**************************************************************************** Note: By default, each nucleotide/amino-acid is identified by chainId.name#. For example, B.DA1689 means adenosine #1689 on chain B, and C.ARG49 denotes arginine #49 on chain C. Use the --idstr=long option to get strictly delineated id strings. Command: x3dna-dssr snap -i=/data/pdb/pdbfiles/5t00.pdb -o=5t00.out --type=base File name: 5t00.pdb no. of peptide chains: 2 [A=143,D=143] no. of DNA/RNA chains: 4 [B=17,C=17,E=17,F=17] no. of amino acids: 286 no. of nucleotides: 68 no. of atoms: 6860 no. of waters: 97 no. of metals: 10 [Zn=10] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5CM-c 4 B.5CM4,C.5CM13,E.5CM4,F.5CM13 **************************************************************************** List of 2 helices Note: a helix is defined by base-stacking interactions, regardless of bp 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'-TAGcGCCCCCTGCTGGC-3' bp-type ||||||||||||||||| strand-2 3'-ATCGcGGGGGACGACCG-5' helix-form .B.......BB.BBBB 1 B.DT1 C.DA17 T-A WC 20-XX cWW cW-W 2 B.DA2 C.DT16 A-T WC 20-XX cWW cW-W 3 B.DG3 C.DC15 G-C WC 19-XIX cWW cW-W 4 B.5CM4 C.DG14 c-G WC 19-XIX cWW cW-W 5 B.DG5 C.5CM13 G-c WC 19-XIX cWW cW-W 6 B.DC6 C.DG12 C-G WC 19-XIX cWW cW-W 7 B.DC7 C.DG11 C-G WC 19-XIX cWW cW-W 8 B.DC8 C.DG10 C-G WC 19-XIX cWW cW-W 9 B.DC9 C.DG9 C-G WC 19-XIX cWW cW-W 10 B.DC10 C.DG8 C-G WC 19-XIX cWW cW-W 11 B.DT11 C.DA7 T-A WC 20-XX cWW cW-W 12 B.DG12 C.DC6 G-C WC 19-XIX cWW cW-W 13 B.DC13 C.DG5 C-G WC 19-XIX cWW cW-W 14 B.DT14 C.DA4 T-A WC 20-XX cWW cW-W 15 B.DG15 C.DC3 G-C WC 19-XIX cWW cW-W 16 B.DG16 C.DC2 G-C WC 19-XIX cWW cW-W 17 B.DC17 C.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=17 strand-1 5'-TAGcGCCCCCTGCTGGC-3' bp-type ||||||||||||||||| strand-2 3'-ATCGcGGGGGACGACCG-5' helix-form .BB......BB.BBBB 1 E.DT1 F.DA17 T-A WC 20-XX cWW cW-W 2 E.DA2 F.DT16 A-T WC 20-XX cWW cW-W 3 E.DG3 F.DC15 G-C WC 19-XIX cWW cW-W 4 E.5CM4 F.DG14 c-G WC 19-XIX cWW cW-W 5 E.DG5 F.5CM13 G-c WC 19-XIX cWW cW-W 6 E.DC6 F.DG12 C-G WC 19-XIX cWW cW-W 7 E.DC7 F.DG11 C-G WC 19-XIX cWW cW-W 8 E.DC8 F.DG10 C-G WC 19-XIX cWW cW-W 9 E.DC9 F.DG9 C-G WC 19-XIX cWW cW-W 10 E.DC10 F.DG8 C-G WC 19-XIX cWW cW-W 11 E.DT11 F.DA7 T-A WC 20-XX cWW cW-W 12 E.DG12 F.DC6 G-C WC 19-XIX cWW cW-W 13 E.DC13 F.DG5 C-G WC 19-XIX cWW cW-W 14 E.DT14 F.DA4 T-A WC 20-XX cWW cW-W 15 E.DG15 F.DC3 G-C WC 19-XIX cWW cW-W 16 E.DG16 F.DC2 G-C WC 19-XIX cWW cW-W 17 E.DC17 F.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 90 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5t00 T-gly B.DT1 A.GLY335 8.78 -134.10 -2.94 8.27 0.11 -15.74 45.19 -129.50 2 5t00 G-arg B.DG3 A.ARG339 -10.21 161.04 -0.71 -10.17 -0.52 12.56 -59.38 158.00 3 5t00 C-glu B.5CM4 A.GLU362 -10.00 -150.82 0.12 9.97 0.85 -37.96 -39.36 -147.06 4 5t00 C-ser B.5CM4 A.SER364 -9.54 -156.93 -4.75 8.26 -0.43 -25.29 48.05 -154.03 5 5t00 G-lys B.DG5 A.LYS365 9.39 -117.22 5.48 6.58 -3.85 36.23 -46.88 -106.37 6 5t00 C-tyr B.DC6 A.TYR392 9.21 -134.88 -4.82 6.97 3.62 -10.77 51.08 -129.42 7 5t00 C-tyr B.DC7 A.TYR392 8.48 -151.19 -3.61 7.65 0.57 6.39 35.72 -149.65 8 5t00 C-tyr B.DC8 A.TYR392 -8.22 169.06 0.28 -7.08 -4.17 2.14 -30.79 168.65 9 5t00 C-lys B.DC8 A.LYS393 -8.69 -101.38 5.31 4.76 -4.97 22.40 -57.13 -85.10 10 5t00 C-arg B.DC9 A.ARG396 -11.18 172.07 0.48 -11.15 -0.63 17.54 -71.73 170.08 11 5t00 C-arg B.DC10 A.ARG396 -10.31 150.54 -3.21 -9.61 -1.89 -12.61 -61.80 145.28 12 5t00 C-ser B.DC13 A.SER450 8.34 -127.32 -4.00 7.32 -0.01 9.48 34.97 -124.34 13 5t00 T-asp B.DT14 A.ASP451 8.78 -130.73 -0.04 5.36 6.95 -73.69 42.56 -111.09 14 5t00 T-val B.DT14 A.VAL454 10.76 -137.36 -5.94 8.44 3.04 -24.41 41.17 -133.12 15 5t00 G-asp B.DG15 A.ASP451 7.58 -156.14 2.48 5.47 4.63 -54.08 50.12 -150.05 16 5t00 C-asp C.DC2 A.ASP451 9.00 178.74 6.47 -5.61 -2.78 -26.73 -73.89 178.37 17 5t00 C-arg C.DC3 A.ARG448 10.15 -149.88 -3.09 9.26 2.79 5.95 -61.92 -144.67 18 5t00 C-asp C.DC3 A.ASP451 -7.39 149.64 2.85 -4.73 -4.91 -47.86 -55.37 141.93 19 5t00 A-thr C.DA4 A.THR421 9.48 -173.97 -2.17 3.17 8.67 13.58 -85.41 -171.72 20 5t00 G-thr C.DG5 A.THR421 8.15 157.64 3.56 -3.53 6.42 16.37 83.30 149.53 21 5t00 C-thr C.DC6 A.THR417 10.51 -176.41 -7.60 5.05 -5.22 24.92 70.96 -175.47 22 5t00 C-gln C.DC6 A.GLN418 8.78 -151.38 -2.48 7.55 3.72 20.51 -53.33 -147.31 23 5t00 C-thr C.DC6 A.THR421 -6.95 123.55 4.34 -3.36 4.28 30.29 71.76 105.09 24 5t00 A-arg C.DA7 A.ARG396 10.65 -131.92 -6.81 7.17 3.96 -36.85 57.26 -121.10 25 5t00 A-gln C.DA7 A.GLN418 8.58 -179.48 -1.86 8.33 0.91 9.82 -56.96 -179.41 26 5t00 G-lys C.DG8 A.LYS393 9.30 161.54 2.71 -3.44 8.21 6.37 80.24 155.74 27 5t00 G-arg C.DG8 A.ARG396 10.74 -153.09 -3.22 10.11 1.68 -14.58 64.36 -147.79 28 5t00 G-lys C.DG9 A.LYS393 9.02 137.33 4.49 -4.53 6.37 21.92 75.67 123.84 29 5t00 G-arg C.DG9 A.ARG396 -11.20 -174.43 0.55 11.14 -1.10 5.31 64.02 -173.43 30 5t00 G-arg C.DG10 A.ARG368 11.12 -125.39 -6.81 7.61 4.40 -32.62 68.75 -108.75 31 5t00 G-asp C.DG10 A.ASP390 9.57 -178.43 -3.02 8.86 1.98 17.23 -43.39 -178.29 32 5t00 G-lys C.DG10 A.LYS393 -8.61 115.87 5.69 -5.44 3.49 45.84 63.32 93.70 33 5t00 G-lys C.DG11 A.LYS365 9.23 163.72 3.53 -4.03 7.51 12.65 71.06 159.82 34 5t00 G-arg C.DG11 A.ARG368 11.25 -154.03 -2.62 10.90 0.95 -15.30 71.06 -147.60 35 5t00 G-tyr C.DG12 A.TYR343 12.15 -127.62 -10.31 6.32 -1.23 -49.41 71.53 -105.08 36 5t00 G-glu C.DG12 A.GLU362 10.76 -136.88 -2.61 9.95 3.14 36.12 -26.71 -133.14 37 5t00 G-lys C.DG12 A.LYS365 9.43 138.80 5.09 -5.27 5.93 20.37 69.26 128.37 38 5t00 C-arg C.5CM13 A.ARG339 11.46 -127.77 -6.99 7.78 4.68 -42.48 61.97 -112.54 39 5t00 C-tyr C.5CM13 A.TYR343 -12.54 -153.87 -7.90 9.36 2.71 28.39 -84.12 -143.12 40 5t00 C-glu C.5CM13 A.GLU362 9.60 -168.06 -1.32 9.51 -0.25 22.04 -33.95 -167.27 41 5t00 C-lys C.5CM13 A.LYS365 -9.53 116.15 5.55 -7.24 2.73 44.62 61.97 95.44 42 5t00 G-glu C.DG14 A.GLU336 9.24 162.90 2.87 -4.27 7.67 -17.30 76.47 157.88 43 5t00 G-arg C.DG14 A.ARG339 10.85 -143.83 -3.41 9.94 2.69 -13.39 64.24 -136.65 44 5t00 G-glu C.DG14 A.GLU362 -9.72 158.53 0.24 -9.45 -2.22 -25.36 38.36 156.65 45 5t00 C-glu C.DC15 A.GLU336 8.10 137.08 4.35 -3.70 5.75 6.02 79.19 123.20 46 5t00 C-arg C.DC15 A.ARG339 -9.76 -172.68 0.07 9.72 -0.87 5.86 64.36 -171.34 47 5t00 T-thr C.DT16 A.THR333 9.50 -176.86 -2.95 8.46 3.17 8.34 -55.88 -176.43 48 5t00 T-gly E.DT1 D.GLY335 8.82 -132.99 -3.64 8.00 0.72 -26.99 47.60 -126.63 49 5t00 G-arg E.DG3 D.ARG339 -9.69 166.26 -0.46 -9.68 0.41 13.00 -57.95 164.17 50 5t00 G-glu E.DG3 D.GLU362 9.35 -130.90 -0.19 8.54 3.80 -21.38 -49.55 -124.42 51 5t00 C-glu E.5CM4 D.GLU362 -9.80 -159.62 0.62 9.77 0.50 -42.52 -41.63 -156.49 52 5t00 C-ser E.5CM4 D.SER364 -9.17 -164.90 -4.00 8.21 -0.84 -24.86 49.18 -162.95 53 5t00 C-tyr E.DC6 D.TYR392 9.14 -139.16 -4.55 7.09 3.56 -6.59 47.21 -135.16 54 5t00 C-tyr E.DC7 D.TYR392 8.19 -154.74 -3.58 7.34 0.62 14.57 33.87 -153.35 55 5t00 C-tyr E.DC8 D.TYR392 -7.57 164.06 0.50 -6.36 -4.07 -1.63 -23.13 163.73 56 5t00 C-lys E.DC8 D.LYS393 -8.03 -96.69 5.36 4.16 -4.31 20.85 -57.61 -78.86 57 5t00 C-lys E.DC9 D.LYS393 -8.42 -126.60 3.09 3.89 -6.80 18.01 -62.96 -115.42 58 5t00 C-ser E.DC13 D.SER450 8.59 -118.98 -4.18 7.51 0.17 12.55 32.41 -115.72 59 5t00 T-asp E.DT14 D.ASP451 8.62 -131.20 -0.40 5.40 6.70 -73.39 44.59 -111.30 60 5t00 T-val E.DT14 D.VAL454 10.99 -137.07 -6.13 8.49 3.33 -26.63 40.39 -132.70 61 5t00 G-asp E.DG15 D.ASP451 7.68 -157.24 2.21 5.80 4.53 -54.55 50.37 -151.34 62 5t00 C-asp F.DC2 D.ASP451 9.35 178.44 6.53 -5.94 -3.09 -26.98 -74.40 177.97 63 5t00 C-arg F.DC3 D.ARG448 9.91 -151.09 -2.31 9.10 3.17 9.22 -60.48 -146.29 64 5t00 C-asp F.DC3 D.ASP451 -7.55 150.91 2.69 -5.18 -4.79 -54.28 -59.97 141.46 65 5t00 A-thr F.DA4 D.THR421 9.25 -172.49 -2.04 3.55 8.29 14.07 -86.90 -169.55 66 5t00 G-thr F.DG5 D.THR421 7.91 159.11 3.42 -3.49 6.22 13.10 82.73 151.82 67 5t00 C-gln F.DC6 D.GLN418 8.62 -154.70 -2.63 7.34 3.67 22.17 -44.77 -152.04 68 5t00 C-thr F.DC6 D.THR421 -6.60 125.40 4.33 -3.26 3.78 33.47 67.29 109.27 69 5t00 A-arg F.DA7 D.ARG396 10.77 -130.76 -6.76 7.13 4.42 -34.96 50.98 -121.90 70 5t00 A-gln F.DA7 D.GLN418 8.85 179.67 1.97 -8.55 1.14 -12.78 59.60 179.62 71 5t00 G-lys F.DG8 D.LYS393 9.50 158.10 2.91 -3.49 8.34 5.53 82.11 150.78 72 5t00 G-arg F.DG8 D.ARG396 11.01 -153.47 -2.96 10.37 2.18 -16.68 61.28 -148.69 73 5t00 G-lys F.DG9 D.LYS393 9.18 132.02 4.56 -4.36 6.68 21.14 76.47 116.23 74 5t00 G-arg F.DG10 D.ARG368 11.31 -126.18 -7.74 7.52 3.38 -31.63 66.71 -111.05 75 5t00 G-asp F.DG10 D.ASP390 9.05 178.46 3.11 -8.35 1.53 -32.60 51.79 178.21 76 5t00 G-lys F.DG10 D.LYS393 -8.21 107.25 5.35 -4.94 3.79 41.34 61.89 83.74 77 5t00 G-lys F.DG11 D.LYS365 9.89 168.14 3.82 -4.09 8.15 3.01 74.02 165.13 78 5t00 G-arg F.DG11 D.ARG368 11.78 -148.64 -3.99 11.08 0.33 -14.53 72.58 -140.44 79 5t00 G-tyr F.DG12 D.TYR343 12.56 -126.40 -10.83 6.29 -0.88 -54.50 68.05 -103.00 80 5t00 G-glu F.DG12 D.GLU362 11.17 -131.59 -3.31 10.35 2.61 37.13 -27.96 -127.00 81 5t00 G-lys F.DG12 D.LYS365 9.84 145.24 5.60 -5.27 6.13 16.72 75.53 135.00 82 5t00 C-arg F.5CM13 D.ARG339 11.08 -130.95 -6.95 7.65 3.98 -37.10 61.75 -118.25 83 5t00 C-tyr F.5CM13 D.TYR343 -12.62 -156.48 -6.25 10.04 -4.42 -28.46 82.97 -147.16 84 5t00 C-glu F.5CM13 D.GLU362 9.62 -168.92 -1.39 9.51 -0.29 22.48 -40.01 -167.96 85 5t00 C-lys F.5CM13 D.LYS365 -9.37 116.04 5.36 -7.09 2.98 43.67 66.68 92.75 86 5t00 G-glu F.DG14 D.GLU336 9.32 156.08 3.55 -2.46 8.26 5.15 66.78 151.23 87 5t00 G-arg F.DG14 D.ARG339 10.99 -145.87 -3.35 10.21 2.32 -8.92 65.41 -139.04 88 5t00 C-glu F.DC15 D.GLU336 7.97 127.30 5.16 -2.49 5.55 25.93 62.14 115.54 89 5t00 C-arg F.DC15 D.ARG339 -9.60 -176.05 0.35 9.50 -1.32 11.26 65.08 -175.29 90 5t00 T-thr F.DT16 D.THR333 9.08 -174.03 -2.50 8.30 2.73 9.55 -55.13 -173.23 **************************************************************************** List of 79 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5t00 AT-arg C.DA7 B.DT11 A.ARG396 10.47 -128.11 -6.95 6.76 3.96 -36.37 54.55 -117.28 2 5t00 AT-arg F.DA7 E.DT11 D.ARG396 10.61 -125.06 -6.85 6.63 4.67 -34.38 50.15 -115.34 3 5t00 AT-asp C.DA4 B.DT14 A.ASP451 -8.43 133.32 -0.32 -4.88 -6.87 -69.82 -38.62 117.82 4 5t00 AT-asp F.DA4 E.DT14 D.ASP451 -8.56 133.53 -0.91 -5.14 -6.79 -69.78 -37.45 118.41 5 5t00 AT-gln C.DA7 B.DT11 A.GLN418 8.46 -177.91 -1.94 8.17 1.01 13.87 -57.02 -177.60 6 5t00 AT-gln F.DA7 E.DT11 D.GLN418 8.83 -177.44 -2.14 8.48 1.19 17.16 -56.86 -177.05 7 5t00 AT-gly C.DA17 B.DT1 A.GLY335 -8.77 127.62 -3.35 -8.08 -0.66 -8.54 -30.97 125.32 8 5t00 AT-gly F.DA17 E.DT1 D.GLY335 -8.61 131.64 -3.47 -7.71 -1.62 -13.96 -41.40 127.63 9 5t00 AT-thr B.DA2 C.DT16 A.THR333 -9.94 172.91 -3.23 -8.71 -3.54 15.57 55.89 171.89 10 5t00 AT-thr C.DA4 B.DT14 A.THR421 9.48 179.83 1.50 -3.04 8.85 -15.81 81.82 179.78 11 5t00 AT-thr E.DA2 F.DT16 D.THR333 -9.46 170.15 -2.67 -8.57 -2.99 14.25 53.46 168.88 12 5t00 AT-thr F.DA4 E.DT14 D.THR421 9.34 -178.89 -1.26 3.00 8.76 18.68 -81.37 -178.51 13 5t00 AT-val C.DA4 B.DT14 A.VAL454 -10.44 138.87 -5.87 -8.08 -3.04 -19.90 -35.81 135.96 14 5t00 AT-val F.DA4 E.DT14 D.VAL454 -10.94 137.38 -6.28 -8.32 -3.32 -22.16 -32.24 134.63 15 5t00 GC-arg B.DG3 C.DC15 A.ARG339 -9.99 166.87 -0.30 -9.98 0.18 9.17 -61.82 164.63 16 5t00 GC-arg C.DG14 B.5CM4 A.ARG339 11.08 -141.75 -3.54 10.02 3.14 -6.67 60.40 -135.36 17 5t00 GC-arg B.DG5 C.5CM13 A.ARG339 -11.48 119.24 -7.39 -6.92 -5.40 -35.84 -60.02 103.80 18 5t00 GC-arg C.DG11 B.DC7 A.ARG368 11.05 -153.56 -2.63 10.71 0.68 -18.03 69.06 -147.29 19 5t00 GC-arg C.DG10 B.DC8 A.ARG368 11.06 -119.80 -7.23 7.30 4.08 -28.87 57.09 -107.50 20 5t00 GC-arg C.DG9 B.DC9 A.ARG396 11.19 -173.29 0.50 11.18 -0.25 11.34 68.02 -171.85 21 5t00 GC-arg C.DG8 B.DC10 A.ARG396 10.52 -151.81 -3.22 9.86 1.79 -13.60 63.08 -146.53 22 5t00 GC-arg B.DG15 C.DC3 A.ARG448 -10.15 150.81 -3.00 -9.32 -2.70 7.29 66.74 144.79 23 5t00 GC-arg E.DG3 F.DC15 D.ARG339 -9.64 171.20 -0.04 -9.61 0.86 12.04 -61.49 169.69 24 5t00 GC-arg F.DG14 E.5CM4 D.ARG339 10.72 -139.20 -3.96 9.56 2.82 -4.38 59.75 -132.56 25 5t00 GC-arg E.DG5 F.5CM13 D.ARG339 -11.16 120.57 -7.20 -7.01 -4.85 -31.13 -57.64 107.77 26 5t00 GC-arg F.DG11 E.DC7 D.ARG368 11.61 -152.84 -3.60 11.03 -0.33 -18.73 72.91 -145.50 27 5t00 GC-arg F.DG10 E.DC8 D.ARG368 11.18 -121.30 -8.07 7.27 2.65 -29.70 56.62 -109.41 28 5t00 GC-arg F.DG8 E.DC10 D.ARG396 10.67 -152.20 -2.96 9.99 2.29 -17.37 62.93 -146.84 29 5t00 GC-arg E.DG15 F.DC3 D.ARG448 -9.88 149.51 -2.27 -9.18 -2.86 7.72 65.80 143.40 30 5t00 GC-asp C.DG10 B.DC8 A.ASP390 9.56 -179.68 -3.05 8.68 2.62 27.84 -49.69 -179.63 31 5t00 GC-asp B.DG15 C.DC3 A.ASP451 7.48 -152.87 2.66 5.10 4.78 -51.00 52.78 -145.98 32 5t00 GC-asp B.DG16 C.DC2 A.ASP451 -8.97 178.19 -6.44 -5.80 2.34 33.21 -71.29 177.66 33 5t00 GC-asp F.DG10 E.DC8 D.ASP390 8.89 178.86 3.41 -8.00 1.83 -41.61 57.01 178.60 34 5t00 GC-asp E.DG15 F.DC3 D.ASP451 7.61 -154.02 2.44 5.49 4.67 -54.44 55.19 -146.49 35 5t00 GC-asp E.DG16 F.DC2 D.ASP451 -9.34 178.18 -6.41 -6.19 2.77 31.29 -70.68 177.67 36 5t00 GC-gln B.DG12 C.DC6 A.GLN418 -8.67 148.20 -2.67 -7.57 -3.28 20.31 55.77 143.24 37 5t00 GC-gln E.DG12 F.DC6 D.GLN418 -8.92 149.68 -2.96 -7.74 -3.30 22.37 50.66 145.64 38 5t00 GC-glu B.DG3 C.DC15 A.GLU336 -8.28 -135.24 4.31 3.48 -6.16 -1.27 -78.32 -121.18 39 5t00 GC-glu C.DG14 B.5CM4 A.GLU336 9.44 157.05 2.83 -3.89 8.12 -22.07 76.81 149.91 40 5t00 GC-glu C.DG14 B.5CM4 A.GLU362 9.86 154.59 0.19 -9.73 -1.55 -31.67 38.80 151.90 41 5t00 GC-glu B.DG5 C.5CM13 A.GLU362 -9.56 168.33 -1.47 -9.43 -0.59 30.77 29.18 167.48 42 5t00 GC-glu C.DG12 B.DC6 A.GLU362 10.56 -136.66 -2.72 9.48 3.79 41.21 -22.14 -132.55 43 5t00 GC-glu E.DG3 F.DC15 D.GLU336 -8.03 -127.20 5.20 2.15 -5.73 19.89 -64.07 -115.52 44 5t00 GC-glu E.DG3 F.DC15 D.GLU362 9.36 -128.99 -0.26 8.28 4.34 -15.48 -48.45 -123.05 45 5t00 GC-glu F.DG14 E.5CM4 D.GLU336 9.18 153.70 3.42 -1.39 8.41 -4.06 67.07 148.30 46 5t00 GC-glu F.DG14 E.5CM4 D.GLU362 10.13 159.48 0.67 -10.01 -1.38 -33.29 41.82 156.99 47 5t00 GC-glu E.DG5 F.5CM13 D.GLU362 -9.99 167.75 -1.53 -9.87 -0.44 33.35 36.42 166.52 48 5t00 GC-glu F.DG12 E.DC6 D.GLU362 11.17 -133.34 -3.10 10.25 3.16 41.70 -24.12 -128.58 49 5t00 GC-lys B.DG5 C.5CM13 A.LYS365 9.46 -116.27 5.55 6.91 -3.30 40.25 -54.51 -101.02 50 5t00 GC-lys C.DG12 B.DC6 A.LYS365 9.13 140.50 4.79 -4.86 6.06 18.24 63.83 132.37 51 5t00 GC-lys C.DG11 B.DC7 A.LYS365 9.02 165.78 3.65 -3.92 7.26 12.26 73.69 162.08 52 5t00 GC-lys C.DG10 B.DC8 A.LYS393 -8.65 108.32 5.53 -5.14 4.22 34.05 60.61 89.09 53 5t00 GC-lys C.DG9 B.DC9 A.LYS393 9.02 133.47 3.86 -4.44 6.84 20.55 68.90 121.59 54 5t00 GC-lys C.DG8 B.DC10 A.LYS393 9.10 160.82 2.62 -3.14 8.12 4.50 80.60 154.74 55 5t00 GC-lys E.DG5 F.5CM13 D.LYS365 9.81 -115.68 5.58 7.06 -3.90 36.17 -59.87 -98.98 56 5t00 GC-lys F.DG12 E.DC6 D.LYS365 9.85 145.19 5.29 -5.29 6.41 15.79 69.76 136.74 57 5t00 GC-lys F.DG11 E.DC7 D.LYS365 9.71 170.56 3.90 -4.42 7.71 7.94 76.38 167.95 58 5t00 GC-lys F.DG10 E.DC8 D.LYS393 -8.12 101.72 5.37 -4.54 4.05 31.02 60.11 81.10 59 5t00 GC-lys F.DG9 E.DC9 D.LYS393 8.80 129.24 3.82 -4.13 6.77 19.60 69.71 115.83 60 5t00 GC-lys F.DG8 E.DC10 D.LYS393 9.20 159.51 2.63 -3.31 8.18 5.17 80.48 153.01 61 5t00 GC-ser C.DG14 B.5CM4 A.SER364 -9.51 155.52 -4.91 -8.15 -0.04 -17.56 -48.16 152.80 62 5t00 GC-ser C.DG5 B.DC13 A.SER450 -8.20 122.37 -3.92 -7.19 -0.41 16.33 -31.28 119.24 63 5t00 GC-ser F.DG14 E.5CM4 D.SER364 -9.40 158.56 -4.25 -8.39 -0.02 -18.01 -49.02 156.09 64 5t00 GC-ser F.DG5 E.DC13 D.SER450 -8.53 117.91 -4.23 -7.39 -0.57 18.52 -29.60 114.55 65 5t00 GC-thr B.DG12 C.DC6 A.THR417 -10.40 174.06 -7.31 -4.93 5.50 22.43 -68.20 172.67 66 5t00 GC-thr B.DG12 C.DC6 A.THR421 7.02 -124.95 4.52 3.47 -4.10 27.51 -75.35 -105.65 67 5t00 GC-thr C.DG5 B.DC13 A.THR421 7.83 153.39 3.23 -2.83 6.55 7.64 81.41 144.55 68 5t00 GC-thr E.DG12 F.DC6 D.THR421 7.03 -126.35 4.67 3.37 -4.04 27.61 -73.73 -108.58 69 5t00 GC-thr F.DG5 E.DC13 D.THR421 7.98 154.06 3.21 -3.22 6.55 8.40 81.44 145.43 70 5t00 GC-tyr B.DG5 C.5CM13 A.TYR343 -12.54 158.12 -7.73 -9.01 -4.05 37.69 81.21 148.99 71 5t00 GC-tyr C.DG12 B.DC6 A.TYR343 12.15 -121.68 -10.73 5.65 -0.71 -46.75 72.02 -96.55 72 5t00 GC-tyr C.DG12 B.DC6 A.TYR392 -9.35 131.72 -4.99 -7.13 -3.43 -12.13 -44.82 127.15 73 5t00 GC-tyr C.DG11 B.DC7 A.TYR392 -8.48 149.89 -3.52 -7.69 -0.63 5.27 -38.32 148.04 74 5t00 GC-tyr C.DG10 B.DC8 A.TYR392 8.15 -173.74 0.60 7.38 3.41 -7.07 37.69 -173.37 75 5t00 GC-tyr E.DG5 F.5CM13 D.TYR343 -12.73 145.69 -6.93 -10.27 2.92 -24.35 -81.41 132.85 76 5t00 GC-tyr F.DG12 E.DC6 D.TYR343 12.50 -121.79 -10.97 6.00 -0.07 -50.62 69.52 -96.62 77 5t00 GC-tyr F.DG12 E.DC6 D.TYR392 -9.08 137.74 -4.75 -6.99 -3.33 -6.84 -41.23 134.60 78 5t00 GC-tyr F.DG11 E.DC7 D.TYR392 -8.18 157.45 -3.28 -7.48 -0.40 10.23 -36.48 156.14 79 5t00 GC-tyr F.DG10 E.DC8 D.TYR392 7.75 -168.24 0.84 6.68 3.84 -8.44 29.84 -167.80 **************************************************************************** List of 47 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5t00 OP2@B.DC7 OH@A.TYR392 2.41 po4:sidechain 2 5t00 OP2@B.DC7 NZ@A.LYS395 2.54 po4:sidechain:salt-bridge 3 5t00 O5'@B.DC7 OH@A.TYR392 2.72 po4:sidechain 4 5t00 OP2@B.DC8 OH@A.TYR407 2.40 po4:sidechain 5 5t00 OP2@B.DC9 OG@A.SER419 2.78 po4:sidechain 6 5t00 OP2@B.DC10 NZ@A.LYS423 3.11 po4:sidechain:salt-bridge 7 5t00 O5'@B.DC13 NH1@A.ARG457 3.89 po4:sidechain 8 5t00 OP2@B.DT14 NH1@A.ARG457 3.07 po4:sidechain:salt-bridge 9 5t00 OP2@C.DC2 N@A.ALA447 2.91 po4:backbone 10 5t00 OP2@C.DC3 NH2@A.ARG448 3.10 po4:sidechain:salt-bridge 11 5t00 OP1@C.DA4 ND1@A.HIS425 2.65 po4:sidechain:salt-bridge 12 5t00 OP1@C.DG5 NZ@A.LYS405 2.40 po4:sidechain:salt-bridge 13 5t00 OP2@C.DG5 N@A.THR417 3.23 po4:backbone 14 5t00 OP1@C.DA7 ND1@A.HIS397 2.39 po4:sidechain:salt-bridge 15 5t00 OP1@C.DG8 NH1@A.ARG377 2.58 po4:sidechain:salt-bridge 16 5t00 OP1@C.DG8 NH2@A.ARG377 2.74 po4:sidechain:salt-bridge 17 5t00 OP2@C.DG8 OH@A.TYR386 2.49 po4:sidechain 18 5t00 OP2@C.DG9 OG@A.SER372 3.45 po4:sidechain 19 5t00 OP2@C.DG9 NH1@A.ARG389 2.93 po4:sidechain:salt-bridge 20 5t00 OP2@C.DG10 ND1@A.HIS369 2.80 po4:sidechain:salt-bridge 21 5t00 OP2@C.DG11 OH@A.TYR358 2.48 po4:sidechain 22 5t00 OP1@C.5CM13 ND1@A.HIS340 2.67 po4:sidechain:salt-bridge 23 5t00 OP2@E.DG5 OG1@D.THR391 3.45 po4:sidechain 24 5t00 OP1@E.DC6 NZ@D.LYS395 3.12 po4:sidechain:salt-bridge 25 5t00 OP2@E.DC7 OH@D.TYR392 2.35 po4:sidechain 26 5t00 OP2@E.DC7 NZ@D.LYS395 2.86 po4:sidechain:salt-bridge 27 5t00 O5'@E.DC7 OH@D.TYR392 2.87 po4:sidechain 28 5t00 OP2@E.DC8 OH@D.TYR407 2.49 po4:sidechain 29 5t00 OP1@E.DC9 NZ@D.LYS423 2.58 po4:sidechain:salt-bridge 30 5t00 OP2@E.DC9 OG@D.SER419 2.61 po4:sidechain 31 5t00 OP2@E.DC10 NZ@D.LYS423 2.94 po4:sidechain:salt-bridge 32 5t00 OP1@E.DG12 NZ@D.LYS449 3.39 po4:sidechain:salt-bridge 33 5t00 OP2@E.DG12 NZ@D.LYS449 2.92 po4:sidechain:salt-bridge 34 5t00 OP2@F.DC2 N@D.ALA447 3.07 po4:backbone 35 5t00 OP2@F.DC3 NH2@D.ARG448 3.25 po4:sidechain:salt-bridge 36 5t00 OP1@F.DA4 ND1@D.HIS425 2.62 po4:sidechain:salt-bridge 37 5t00 OP1@F.DA4 NZ@D.LYS429 3.54 po4:sidechain:salt-bridge 38 5t00 OP2@F.DG5 N@D.THR417 3.28 po4:backbone 39 5t00 OP1@F.DA7 ND1@D.HIS397 2.47 po4:sidechain:salt-bridge 40 5t00 OP1@F.DG8 NH1@D.ARG377 2.47 po4:sidechain:salt-bridge 41 5t00 OP1@F.DG8 NH2@D.ARG377 3.25 po4:sidechain:salt-bridge 42 5t00 OP2@F.DG8 OH@D.TYR386 2.49 po4:sidechain 43 5t00 OP2@F.DG9 NH1@D.ARG389 2.81 po4:sidechain:salt-bridge 44 5t00 OP2@F.DG10 ND1@D.HIS369 3.70 po4:sidechain:salt-bridge 45 5t00 OP2@F.DG10 OG@D.SER372 3.31 po4:sidechain 46 5t00 OP2@F.DG11 OH@D.TYR358 2.79 po4:sidechain 47 5t00 OP1@F.5CM13 ND1@D.HIS340 2.41 po4:sidechain:salt-bridge **************************************************************************** List of 38 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5t00 O6@B.DG3 NH2@A.ARG339 3.77 base:sidechain 2 5t00 O6@B.DG5 NZ@A.LYS365 3.54 base:sidechain 3 5t00 N4@B.DC13 OG@A.SER450 3.60 base:sidechain 4 5t00 N4@C.DC3 OD1@A.ASP451 3.16 base:sidechain 5 5t00 N4@C.DC3 OD2@A.ASP451 2.53 base:sidechain 6 5t00 N4@C.DC6 OG1@A.THR421 3.06 base:sidechain 7 5t00 N7@C.DA7 NE2@A.GLN418 2.96 base:sidechain 8 5t00 N6@C.DA7 OE1@A.GLN418 2.69 base:sidechain 9 5t00 N7@C.DG8 NH2@A.ARG396 2.53 base:sidechain 10 5t00 O6@C.DG8 NH1@A.ARG396 2.54 base:sidechain 11 5t00 O6@C.DG9 NZ@A.LYS393 2.74 base:sidechain 12 5t00 O6@C.DG10 NZ@A.LYS393 2.89 base:sidechain 13 5t00 N7@C.DG11 NH2@A.ARG368 2.92 base:sidechain 14 5t00 O6@C.DG11 NH1@A.ARG368 3.11 base:sidechain 15 5t00 O6@C.DG12 NZ@A.LYS365 2.66 base:sidechain 16 5t00 N4@C.5CM13 OE1@A.GLU362 3.14 base:sidechain 17 5t00 N4@C.5CM13 OE2@A.GLU362 3.34 base:sidechain 18 5t00 N7@C.DG14 NH1@A.ARG339 2.45 base:sidechain 19 5t00 O6@C.DG14 NH2@A.ARG339 2.69 base:sidechain 20 5t00 O6@E.DG3 NH2@D.ARG339 3.59 base:sidechain 21 5t00 N4@E.DC13 OG@D.SER450 3.95 base:sidechain 22 5t00 N4@F.DC3 OD1@D.ASP451 3.18 base:sidechain 23 5t00 N4@F.DC3 OD2@D.ASP451 2.76 base:sidechain 24 5t00 N4@F.DC6 OG1@D.THR421 2.74 base:sidechain 25 5t00 N7@F.DA7 NH1@D.ARG396 2.52 base:sidechain 26 5t00 N7@F.DA7 NE2@D.GLN418 3.19 base:sidechain 27 5t00 N6@F.DA7 OE1@D.GLN418 2.98 base:sidechain 28 5t00 N7@F.DG8 NH2@D.ARG396 3.09 base:sidechain 29 5t00 O6@F.DG9 NZ@D.LYS393 2.66 base:sidechain 30 5t00 O6@F.DG10 NZ@D.LYS393 2.23 base:sidechain 31 5t00 N7@F.DG11 NH1@D.ARG368 3.22 base:sidechain 32 5t00 N7@F.DG11 NH2@D.ARG368 3.06 base:sidechain 33 5t00 O6@F.DG11 NH2@D.ARG368 3.27 base:sidechain 34 5t00 O6@F.DG12 NZ@D.LYS365 2.60 base:sidechain 35 5t00 N4@F.5CM13 OE1@D.GLU362 3.37 base:sidechain 36 5t00 N4@F.5CM13 OE2@D.GLU362 3.07 base:sidechain 37 5t00 N7@F.DG14 NH1@D.ARG339 2.57 base:sidechain 38 5t00 O6@F.DG14 NH2@D.ARG339 2.81 base:sidechain **************************************************************************** List of 11 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5t00 G-arg B.DG3 A.ARG339 1.85 21 2 5t00 C-asp C.DC3 A.ASP451 0.44 16 3 5t00 A-gln C.DA7 A.GLN418 0.16 10 4 5t00 G-arg C.DG8 A.ARG396 0.20 15 5 5t00 G-arg C.DG11 A.ARG368 0.18 7 6 5t00 G-arg C.DG14 A.ARG339 0.57 8 7 5t00 G-arg E.DG3 D.ARG339 1.86 17 8 5t00 C-asp F.DC3 D.ASP451 0.14 19 9 5t00 A-gln F.DA7 D.GLN418 0.09 11 10 5t00 G-arg F.DG11 D.ARG368 0.20 20 11 5t00 G-arg F.DG14 D.ARG339 0.59 7 **************************************************************************** List of 8 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5t00 C-asp C.DC2 A.ASP451 3.01 11 2 5t00 C-gln C.DC6 A.GLN418 3.23 7 3 5t00 A-arg C.DA7 A.ARG396 3.35 16 4 5t00 G-arg C.DG10 A.ARG368 3.49 11 5 5t00 C-arg C.5CM13 A.ARG339 3.65 7 6 5t00 C-gln F.DC6 D.GLN418 3.43 6 7 5t00 G-arg F.DG10 D.ARG368 3.48 20 8 5t00 C-arg F.5CM13 D.ARG339 3.53 7 **************************************************************************** List of 3 additional files 1 -- 5t00-baseAA-pairs.pdb 2 -- 5t00-baseAA-stacks.pdb 3 -- 5t00-pairs.pdb