**************************************************************************** File name: 3v6t.pdb no. of peptide chains: 2 [A=491,B=487] no. of DNA/RNA chains: 4 [G=17,H=17,I=17,J=17] no. of amino acids: 978 no. of nucleotides: 68 no. of atoms: 9492 no. of waters: 1046 no. of metals: 0 **************************************************************************** List of 2 helices Note: A helix is defined by base-stacking interactions, regardless of pair type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[0] bps=17 strand-1 5'-TGTCCCTTTATCTCTCT-3' bp-type ||||||||||||||||| strand-2 3'-ACAGGGAAATAGAGAGA-5' helix-form .BBBBBBBB.BBBBBB 1 G.DT-2 H.DA2 T-A WC 20-XX cWW cW-W 2 G.DG-1 H.DC1 G-C WC 19-XIX cWW cW-W 3 G.DT0 H.DA0 T-A WC 20-XX cWW cW-W 4 G.DC1 H.DG-1 C-G WC 19-XIX cWW cW-W 5 G.DC2 H.DG-2 C-G WC 19-XIX cWW cW-W 6 G.DC3 H.DG-3 C-G WC 19-XIX cWW cW-W 7 G.DT4 H.DA-4 T-A WC 20-XX cWW cW-W 8 G.DT5 H.DA-5 T-A WC 20-XX cWW cW-W 9 G.DT6 H.DA-6 T-A WC 20-XX cWW cW-W 10 G.DA7 H.DT-7 A-T WC 20-XX cWW cW-W 11 G.DT8 H.DA-8 T-A WC 20-XX cWW cW-W 12 G.DC9 H.DG-9 C-G WC 19-XIX cWW cW-W 13 G.DT10 H.DA-10 T-A WC 20-XX cWW cW-W 14 G.DC11 H.DG-11 C-G WC 19-XIX cWW cW-W 15 G.DT12 H.DA-12 T-A WC 20-XX cWW cW-W 16 G.DC13 H.DG-13 C-G WC 19-XIX cWW cW-W 17 G.DT14 H.DA-14 T-A WC 20-XX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=17 strand-1 5'-TGTCCCTTTATCTCTCT-3' bp-type ||||||||||||||||| strand-2 3'-ACAGGGAAATAGAGAGA-5' helix-form BBBBBBBBBBBBBBBB 1 I.DT-2 J.DA2 T-A WC 20-XX cWW cW-W 2 I.DG-1 J.DC1 G-C WC 19-XIX cWW cW-W 3 I.DT0 J.DA0 T-A WC 20-XX cWW cW-W 4 I.DC1 J.DG-1 C-G WC 19-XIX cWW cW-W 5 I.DC2 J.DG-2 C-G WC 19-XIX cWW cW-W 6 I.DC3 J.DG-3 C-G WC 19-XIX cWW cW-W 7 I.DT4 J.DA-4 T-A WC 20-XX cWW cW-W 8 I.DT5 J.DA-5 T-A WC 20-XX cWW cW-W 9 I.DT6 J.DA-6 T-A WC 20-XX cWW cW-W 10 I.DA7 J.DT-7 A-T WC 20-XX cWW cW-W 11 I.DT8 J.DA-8 T-A WC 20-XX cWW cW-W 12 I.DC9 J.DG-9 C-G WC 19-XIX cWW cW-W 13 I.DT10 J.DA-10 T-A WC 20-XX cWW cW-W 14 I.DC11 J.DG-11 C-G WC 19-XIX cWW cW-W 15 I.DT12 J.DA-12 T-A WC 20-XX cWW cW-W 16 I.DC13 J.DG-13 C-G WC 19-XIX cWW cW-W 17 I.DT14 J.DA-14 T-A WC 20-XX cWW cW-W **************************************************************************** List of 72 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 3v6t T-asp G.DT0 B.ASP301 9.25 -109.18 -3.43 8.24 2.42 43.40 -48.53 -93.15 2 3v6t C-asp G.DC1 B.ASP301 -8.69 -134.46 -3.44 7.98 0.07 24.54 -66.15 -123.40 3 3v6t C-arg G.DC2 B.ARG266 -10.20 -124.93 7.03 5.57 -4.87 59.11 13.26 -115.26 4 3v6t C-asp G.DC2 B.ASP301 -8.39 -163.76 -3.39 7.40 -2.01 3.18 -79.28 -158.85 5 3v6t C-asp G.DC2 B.ASP335 -8.20 -141.84 -2.89 7.67 0.14 22.99 -72.22 -131.06 6 3v6t C-asp G.DC2 B.ASP369 8.92 -116.02 -2.85 8.07 2.53 40.44 -47.32 -103.54 7 3v6t C-arg G.DC3 B.ARG266 -10.63 -146.33 7.79 2.26 -6.87 63.52 -9.40 -140.01 8 3v6t C-asp G.DC3 B.ASP335 -8.77 -167.73 -3.28 7.97 -1.64 7.52 -83.12 -163.53 9 3v6t C-asp G.DC3 B.ASP369 8.43 -141.19 -3.02 7.87 0.17 29.46 -64.17 -131.95 10 3v6t T-asp G.DT4 B.ASP369 -8.85 -169.16 -3.35 8.01 -1.72 11.73 -74.37 -166.29 11 3v6t T-gly G.DT4 B.GLY403 8.49 -140.35 -2.71 8.04 0.19 35.45 -62.64 -130.43 12 3v6t T-gly G.DT4 B.GLY404 -10.19 -176.69 -8.86 4.70 1.80 -18.67 -23.23 -176.57 13 3v6t T-gly G.DT5 B.GLY437 9.76 -128.76 0.52 9.11 3.45 4.43 -80.15 -111.11 14 3v6t T-gly G.DT5 B.GLY472 9.59 -141.31 -8.36 2.34 4.07 -10.49 -16.98 -140.69 15 3v6t T-gly G.DT6 B.GLY471 8.22 -143.54 -3.29 7.50 -0.68 41.11 -59.45 -134.42 16 3v6t T-gly G.DT6 B.GLY472 -10.11 -173.80 -8.81 4.90 0.74 -15.09 -18.54 -173.66 17 3v6t T-ser G.DT6 B.SER505 8.68 -119.72 -2.68 7.54 3.35 49.28 -51.49 -103.69 18 3v6t A-ser G.DA7 B.SER505 7.75 -147.77 -2.89 7.08 1.20 33.20 -67.16 -139.07 19 3v6t T-gly G.DT8 B.GLY539 8.71 -139.61 -3.10 8.12 0.46 37.36 -66.30 -127.99 20 3v6t T-gly G.DT8 B.GLY540 -10.45 -176.99 -9.32 4.40 1.72 -14.29 -25.95 -176.88 21 3v6t T-asp G.DT8 B.ASP573 9.23 -116.58 -3.25 8.13 2.92 50.98 -48.48 -99.96 22 3v6t C-asp G.DC9 B.ASP573 8.55 -144.47 -3.12 7.94 0.62 36.69 -65.93 -134.62 23 3v6t T-gly G.DT10 B.GLY607 8.85 -139.35 -3.02 8.31 0.21 37.17 -69.16 -126.69 24 3v6t T-gly G.DT10 B.GLY608 -10.51 -174.17 -9.14 4.99 1.42 -8.69 -29.91 -173.95 25 3v6t T-asp G.DT10 B.ASP641 9.15 -114.58 -2.97 8.15 2.90 47.19 -50.02 -98.19 26 3v6t C-asp G.DC11 B.ASP641 8.36 -137.80 -2.88 7.85 0.19 27.33 -63.53 -128.14 27 3v6t T-gly G.DT12 B.GLY675 8.25 -143.51 -2.18 7.96 0.14 29.30 -52.26 -137.63 28 3v6t T-gly G.DT12 B.GLY676 -9.94 -178.12 -8.32 5.04 2.05 -26.20 -12.43 -178.06 29 3v6t T-lys G.DT14 A.LYS720 9.86 -93.39 -2.35 8.76 3.88 22.04 -66.81 -65.92 30 3v6t T-leu G.DT14 A.LEU721 7.35 27.63 3.25 6.41 1.55 25.99 -2.69 9.07 31 3v6t A-asp H.DA-12 B.ASP641 8.67 -74.86 8.21 -2.48 1.30 -72.17 18.30 -8.45 32 3v6t A-arg H.DA-4 B.ARG266 11.26 -83.41 -0.44 7.48 8.41 -32.90 75.15 -16.63 33 3v6t A-asp H.DA-4 B.ASP369 8.42 -85.30 7.70 -3.31 0.81 -79.90 27.55 -12.81 34 3v6t G-arg H.DG-3 B.ARG266 11.03 -82.18 2.97 8.44 6.45 -14.07 71.98 -40.01 35 3v6t G-asp H.DG-3 B.ASP335 9.03 -86.57 8.60 -2.61 0.91 -85.25 13.90 -6.56 36 3v6t G-arg H.DG-2 B.ARG266 10.22 -94.70 6.05 7.35 3.72 5.20 65.05 -72.88 37 3v6t G-asp H.DG-2 B.ASP301 8.33 -87.56 7.63 -3.04 1.39 -85.69 12.53 -14.49 38 3v6t T-asp I.DT0 A.ASP301 8.98 -112.00 -3.22 7.90 2.81 42.59 -50.76 -96.21 39 3v6t C-asp I.DC1 A.ASP301 8.70 -136.04 -3.42 7.99 0.33 25.49 -66.56 -125.16 40 3v6t C-arg I.DC2 A.ARG266 -10.88 -123.71 7.70 6.44 -4.21 68.45 22.74 -108.60 41 3v6t C-asp I.DC2 A.ASP301 -8.79 -165.50 -3.67 7.85 -1.47 8.31 -76.77 -161.41 42 3v6t C-asp I.DC2 A.ASP335 8.47 -144.16 -3.17 7.85 0.24 32.71 -69.33 -133.82 43 3v6t C-arg I.DC3 A.ARG266 -10.93 -145.78 8.54 2.42 -6.38 73.15 -2.36 -137.01 44 3v6t C-asp I.DC3 A.ASP335 -9.00 -170.75 -3.58 8.11 -1.57 14.09 -81.08 -167.71 45 3v6t C-asp I.DC3 A.ASP369 8.53 -143.45 -3.25 7.88 0.40 32.90 -62.88 -134.70 46 3v6t T-asp I.DT4 A.ASP369 -8.97 -172.18 -3.45 8.11 -1.66 14.73 -72.87 -170.18 47 3v6t T-gly I.DT4 A.GLY403 8.42 -142.97 -2.74 7.95 0.38 36.46 -63.97 -133.27 48 3v6t T-gly I.DT4 A.GLY404 -10.21 -179.16 -8.89 4.66 1.82 -14.99 -24.96 -179.13 49 3v6t T-gly I.DT5 A.GLY437 8.63 -138.53 -2.97 8.10 -0.08 35.06 -66.14 -127.04 50 3v6t T-gly I.DT5 A.GLY438 -10.27 -175.44 -9.00 4.69 1.62 -20.70 -27.86 -175.22 51 3v6t T-gly I.DT6 A.GLY471 9.83 -84.99 3.97 8.99 0.01 70.74 46.14 -10.56 52 3v6t T-ser I.DT6 A.SER505 8.83 -116.62 -2.83 7.64 3.43 41.65 -51.70 -102.22 53 3v6t A-ser I.DA7 A.SER505 8.09 -143.20 -3.13 7.37 1.20 29.32 -65.77 -134.07 54 3v6t T-gly I.DT8 A.GLY539 8.97 -135.55 -3.10 8.40 0.47 36.12 -66.74 -122.68 55 3v6t T-gly I.DT8 A.GLY540 -10.61 -173.12 -9.41 4.53 1.86 -13.10 -29.05 -172.84 56 3v6t T-asp I.DT8 A.ASP573 9.37 -114.71 -3.19 8.40 2.67 52.54 -48.17 -96.83 57 3v6t C-asp I.DC9 A.ASP573 8.48 -143.15 -3.01 7.91 0.52 33.36 -67.35 -133.00 58 3v6t T-gly I.DT10 A.GLY607 8.67 -139.23 -3.17 8.07 -0.13 38.40 -66.32 -127.28 59 3v6t T-gly I.DT10 A.GLY608 -10.42 -173.88 -9.14 4.85 1.24 -12.12 -27.11 -173.67 60 3v6t T-asp I.DT10 A.ASP641 8.91 -114.78 -3.21 7.86 2.72 48.40 -45.91 -99.64 61 3v6t C-asp I.DC11 A.ASP641 8.30 -138.17 -3.00 7.73 -0.12 27.39 -61.96 -129.07 62 3v6t T-gly I.DT12 A.GLY675 8.20 -143.30 -2.44 7.82 -0.08 30.44 -49.60 -137.76 63 3v6t T-gly I.DT12 A.GLY676 -9.95 -177.23 -8.41 4.92 1.99 -27.88 -12.01 -177.13 64 3v6t T-lys I.DT14 B.LYS720 10.51 -80.15 -2.55 9.58 3.47 18.85 -63.29 -48.28 65 3v6t T-leu I.DT14 B.LEU721 8.35 28.06 3.64 7.38 1.39 21.32 -3.61 17.99 66 3v6t G-asp J.DG-9 A.ASP573 -7.98 -91.20 7.37 -3.00 -0.61 -71.61 37.34 -46.59 67 3v6t A-arg J.DA-4 A.ARG266 11.52 -88.96 -1.36 8.86 7.24 -38.47 78.29 -19.53 68 3v6t A-asp J.DA-4 A.ASP369 8.74 -89.18 8.08 -3.02 1.35 -86.40 21.19 -7.06 69 3v6t G-arg J.DG-3 A.ARG266 11.20 -89.12 2.93 9.37 5.40 -10.91 75.78 -49.62 70 3v6t G-asp J.DG-3 A.ASP335 9.13 163.47 0.75 -9.00 1.34 -6.37 -88.29 156.85 71 3v6t G-arg J.DG-2 A.ARG266 -10.94 -100.51 6.63 8.07 3.26 12.09 65.44 -80.23 72 3v6t G-asp J.DG-2 A.ASP301 8.78 -91.12 7.92 -3.42 1.64 -88.95 12.39 -17.38 **************************************************************************** List of 61 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 3v6t AT-ser G.DA7 H.DT-7 B.SER505 7.65 -147.98 -2.99 6.94 1.17 35.96 -70.55 -138.05 2 3v6t AT-lys H.DA-14 G.DT14 A.LYS720 -9.75 -130.95 8.41 -2.79 -4.07 -65.14 24.50 -119.27 3 3v6t AT-leu H.DA-14 G.DT14 A.LEU721 -7.16 166.44 -6.43 -2.68 -1.65 0.78 -26.08 166.08 4 3v6t AT-asp H.DA-12 G.DT12 B.ASP641 8.85 -71.42 8.25 -2.67 1.75 -69.63 12.78 -10.20 5 3v6t AT-gly H.DA-12 G.DT12 B.GLY675 -8.11 -77.04 7.81 -2.13 -0.48 -56.02 33.99 -43.02 6 3v6t AT-gly H.DA-12 G.DT12 B.GLY676 -9.78 -25.81 4.73 -8.27 -2.18 -15.10 -20.80 -2.33 7 3v6t GC-asp H.DG-11 G.DC11 B.ASP641 -8.38 -84.03 7.96 -2.53 -0.63 -63.92 33.41 -46.42 8 3v6t AT-gly H.DA-10 G.DT10 B.GLY607 -8.74 -92.07 8.22 -2.88 -0.62 -68.58 40.57 -50.57 9 3v6t AT-gly H.DA-10 G.DT10 B.GLY608 10.39 -28.83 4.85 -9.03 -1.73 -27.73 -5.52 -5.66 10 3v6t AT-asp H.DA-10 G.DT10 B.ASP641 -9.08 -103.34 7.96 -2.90 -3.27 -50.32 50.91 -80.26 11 3v6t GC-asp H.DG-9 G.DC9 B.ASP573 -8.48 -88.57 7.89 -3.04 -0.68 -68.61 38.61 -44.37 12 3v6t AT-gly H.DA-8 G.DT8 B.GLY539 -8.63 -92.10 8.02 -3.01 -0.96 -67.49 43.47 -49.58 13 3v6t AT-gly H.DA-8 G.DT8 B.GLY540 10.36 -26.23 4.21 -9.24 -2.05 -24.75 -8.11 -3.12 14 3v6t AT-asp H.DA-8 G.DT8 B.ASP573 -9.17 -105.87 7.89 -3.31 -3.30 -50.80 56.84 -79.98 15 3v6t AT-gly H.DA-6 G.DT6 B.GLY471 -8.17 -86.44 7.45 -3.25 0.79 -62.64 42.09 -45.73 16 3v6t AT-gly H.DA-6 G.DT6 B.GLY472 10.07 -25.27 4.95 -8.75 -0.54 -20.98 -13.10 -5.20 17 3v6t AT-ser H.DA-6 G.DT6 B.SER505 -8.58 -102.77 7.46 -2.79 -3.19 -54.78 49.53 -77.36 18 3v6t AT-gly H.DA-5 G.DT5 B.GLY437 -9.67 -105.66 8.89 0.31 -3.78 -86.29 8.38 -67.63 19 3v6t AT-gly H.DA-5 G.DT5 B.GLY472 -9.52 -45.40 2.04 -8.51 -3.74 -22.16 -5.41 -39.52 20 3v6t AT-arg H.DA-4 G.DT4 B.ARG266 11.26 -76.01 -1.01 7.09 8.69 -32.27 67.83 -12.57 21 3v6t AT-asp H.DA-4 G.DT4 B.ASP369 8.64 -80.79 7.87 -3.32 1.28 -77.44 19.51 -13.41 22 3v6t AT-gly H.DA-4 G.DT4 B.GLY403 -8.30 -92.23 7.76 -2.89 -0.50 -66.61 42.07 -52.46 23 3v6t AT-gly H.DA-4 G.DT4 B.GLY404 10.01 -29.57 4.18 -8.91 -1.82 -26.61 -11.69 -5.51 24 3v6t GC-arg H.DG-3 G.DC3 B.ARG266 10.83 -78.29 2.62 8.12 6.67 -11.69 67.77 -39.98 25 3v6t GC-asp H.DG-3 G.DC3 B.ASP335 8.90 -85.54 8.30 -2.95 1.30 -84.22 10.71 -11.56 26 3v6t GC-asp H.DG-3 G.DC3 B.ASP369 -8.48 -85.30 8.02 -2.73 -0.36 -66.77 32.82 -45.14 27 3v6t GC-arg H.DG-2 G.DC2 B.ARG266 10.21 -90.43 5.82 7.20 4.30 9.24 62.11 -68.77 28 3v6t GC-asp H.DG-2 G.DC2 B.ASP301 8.36 -84.52 7.52 -3.21 1.72 -82.58 7.81 -17.94 29 3v6t GC-asp H.DG-2 G.DC2 B.ASP335 -8.14 -92.09 7.63 -2.84 -0.32 -76.57 27.06 -47.82 30 3v6t GC-asp H.DG-2 G.DC2 B.ASP369 -8.87 -99.81 7.94 -2.99 -2.57 -52.17 43.58 -78.07 31 3v6t GC-asp H.DG-1 G.DC1 B.ASP301 -8.70 -89.67 8.06 -3.25 -0.30 -69.23 28.37 -53.54 32 3v6t AT-asp H.DA0 G.DT0 B.ASP301 -9.23 -107.35 8.14 -3.51 -2.58 -52.58 46.28 -87.34 33 3v6t AT-ser I.DA7 J.DT-7 A.SER505 8.02 -145.95 -3.08 7.29 1.29 32.97 -69.92 -135.97 34 3v6t AT-lys J.DA-14 I.DT14 B.LYS720 -10.15 -136.59 9.37 -2.06 -3.32 -58.36 18.06 -129.14 35 3v6t AT-leu J.DA-14 I.DT14 B.LEU721 -8.07 164.80 -6.91 -3.96 -1.29 -0.29 -24.32 164.45 36 3v6t AT-gly J.DA-12 I.DT12 A.GLY675 -8.09 -78.48 7.73 -2.37 -0.34 -56.78 37.70 -41.52 37 3v6t AT-gly J.DA-12 I.DT12 A.GLY676 -9.83 -24.88 4.70 -8.38 -2.07 -16.36 -18.69 -1.40 38 3v6t GC-asp J.DG-11 I.DC11 A.ASP641 -8.31 -81.98 7.80 -2.83 -0.40 -60.73 34.85 -45.68 39 3v6t AT-gly J.DA-10 I.DT10 A.GLY607 -8.57 -89.84 8.03 -2.96 -0.43 -65.58 42.70 -48.20 40 3v6t AT-gly J.DA-10 I.DT10 A.GLY608 10.32 -25.67 4.77 -9.00 -1.69 -23.86 -7.93 -5.23 41 3v6t AT-asp J.DA-10 I.DT10 A.ASP641 -8.87 -100.99 7.67 -3.07 -3.21 -46.43 53.32 -77.49 42 3v6t GC-asp J.DG-9 I.DC9 A.ASP573 -8.23 -88.97 7.64 -3.01 -0.57 -69.49 35.34 -46.81 43 3v6t AT-gly J.DA-8 I.DT8 A.GLY539 -8.94 -93.25 8.44 -2.86 -0.71 -69.87 38.61 -52.87 44 3v6t AT-gly J.DA-8 I.DT8 A.GLY540 10.58 -30.57 4.72 -9.26 -1.97 -28.99 -9.03 -3.61 45 3v6t AT-asp J.DA-8 I.DT8 A.ASP573 -9.31 -106.22 8.34 -3.06 -2.79 -52.37 55.13 -80.73 46 3v6t AT-gly J.DA-6 I.DT6 A.GLY471 -9.71 -173.93 8.91 3.86 -0.16 42.21 69.83 -171.98 47 3v6t AT-ser J.DA-6 I.DT6 A.SER505 -8.72 -101.03 7.44 -2.91 -3.48 -55.23 44.11 -77.57 48 3v6t AT-gly J.DA-5 I.DT5 A.GLY437 -8.53 -93.23 8.02 -2.93 -0.02 -70.59 38.60 -51.77 49 3v6t AT-gly J.DA-5 I.DT5 A.GLY438 10.20 -34.05 4.67 -8.94 -1.52 -30.11 -15.64 -2.89 50 3v6t AT-arg J.DA-4 I.DT4 A.ARG266 11.56 -82.76 -1.65 8.20 7.97 -32.53 74.92 -14.69 51 3v6t AT-asp J.DA-4 I.DT4 A.ASP369 8.85 -82.02 8.10 -3.23 1.52 -79.66 17.92 -8.53 52 3v6t AT-gly J.DA-4 I.DT4 A.GLY403 -8.34 -92.21 7.86 -2.78 -0.30 -71.17 37.88 -49.19 53 3v6t AT-gly J.DA-4 I.DT4 A.GLY404 10.11 33.34 4.56 -8.89 -1.55 -31.39 -11.21 0.65 54 3v6t GC-arg J.DG-3 I.DC3 A.ARG266 11.07 -86.15 2.68 8.97 5.91 -6.62 74.53 -46.27 55 3v6t GC-asp J.DG-3 I.DC3 A.ASP335 9.06 -87.38 8.29 -3.34 1.50 -85.36 16.22 -10.34 56 3v6t GC-asp J.DG-3 I.DC3 A.ASP369 -8.55 -86.77 7.95 -3.13 -0.29 -67.67 34.19 -45.80 57 3v6t GC-arg J.DG-2 I.DC2 A.ARG266 10.91 -99.06 6.53 7.90 3.73 17.41 67.01 -75.88 58 3v6t GC-asp J.DG-2 I.DC2 A.ASP301 8.79 -85.09 7.88 -3.55 1.57 -82.87 10.31 -18.04 59 3v6t GC-asp J.DG-2 I.DC2 A.ASP335 -8.44 -93.58 7.79 -3.22 0.02 -75.43 33.65 -48.62 60 3v6t GC-asp J.DG-1 I.DC1 A.ASP301 -8.75 -90.07 8.10 -3.27 -0.55 -69.59 30.58 -52.51 61 3v6t AT-asp J.DA0 I.DT0 A.ASP301 -8.95 -108.05 7.71 -3.44 -2.95 -55.42 47.26 -86.22 **************************************************************************** List of 30 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 3v6t OP1@G.DT0 NE2@B.GLN305 2.92 po4:sidechain 2 3v6t OP2@G.DT0 N@B.GLY302 3.79 po4:backbone 3 3v6t OP1@G.DC1 NE2@B.GLN339 2.78 po4:sidechain 4 3v6t OP1@G.DC2 NE2@B.GLN373 2.87 po4:sidechain 5 3v6t OP1@G.DC3 NE2@B.GLN407 2.88 po4:sidechain 6 3v6t OP1@G.DT4 NE2@B.GLN441 2.86 po4:sidechain 7 3v6t OP1@G.DT5 NE2@B.GLN475 2.77 po4:sidechain 8 3v6t OP1@G.DT6 NE2@B.GLN509 2.82 po4:sidechain 9 3v6t OP1@G.DA7 NE2@B.GLN543 2.96 po4:sidechain 10 3v6t OP1@G.DT8 NE2@B.GLN577 2.83 po4:sidechain 11 3v6t OP1@G.DC9 NE2@B.GLN611 2.87 po4:sidechain 12 3v6t OP1@G.DT10 NE2@B.GLN645 2.86 po4:sidechain 13 3v6t OP1@G.DT12 NE@B.ARG712 2.95 po4:sidechain:salt-bridge 14 3v6t OP1@G.DT12 NH2@B.ARG712 3.08 po4:sidechain:salt-bridge 15 3v6t O3'@G.DC11 NH2@B.ARG712 3.19 po4:sidechain 16 3v6t OP1@I.DT0 NE2@A.GLN305 2.68 po4:sidechain 17 3v6t OP1@I.DC1 NE2@A.GLN339 2.85 po4:sidechain 18 3v6t OP1@I.DC2 NE2@A.GLN373 2.75 po4:sidechain 19 3v6t OP1@I.DC3 NE2@A.GLN407 2.95 po4:sidechain 20 3v6t OP1@I.DT4 NE2@A.GLN441 2.92 po4:sidechain 21 3v6t OP1@I.DT5 NE2@A.GLN475 2.89 po4:sidechain 22 3v6t OP1@I.DT6 NE2@A.GLN509 2.91 po4:sidechain 23 3v6t OP1@I.DA7 NE2@A.GLN543 2.86 po4:sidechain 24 3v6t OP1@I.DT8 NE2@A.GLN577 2.87 po4:sidechain 25 3v6t OP1@I.DC9 NE2@A.GLN611 2.94 po4:sidechain 26 3v6t OP1@I.DT10 NE2@A.GLN645 2.81 po4:sidechain 27 3v6t OP1@I.DC11 NE@A.ARG678 3.62 po4:sidechain:salt-bridge 28 3v6t OP1@I.DT12 NE@A.ARG712 2.90 po4:sidechain:salt-bridge 29 3v6t OP1@I.DT12 NH2@A.ARG712 3.19 po4:sidechain:salt-bridge 30 3v6t O3'@I.DC11 NH2@A.ARG712 3.14 po4:sidechain **************************************************************************** List of 19 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 3v6t N4@G.DC1 OD2@B.ASP301 2.93 base:sidechain 2 3v6t N4@G.DC2 OD2@B.ASP335 2.61 base:sidechain 3 3v6t N4@G.DC3 OD2@B.ASP335 3.84 base:sidechain 4 3v6t N4@G.DC3 OD2@B.ASP369 2.88 base:sidechain 5 3v6t N7@G.DA7 OG@B.SER505 2.68 base:sidechain 6 3v6t N4@G.DC9 OD2@B.ASP573 2.89 base:sidechain 7 3v6t N4@G.DC11 OD1@B.ASP641 2.77 base:sidechain 8 3v6t N6@H.DA-4 OD2@B.ASP369 3.95 base:sidechain 9 3v6t N7@H.DG-3 NH2@B.ARG266 3.00 base:sidechain 10 3v6t O6@H.DG-3 NH1@B.ARG266 2.69 base:sidechain 11 3v6t N4@I.DC1 OD2@A.ASP301 2.90 base:sidechain 12 3v6t N4@I.DC2 OD2@A.ASP335 2.89 base:sidechain 13 3v6t N4@I.DC3 OD2@A.ASP335 3.99 base:sidechain 14 3v6t N4@I.DC3 OD2@A.ASP369 2.81 base:sidechain 15 3v6t N7@I.DA7 OG@A.SER505 2.75 base:sidechain 16 3v6t N4@I.DC9 OD2@A.ASP573 2.89 base:sidechain 17 3v6t N4@I.DC11 OD2@A.ASP641 2.80 base:sidechain 18 3v6t N7@J.DG-3 NH1@A.ARG266 3.08 base:sidechain 19 3v6t O6@J.DG-3 NH2@A.ARG266 2.90 base:sidechain **************************************************************************** List of 15 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 3v6t C-asp G.DC1 B.ASP301 0.68 16 2 3v6t C-asp G.DC2 B.ASP335 0.83 21 3 3v6t C-asp G.DC3 B.ASP335 1.98 21 4 3v6t C-asp G.DC3 B.ASP369 0.69 9 5 3v6t C-asp G.DC9 B.ASP573 0.10 20 6 3v6t C-asp G.DC11 B.ASP641 0.19 7 7 3v6t A-asp H.DA-4 B.ASP369 1.09 18 8 3v6t G-arg H.DG-3 B.ARG266 0.36 6 9 3v6t C-asp I.DC1 A.ASP301 0.76 13 10 3v6t C-asp I.DC2 A.ASP335 0.93 16 11 3v6t C-asp I.DC3 A.ASP335 2.09 18 12 3v6t C-asp I.DC3 A.ASP369 0.83 6 13 3v6t C-asp I.DC9 A.ASP573 0.06 20 14 3v6t C-asp I.DC11 A.ASP641 0.10 2 15 3v6t G-arg J.DG-3 A.ARG266 0.43 8 **************************************************************************** List of 7 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 3v6t T-asp G.DT0 B.ASP301 3.97 11 2 3v6t T-asp G.DT8 B.ASP573 3.72 19 3 3v6t T-asp G.DT10 B.ASP641 3.91 11 4 3v6t A-arg H.DA-4 B.ARG266 3.44 4 5 3v6t T-asp I.DT0 A.ASP301 4.06 9 6 3v6t T-asp I.DT10 A.ASP641 3.80 8 7 3v6t A-arg J.DA-4 A.ARG266 3.39 9 **************************************************************************** List of 3 additional files 1 -- 3v6t-baseAA-pairs.pdb 2 -- 3v6t-baseAA-stacks.pdb 3 -- 3v6t-pairs.pdb