PDB data file name: 437D.py.pdb Base-pair criteria used: 3.35 3.35 15.00 1.50 65.00 4.50 7.50 [ O N] Six-line information for each base-pair as follows: #1: Overall serial number, local serial number, paired residue numbers, detailed pairing residue information. #2: One-letter base-pair followed by six base-pair parameters (shear, stretch, stagger, buckle, propeller, opening). The parameters are with respect to the Watson-Crick base reference frame. There are two types of base-pair orientation: M-N means the two bases have opposite orientations as in Watson-Crick base-pair; M+N means the two bases have the same local orientations as in Hoogsteen base- pair. All possible base pairing patterns can then be classified based on the six parameters, among which shear, stretch and opening are most discriminative. #3: H-bonding information (atom pair followed by their distance). #4: Overall classification of the base-pair (anti-parallel vs parallel based on relative z-axis of the two bases, cis vs trans based on x-axis and C1-RN9/YN1 directions). #5: Relative directions of the three axes and their numerical values. The last 3 numbers are the angles between the glycosidic bonds, and the two chi torsion angles. #6: The actual parameters used to locate the base-pair in question. 1 1 2 157 ....>A:...2_:[..G]G-**--C[..C]:...3_:A<.... G-C 1.51 3.18 -0.22 6.62 -12.05 -92.01 G-C [1] O6 - N4 2.91 anti-parallel trans trans -+- 92.4 88.5 166.2 163.3 177.6 -166.8 3.52 0.22 13.75 11.44 3.64 7.79 27.22 22.00 2 2 2 159 ....>A:...2_:[..G]G-**+-G[..G]:..18_:A<.... G+G 1.58 3.31 0.02 8.92 -5.11 -92.47 G+G [2] N1 - O6 2.74 N2 - N7 2.88 parallel trans cis --+ 92.2 92.7 10.3 89.6 177.6 -131.5 3.67 0.02 10.28 9.67 1.23 7.74 27.20 21.85 3 1 3 17 ....>A:...3_:[..C]C-----G[..G]:..18_:A<.... C-G 0.13 -0.04 -0.28 6.60 -3.15 -0.19 C-G [3] O2 - N2 2.85 N3 - N1 3.00 N4 - O6 3.07 anti-parallel cis cis +-- 3.2 173.4 172.7 75.5 -166.8 -131.5 0.31 0.28 7.32 9.05 -3.77 6.59 26.23 25.02 4 2 3 156 ....>A:...3_:[..C]C-**--G[..G]:...2_:A<.... C-G -1.51 3.18 -0.22 -6.62 -12.05 -92.01 C-G [1] N4 - O6 2.91 anti-parallel trans trans -+- 92.4 88.5 166.2 163.3 -166.8 177.6 3.52 0.22 13.75 11.44 3.64 7.79 24.88 24.70 5 1 4 16 ....>A:...4_:[..G]G-----C[..C]:..17_:A<.... G-C -0.26 -0.10 0.02 -3.71 -19.48 3.82 G-C [3] O6 - N4 2.97 N1 - N3 2.90 N2 - O2 2.70 anti-parallel cis cis +-- 19.8 174.7 160.2 66.8 -170.3 -170.3 0.28 0.02 19.83 8.91 -3.68 6.87 23.58 28.14 6 2 4 19 ....>A:...4_:[..G]G-**+-A[..A]:..20_:A<.... G+A -2.55 -7.35 1.23 -35.98 -9.94 -150.79 G+A [2] O2'- N1 2.70 N2 - N3 3.02 parallel trans trans --+ 134.1 150.6 37.3 146.6 -170.3 -130.9 7.88 1.23 37.33 7.89 9.20 3.34 25.46 28.57 7 1 5 15 ....>A:...5_:[..C]C-----G[..G]:..16_:A<.... C-G 0.07 -0.12 -0.04 3.91 -15.80 2.37 C-G [3] O2 - N2 2.65 N3 - N1 2.84 N4 - O6 2.93 anti-parallel cis cis +-- 16.0 175.5 163.7 72.7 -161.8 -162.2 0.14 0.04 16.27 8.95 -3.96 6.65 21.03 30.89 8 1 6 14 ....>A:...6_:[..G]G-----C[..C]:..15_:A<.... G-C -0.24 -0.09 0.07 -6.25 -14.36 -1.92 G-C [3] O6 - N4 2.96 N1 - N3 2.97 N2 - O2 2.96 anti-parallel cis cis +-- 14.5 173.5 164.3 73.7 -169.8 -158.0 0.27 0.07 15.66 9.03 -3.82 8.16 19.50 34.05 9 1 7 13 ....>A:...7_:[..G]G-----C[..C]:..14_:A<.... G-C -0.18 -0.05 -0.06 -10.89 -11.77 1.66 G-C [3] O6 - N4 3.09 N1 - N3 2.93 N2 - O2 2.73 anti-parallel cis cis +-- 11.9 169.0 164.0 72.8 -155.2 -166.4 0.20 0.06 16.03 8.99 -3.88 10.51 19.70 36.93 10 2 7 23 ....>A:...7_:[..G]G-**+-A[..A]:..24_:A<.... G+A 3.77 -3.78 0.00 -12.81 9.13 -60.00 G+A [3] O2'- N6 2.91 N2 - N1 3.16 N3 - N6 3.01 parallel cis cis +++ 60.2 61.0 15.7 61.8 -155.2 -164.8 5.34 0.00 15.73 8.68 3.13 10.20 16.97 36.92 11 1 8 12 ....>A:...8_:[..C]C-**--G[..G]:..12_:A<.... C-G 3.11 -0.60 -0.20 3.02 2.00 -86.56 C-G [3] O2 * O6 3.08 N3 * O6 2.82 N4 - N7 3.10 anti-parallel cis trans +-- 86.5 93.4 176.4 152.2 -170.3 -154.9 3.17 0.20 3.63 8.38 2.76 15.46 18.21 38.89 12 2 8 25 ....>A:...8_:[..C]C-**+-C[..C]:..26_:A<.... C+C 2.66 -1.00 -0.32 -22.80 14.93 -90.56 C+C [1] O2 - N4 3.23 parallel cis cis +-+ 89.3 91.8 27.3 87.7 -170.3 -157.8 2.86 0.32 27.25 9.15 3.86 15.24 18.23 38.97 13 1 9 172 ....>A:...9_:[..A]A-**--C[..C]:..11_:A<.... A-C -6.61 -1.12 1.17 40.33 2.74 51.72 A-C [2] N6 - O2 2.91 N1 - O2' 2.90 anti-parallel cis cis +-- 48.4 115.3 139.6 16.9 173.0 -171.8 6.81 1.17 40.42 8.63 8.16 16.83 21.63 51.30 14 1 10 27 ....>A:..10_:[..C]C-----G[..G]:..28_:A<.... C-G 0.30 -0.12 -0.42 13.77 -20.56 -1.19 C-G [3] O2 - N2 3.02 N3 - N1 2.96 N4 - O6 2.91 anti-parallel cis cis +-- 20.5 166.3 155.3 78.2 -163.7 179.0 0.53 0.42 24.75 8.97 -2.39 16.20 19.81 45.95 15 1 11 26 ....>A:..11_:[..C]C-----G[..G]:..27_:A<.... C-G 0.33 -0.20 0.34 -6.45 -13.56 -1.05 C-G [3] O2 - N2 2.78 N3 - N1 2.86 N4 - O6 2.85 anti-parallel cis cis +-- 13.6 173.5 165.0 75.4 -171.8 -158.6 0.52 0.34 15.01 8.89 -3.04 17.26 19.22 41.70 16 2 11 170 ....>A:..11_:[..C]C-**--A[..A]:...9_:A<.... C-A 6.61 -1.12 1.17 -40.33 2.74 51.72 C-A [2] O2'- N1 2.90 O2 - N6 2.90 anti-parallel cis cis +-- 48.4 115.3 139.6 16.9 -171.8 173.0 6.81 1.17 40.43 8.63 8.16 17.97 22.29 42.09 17 1 12 25 ....>A:..12_:[..G]G-----C[..C]:..26_:A<.... G-C -0.45 -0.10 -0.07 -9.86 -27.25 3.21 G-C [3] O6 - N4 3.17 N1 - N3 2.93 N2 - O2 2.91 anti-parallel cis cis +-- 27.4 169.8 151.0 70.9 -154.9 -157.8 0.47 0.07 28.97 8.87 -2.95 16.35 17.10 38.90 18 1 13 24 ....>A:..14_:[..C]C-**--A[..A]:..25_:A<.... C-A 6.59 -0.92 0.90 -26.93 -12.59 52.30 C-A [2] O2'- N1 2.70 O2 - N6 2.84 anti-parallel cis cis +-- 52.2 121.9 150.3 26.6 -166.4 -162.6 6.72 0.90 29.73 8.88 7.01 12.68 17.27 36.62 19 1 14 22 ....>A:..15_:[..C]C-**--A[..A]:..23_:A<.... C-A 7.02 -0.97 0.14 -5.51 -10.97 54.59 C-A [2] O2'- N1 2.69 O2 - N6 2.98 anti-parallel cis cis +-- 55.5 125.4 167.7 23.3 -158.0 -170.7 7.09 0.14 12.27 9.18 4.99 8.54 16.10 33.89 20 1 17 156 ....>A:..18_:[..G]G-**+-G[..G]:...2_:A<.... G+G -1.58 -3.31 -0.02 -8.92 5.11 92.47 G+G [2] N7 - N2 2.88 O6 - N1 2.74 parallel trans cis --+ 92.2 92.7 10.3 89.6 -131.5 177.6 3.67 0.02 10.28 9.67 1.23 7.74 24.90 24.84 21 1 157 159 ....>A:...3_:[..C]C-----G[..G]:..18_:A<.... C-G 0.13 -0.04 -0.28 6.60 -3.15 -0.19 C-G [3] O2 - N2 2.85 N3 - N1 3.00 N4 - O6 3.07 anti-parallel cis cis +-- 3.2 173.4 172.7 75.5 -166.8 -131.5 0.31 0.28 7.32 9.05 -3.77 6.59 25.87 21.68 22 1 171 174 ....>A:..10_:[..C]C-----G[..G]:..28_:A<.... C-G 0.29 -0.12 -0.42 13.77 -20.56 -1.19 C-G [3] O2 - N2 3.03 N3 - N1 2.96 N4 - O6 2.91 anti-parallel cis cis +-- 20.5 166.3 155.3 78.2 -163.7 179.0 0.53 0.42 24.74 8.97 -2.39 19.87 21.93 47.44 23 1 172 173 ....>A:..11_:[..C]C-----G[..G]:..27_:A<.... C-G 0.33 -0.20 0.34 -6.45 -13.56 -1.05 C-G [3] O2 - N2 2.78 N3 - N1 2.86 N4 - O6 2.85 anti-parallel cis cis +-- 13.6 173.5 165.0 75.4 -171.8 -158.5 0.52 0.34 15.01 8.89 -3.04 19.85 20.71 51.69 Detailed pairing information for each base 1 ....>A:...1_:[GTP]g: [ 0] [ 0] [ 0] [ 0] 2 ....>A:...2_:[..G]G: [ 2] 157 159 [ 2] 157 159 [ 2] 159 157 [ 2] 159 157 3 ....>A:...3_:[..C]C: [ 2] 17 156 [ 2] 17 156 [ 2] 156 17 [ 2] 156 17 4 ....>A:...4_:[..G]G: [ 2] 16 19 [ 2] 16 19 [ 2] 16 19 [ 2] 16 19 5 ....>A:...5_:[..C]C: [ 1] 15 [ 1] 15 [ 1] 15 [ 1] 15 6 ....>A:...6_:[..G]G: [ 1] 14 [ 2] 14 22 [ 2] 14 22 [ 2] 14 22 7 ....>A:...7_:[..G]G: [ 2] 13 23 [ 3] 13 23 24 [ 2] 23 13 [ 2] 23 13 8 ....>A:...8_:[..C]C: [ 2] 12 25 [ 2] 12 25 [ 2] 12 25 [ 2] 12 25 9 ....>A:...9_:[..A]A: [ 1] 172 [ 2] 172 173 [ 2] 172 173 [ 2] 172 173 10 ....>A:..10_:[..C]C: [ 1] 27 [ 1] 27 [ 1] 27 [ 1] 27 11 ....>A:..11_:[..C]C: [ 2] 26 170 [ 2] 26 170 [ 2] 26 170 [ 2] 26 170 12 ....>A:..12_:[..G]G: [ 2] 8 25 [ 2] 8 25 [ 2] 25 8 [ 2] 25 8 13 ....>A:..14_:[..C]C: [ 2] 7 24 [ 3] 7 24 23 [ 2] 7 23 [ 2] 7 23 14 ....>A:..15_:[..C]C: [ 2] 6 22 [ 2] 6 22 [ 2] 6 22 [ 2] 6 22 15 ....>A:..16_:[..G]G: [ 1] 5 [ 1] 5 [ 1] 5 [ 1] 5 16 ....>A:..17_:[..C]C: [ 1] 4 [ 2] 4 19 [ 2] 4 19 [ 2] 4 19 17 ....>A:..18_:[..G]G: [ 2] 3 156 [ 2] 3 156 [ 2] 156 3 [ 2] 156 3 18 ....>A:..19_:[..G]G: [ 0] [ 0] [ 0] [ 0] 19 ....>A:..20_:[..A]A: [ 1] 4 [ 2] 4 16 [ 2] 4 16 [ 2] 4 16 20 ....>A:..21_:[..A]A: [ 0] [ 0] [ 0] [ 0] 21 ....>A:..22_:[..C]C: [ 0] [ 0] [ 0] [ 0] 22 ....>A:..23_:[..A]A: [ 1] 14 [ 2] 14 6 [ 2] 14 6 [ 2] 14 6 23 ....>A:..24_:[..A]A: [ 1] 7 [ 2] 7 13 [ 2] 7 13 [ 2] 7 13 24 ....>A:..25_:[..A]A: [ 1] 13 [ 3] 13 7 23 [ 2] 13 7 [ 2] 13 7 25 ....>A:..26_:[..C]C: [ 2] 8 12 [ 2] 8 12 [ 2] 12 8 [ 2] 12 8 26 ....>A:..27_:[..G]G: [ 1] 11 [ 2] 11 170 [ 2] 11 170 [ 2] 11 170 27 ....>A:..28_:[..G]G: [ 1] 10 [ 1] 10 [ 1] 10 [ 1] 10 138 ....>A:...1_:[GTP]g: [ 0] [ 0] [ 0] [ 0] 139 ....>A:...3_:[..C]C: [ 0] [ 0] [ 0] [ 0] 143 ....>A:...1_:[GTP]g: [ 0] [ 0] [ 0] [ 0] 149 ....>A:...1_:[GTP]g: [ 0] [ 0] [ 0] [ 0] 155 ....>A:...1_:[GTP]g: [ 0] [ 0] [ 0] [ 0] 156 ....>A:...2_:[..G]G: [ 2] 3 17 [ 2] 3 17 [ 2] 17 3 [ 2] 17 3 157 ....>A:...3_:[..C]C: [ 2] 2 159 [ 2] 2 159 [ 2] 2 159 [ 2] 2 159 158 ....>A:..17_:[..C]C: [ 0] [ 0] [ 0] [ 0] 159 ....>A:..18_:[..G]G: [ 2] 2 157 [ 2] 2 157 [ 2] 2 157 [ 2] 2 157 170 ....>A:...9_:[..A]A: [ 1] 11 [ 2] 11 26 [ 2] 11 26 [ 2] 11 26 171 ....>A:..10_:[..C]C: [ 1] 174 [ 1] 174 [ 1] 174 [ 1] 174 172 ....>A:..11_:[..C]C: [ 2] 9 173 [ 2] 9 173 [ 2] 173 9 [ 2] 173 9 173 ....>A:..27_:[..G]G: [ 1] 172 [ 2] 172 9 [ 2] 172 9 [ 2] 172 9 174 ....>A:..28_:[..G]G: [ 1] 171 [ 1] 171 [ 1] 171 [ 1] 171 179 ....>A:..22_:[..C]C: [ 0] [ 0] [ 0] [ 0] Summary of triplets and higher multiplets ====================== initial lists ====================== 2[+3]: 2 157 159 3[+3]: 3 17 156 4[+3]: 4 16 19 6[+3]: 6 14 22 7[+3]: 7 13 23 8[+3]: 8 12 25 9[+3]: 9 172 173 11[+3]: 11 26 170 12[+3]: 8 12 25 13[+3]: 7 13 23 14[+3]: 6 14 22 16[+3]: 4 16 19 17[+3]: 3 17 156 19[+3]: 4 16 19 22[+3]: 6 14 22 23[+3]: 7 13 23 24[+3]: 7 13 24 25[+3]: 8 12 25 26[+3]: 11 26 170 156[+3]: 3 17 156 157[+3]: 2 157 159 159[+3]: 2 157 159 170[+3]: 11 26 170 172[+3]: 9 172 173 173[+3]: 9 172 173 ====================== perfect match ====================== 1[+3]: 2 157 159 2[+3]: 3 17 156 3[+3]: 4 16 19 4[+3]: 6 14 22 5[+3]: 7 13 23 6[+3]: 8 12 25 7[+3]: 9 172 173 8[+3]: 11 26 170 ====================== partial match ====================== 1[+3]: 7 13 24 ===================== perfect match ===================== 1: #3 [2]....>A:...2_:[..G]G + [157]....>A:...3_:[..C]C + [159]....>A:..18_:[..G]G 2: #3 [3]....>A:...3_:[..C]C + [17]....>A:..18_:[..G]G + [156]....>A:...2_:[..G]G 3: #3 [4]....>A:...4_:[..G]G + [16]....>A:..17_:[..C]C + [19]....>A:..20_:[..A]A 4: #3 [6]....>A:...6_:[..G]G + [14]....>A:..15_:[..C]C + [22]....>A:..23_:[..A]A 5: #3 [7]....>A:...7_:[..G]G + [13]....>A:..14_:[..C]C + [23]....>A:..24_:[..A]A 6: #3 [8]....>A:...8_:[..C]C + [12]....>A:..12_:[..G]G + [25]....>A:..26_:[..C]C 7: #3 [9]....>A:...9_:[..A]A + [172]....>A:..11_:[..C]C + [173]....>A:..27_:[..G]G 8: #3 [11]....>A:..11_:[..C]C + [26]....>A:..27_:[..G]G + [170]....>A:...9_:[..A]A ===================== partial match ===================== 9: #3 [7]....>A:...7_:[..G]G + [13]....>A:..14_:[..C]C + [24]....>A:..25_:[..A]A