'-endo 30 G 5.0 16.5 -30.2 33.5 -24.7 33.8 206.6 C3'-exo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 A -26.6 38.6 -35.6 21.4 3.0 38.7 156.9 C2'-endo 2 T -15.1 31.1 -34.7 26.5 -7.3 34.9 173.4 C2'-endo 3 C 4.1 15.1 -26.9 29.9 -21.6 29.9 206.1 C3'-exo 4 C -14.6 26.7 -28.1 19.8 -3.3 28.8 168.1 C2'-endo 5 A -19.4 33.9 -34.9 24.5 -3.5 35.8 166.7 C2'-endo 6 G -0.9 25.6 -38.9 40.0 -24.3 40.7 197.5 C3'-exo 7 T -26.6 40.4 -37.6 23.8 1.6 40.3 158.9 C2'-endo 8 T 1.4 21.9 -35.3 36.8 -24.3 37.7 200.5 C3'-exo 9 T -10.5 27.7 -33.9 28.2 -11.4 33.9 180.7 C3'-exo 10 C -27.5 37.7 -33.3 18.2 5.5 37.4 152.8 C2'-endo 11 C 0.7 18.6 -29.2 30.4 -19.7 31.0 199.8 C3'-exo 12 A -11.3 29.6 -35.6 29.9 -11.8 35.6 180.4 C3'-exo 13 G -32.0 45.4 -41.1 24.4 4.3 45.1 155.6 C2'-endo 14 T -13.6 27.8 -30.2 23.3 -6.5 30.5 172.9 C2'-endo 15 C -7.9 29.2 -37.8 34.2 -16.7 38.1 186.8 C3'-exo 16 A -22.1 37.5 -38.3 26.9 -3.2 39.5 165.9 C2'-endo 17 T -22.4 36.2 -35.2 23.1 -0.7 37.0 162.2 C2'-endo 18 C -15.4 29.7 -31.6 23.3 -5.1 32.0 170.2 C2'-endo 19 C -42.2 29.7 -6.2 -18.7 38.2 42.3 98.5 O4'-endo 20 A -18.2 33.0 -34.4 24.4 -4.1 35.2 167.9 C2'-endo 21 G -30.1 41.6 -36.5 20.6 5.7 40.9 153.2 C2'-endo 22 T -22.1 35.1 -34.1 22.2 -0.2 35.9 161.6 C2'-endo 23 T -5.4 24.7 -33.1 30.6 -16.1 33.5 189.3 C3'-exo 24 T -19.3 34.2 -35.8 25.4 -4.0 36.7 167.7 C2'-endo 25 C -1.1 22.7 -34.6 34.8 -21.1 36.1 196.8 C3'-exo 26 C -11.3 31.3 -37.8 32.8 -13.6 37.8 181.9 C3'-exo 27 A -15.3 32.2 -35.8 28.0 -8.2 35.9 174.2 C2'-endo 28 G -22.3 38.7 -39.1 28.2 -3.9 40.2 166.5 C2'-endo 29 T -35.8 39.9 -28.3 8.3 17.1 39.4 135.9 C1'-exo 30 C -16.6 30.8 -33.3 23.9 -4.9 33.9 169.7 C2'-endo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II base P--P C1'--C1' base P--P C1'--C1' 1 T/A --- 5.8 1 A/T 6.6 4.6 2 A/G 7.5 4.5 2 T/C 6.6 4.9 3 G/G 5.8 4.9 3 C/C 6.6 5.3 4 G/T 7.3 5.2 4 C/A 7.0 4.9 5 T/C 6.5 5.0 5 A/G 6.8 5.1 6 C/A 6.0 4.9 6 G/T 6.7 5.1 7 A/A 7.1 4.6 7 T/T 6.9 4.6 8 A/A 6.7 5.0 8 T/T 6.9 5.1 9 A/G 6.4 5.0 9 T/C 6.1 5.6 10 G/G 6.0 5.1 10 C/C 7.2 4.9 11 G/T 6.5 6.1 11 C/A 7.0 5.1 12 T/C 6.6 5.1 12 A/G 6.8 5.4 13 C/A 6.1 5.0 13 G/T 6.3 4.8 14 A/G 7.4 5.4 14 T/C --- 5.2 15 G/T 10.9 7.6 15 C/A --- 4.9 16 T/A 7.3 4.1 16 A/T 6.8 4.8 17 A/G 5.2 5.1 17 T/C 6.3 5.1 18 G/G 7.4 5.6 18 C/C 6.6 5.3 19 G/T 7.4 5.3 19 C/A 7.1 4.5 20 T/C 6.0 4.2 20 A/G 6.9 5.7 21 C/A 6.2 5.2 21 G/T 6.6 4.8 22 A/A 7.3 4.3 22 T/T 6.8 4.6 23 A/A 6.6 5.2 23 T/T 7.6 5.2 24 A/G 6.7 4.9 24 T/C 6.3 5.9 25 G/G 6.0 5.3 25 C/C 7.1 4.6 26 G/T 6.5 5.9 26 C/A 6.9 4.9 27 T/C 6.5 4.6 27 A/G 6.7 5.3 28 C/A 6.3 5.5 28 G/T 6.6 5.3 29 A/G 7.5 5.3 29 T/C --- 4.7 **************************************************************************** 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 TA/TA 11.3 8.8 7.8 6.3 3.0 2.5 2 AG/CT 7.5 4.7 4.0 13.1 10.1 9.6 3 GG/CC 9.4 7.3 6.5 9.7 7.8 6.9 4 GT/AC 9.7 7.4 6.6 10.8 7.1 6.7 5 TC/GA 7.2 4.5 4.5 9.2 6.0 5.8 6 CA/TG 9.8 6.9 6.3 8.4 5.2 4.7 7 AA/TT 9.2 5.8 5.2 10.7 7.5 7.1 8 AA/TT 9.5 6.5 5.9 9.5 6.1 5.9 9 AG/CT 6.9 5.9 5.1 10.5 8.1 7.6 10 GG/CC 11.1 9.6 8.8 8.8 7.7 6.7 11 GT/AC 8.8 6.9 6.1 10.8 7.4 6.9 12 TC/GA 8.6 5.4 4.9 9.2 6.7 6.1 13 CA/TG 10.1 7.4 6.7 7.5 4.3 3.7 14 AG/CT 9.8 6.6 6.0 10.5 7.2 6.6 15 GT/AC 12.3 9.2 8.4 ---- 5.2 4.6 16 TA/TA 9.7 6.2 5.5 8.1 4.9 4.8 17 AG/CT 8.7 6.3 5.4 8.8 5.7 5.2 18 GG/CC 8.7 7.8 7.1 10.6 9.0 8.2 19 GT/AC 11.5 8.5 8.0 9.5 6.1 5.5 20 TC/GA 6.5 3.2 3.5 9.9 6.9 6.8 21 CA/TG 10.5 7.8 7.2 7.5 4.4 3.8 22 AA/TT 9.1 5.6 5.0 10.7 7.7 7.3 23 AA/TT 10.1 7.6 6.7 9.3 6.5 5.9 24 AG/CT 6.3 4.7 4.0 11.8 9.1 8.4 25 GG/CC 11.0 9.6 8.8 9.8 7.4 6.6 26 GT/AC 10.6 8.1 7.4 10.1 7.0 6.3 27 TC/GA 7.8 4.5 4.4 9.3 6.2 6.0 28 CA/TG 9.1 6.7 6.0 8.7 5.7 5.1 29 AG/CT 11.2 8.2 7.7 9.1 6.1 5.4 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step bp Px Py Pz Hx Hy Hz 1 TA/TA 19.13 8.79 22.79 -0.23 0.09 0.97 2 AG/CT 22.45 3.18 26.51 0.24 0.39 0.89 3 GG/CC 20.30 3.60 29.16 0.43 -0.01 0.90 4 GT/AC 20.48 4.21 33.27 -0.04 0.20 0.98 5 TC/GA 18.21 6.31 37.14 0.43 -0.39 0.82 6 CA/TG 19.98 4.62 38.91 -0.14 -0.10 0.99 7 AA/TT 19.26 6.66 42.97 -0.01 -0.15 0.99 8 AA/TT 20.28 5.52 46.14 0.13 -0.26 0.96 9 AG/CT 18.85 4.76 49.48 0.06 -0.27 0.96 10 GG/CC 17.63 7.56 52.67 -0.43 -0.31 0.84 11 GT/AC 19.33 5.23 57.01 0.11 0.01 0.99 12 TC/GA 20.86 5.55 60.27 -0.21 -0.37 0.91 13 CA/TG 18.53 6.28 63.56 -0.04 -0.06 1.00 14 AG/CT 20.68 3.90 67.48 -0.21 -0.06 0.98 15 GT/AC 18.71 1.64 70.61 -0.11 0.01 0.99 16 TA/TA 15.84 2.38 73.23 -0.00 -0.39 0.92 17 AG/CT 15.05 1.03 76.95 0.10 -0.04 0.99 18 GG/CC 14.18 6.87 79.93 -0.54 -0.14 0.83 19 GT/AC 16.33 6.05 83.08 -0.23 0.17 0.96 20 TC/GA 17.63 1.94 87.24 0.06 0.37 0.93 21 CA/TG 15.63 5.89 89.91 -0.03 -0.01 1.00 22 AA/TT 16.49 2.67 93.46 -0.03 0.11 0.99 23 AA/TT 14.76 3.28 96.89 0.14 0.25 0.96 24 AG/CT 17.38 5.70 100.36 -0.15 0.15 0.98 25 GG/CC 17.90 1.92 103.93 0.32 0.34 0.89 26 GT/AC 17.45 3.23 107.00 0.15 0.14 0.98 27 TC/GA 13.63 2.42 111.47 0.35 0.11 0.93 28 CA/TG 16.04 3.81 114.00 0.00 -0.12 0.99 29 AG/CT 15.93 6.24 117.58 -0.10 0.20 0.97