**************************************************************************** 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/5cpk.pdb -o=5cpk.out --type=base File name: 5cpk.pdb no. of peptide chains: 8 [A=97,B=79,C=106,D=92,E=98,F=83,G=104,H=91] no. of DNA/RNA chains: 2 [I=145,J=145] no. of amino acids: 750 no. of nucleotides: 290 no. of atoms: 11910 no. of waters: 0 no. of metals: 0 **************************************************************************** List of 1 type of 12 modified nucleotides nt count list 1 5CM-c 12 I.5CM60,I.5CM83,I.5CM93,I.5CM109,I.5CM119,I.5CM132,J.5CM13,J.5CM26,J.5CM36,J.5CM52,J.5CM62,J.5CM85 **************************************************************************** List of 1 helix 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=140 strand-1 5'-ATCATGGAATCATGAATGGAAATGAATGGAATCATTGGTTGGACTCAAATGGAATTTTcGACAGGCTCAAATGGAATCTTcGAATGGATTcGAATGTAATCATTcGATGGATTcGAATGGAATCTTcGAATGGAAATGAT-3' bp-type ||||||||||||||||||.||||||..|||||.||||||||||||.||||||||.|.|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.| strand-2 3'-TAGTACCTTAGTACTTACCTTTACTCTCCTTAGTAACCAACCTGAGTTTACCTTAAAAGcTGTCCGAGTTTACCTTAGAAGcTTACCTAAGcTTACATTAGTAAGcTACCTAAGcTTACCTTAGAAGcTTACCTTTACTA-5' helix-form .BBB..B....xx.B......BBBB...BB....B...BBBB....BB..BBB......xB...BBB..B.BBBBBBB..BB....BBBBB..BBBBBBB.B.x.xx..B..B...B.......B.....BBBBB.... 1 I.DA1 J.DT145 A-T WC 20-XX cWW cW-W 2 I.DT2 J.DA144 T-A WC 20-XX cWW cW-W 3 I.DC3 J.DG143 C-G WC 19-XIX cWW cW-W 4 I.DA4 J.DT142 A-T WC 20-XX cWW cW-W 5 I.DT5 J.DA141 T-A WC 20-XX cWW cW-W 6 I.DG6 J.DC140 G-C WC 19-XIX cWW cW-W 7 I.DG7 J.DC139 G-C WC 19-XIX cWW cW-W 8 I.DA8 J.DT138 A-T WC 20-XX cWW cW-W 9 I.DA9 J.DT137 A-T WC 20-XX cWW cW-W 10 I.DT10 J.DA136 T-A WC 20-XX cWW cW-W 11 I.DC11 J.DG135 C-G WC 19-XIX cWW cW-W 12 I.DA12 J.DT134 A-T WC 20-XX cWW cW-W 13 I.DT13 J.DA132 T-A WC 20-XX cWW cW-W 14 I.DG15 J.DC131 G-C WC 19-XIX cWW cW-W 15 I.DA16 J.DT130 A-T WC 20-XX cWW cW-W 16 I.DA17 J.DT129 A-T WC 20-XX cWW cW-W 17 I.DT18 J.DA128 T-A WC 20-XX cWW cW-W 18 I.DG19 J.DC127 G-C WC 19-XIX cWW cW-W 19 I.DG20 J.DC126 G-C -- -- cWW cW-W 20 I.DA21 J.DT125 A-T WC 20-XX cWW cW-W 21 I.DA22 J.DT124 A-T WC 20-XX cWW cW-W 22 I.DA23 J.DT123 A-T WC 20-XX cWW cW-W 23 I.DT24 J.DA122 T-A WC 20-XX cWW cW-W 24 I.DG25 J.DC121 G-C WC 19-XIX cWW cW-W 25 I.DA26 J.DT120 A-T WC 20-XX cWW cW-W 26 I.DA27 J.DC119 A-C -- -- cWW cW-W 27 I.DT28 J.DT118 T-T -- -- cWW cW-W 28 I.DG29 J.DC117 G-C WC 19-XIX cWW cW-W 29 I.DG30 J.DC116 G-C WC 19-XIX cWW cW-W 30 I.DA31 J.DT115 A-T WC 20-XX cWW cW-W 31 I.DA32 J.DT114 A-T WC 20-XX cWW cW-W 32 I.DT33 J.DA113 T-A WC 20-XX cWW cW-W 33 I.DC34 J.DG112 C-G -- -- cSW cm-W 34 I.DA35 J.DT111 A-T WC 20-XX cWW cW-W 35 I.DT36 J.DA110 T-A WC 20-XX cWW cW-W 36 I.DT37 J.DA109 T-A WC 20-XX cWW cW-W 37 I.DG38 J.DC108 G-C WC 19-XIX cWW cW-W 38 I.DG39 J.DC107 G-C WC 19-XIX cWW cW-W 39 I.DT40 J.DA106 T-A WC 20-XX cWW cW-W 40 I.DT41 J.DA105 T-A WC 20-XX cWW cW-W 41 I.DG42 J.DC104 G-C WC 19-XIX cWW cW-W 42 I.DG43 J.DC103 G-C WC 19-XIX cWW cW-W 43 I.DA44 J.DT102 A-T WC 20-XX cWW cW-W 44 I.DC45 J.DG101 C-G WC 19-XIX cWW cW-W 45 I.DT46 J.DA100 T-A WC 20-XX cWW cW-W 46 I.DC47 J.DG99 C-G ~Wobble -- cWW cW-W 47 I.DA48 J.DT98 A-T WC 20-XX cWW cW-W 48 I.DA49 J.DT97 A-T WC 20-XX cWW cW-W 49 I.DA50 J.DT96 A-T WC 20-XX cWW cW-W 50 I.DT51 J.DA95 T-A WC 20-XX cWW cW-W 51 I.DG52 J.DC94 G-C WC 19-XIX cWW cW-W 52 I.DG53 J.DC93 G-C WC 19-XIX cWW cW-W 53 I.DA54 J.DT92 A-T WC 20-XX cWW cW-W 54 I.DA55 J.DT91 A-T WC 20-XX cWW cW-W 55 I.DT56 J.DA90 T-A -- -- cWW cW-W 56 I.DT57 J.DA89 T-A WC 20-XX cWW cW-W 57 I.DT58 J.DA88 T-A ~Wobble -- cWW cW-W 58 I.DT59 J.DA87 T-A WC 20-XX cWW cW-W 59 I.5CM60 J.DG86 c-G WC 19-XIX cWW cW-W 60 I.DG61 J.5CM85 G-c WC 19-XIX cWW cW-W 61 I.DA63 J.DT83 A-T WC 20-XX cWW cW-W 62 I.DC64 J.DG82 C-G WC 19-XIX cWW cW-W 63 I.DA65 J.DT81 A-T WC 20-XX cWW cW-W 64 I.DG66 J.DC80 G-C WC 19-XIX cWW cW-W 65 I.DG67 J.DC79 G-C WC 19-XIX cWW cW-W 66 I.DC68 J.DG78 C-G WC 19-XIX cWW cW-W 67 I.DT69 J.DA77 T-A WC 20-XX cWW cW-W 68 I.DC70 J.DG76 C-G WC 19-XIX cWW cW-W 69 I.DA71 J.DT75 A-T WC 20-XX cWW cW-W 70 I.DA72 J.DT74 A-T WC 20-XX cWW cW-W 71 I.DA73 J.DT73 A-T WC 20-XX cWW cW-W 72 I.DT74 J.DA72 T-A WC 20-XX cWW cW-W 73 I.DG75 J.DC71 G-C WC 19-XIX cWW cW-W 74 I.DG76 J.DC70 G-C WC 19-XIX cWW cW-W 75 I.DA77 J.DT69 A-T WC 20-XX cWW cW-W 76 I.DA78 J.DT68 A-T WC 20-XX cWW cW-W 77 I.DT79 J.DA67 T-A WC 20-XX cWW cW-W 78 I.DC80 J.DG66 C-G WC 19-XIX cWW cW-W 79 I.DT81 J.DA65 T-A WC 20-XX cWW cW-W 80 I.DT82 J.DA64 T-A WC 20-XX cWW cW-W 81 I.5CM83 J.DG63 c-G WC 19-XIX cWW cW-W 82 I.DG84 J.5CM62 G-c WC 19-XIX cWW cW-W 83 I.DA85 J.DT61 A-T WC 20-XX cWW cW-W 84 I.DA86 J.DT60 A-T WC 20-XX cWW cW-W 85 I.DT87 J.DA59 T-A WC 20-XX cWW cW-W 86 I.DG88 J.DC58 G-C WC 19-XIX cWW cW-W 87 I.DG89 J.DC57 G-C WC 19-XIX cWW cW-W 88 I.DA90 J.DT56 A-T WC 20-XX cWW cW-W 89 I.DT91 J.DA55 T-A WC 20-XX cWW cW-W 90 I.DT92 J.DA54 T-A WC 20-XX cWW cW-W 91 I.5CM93 J.DG53 c-G WC 19-XIX cWW cW-W 92 I.DG94 J.5CM52 G-c WC 19-XIX cWW cW-W 93 I.DA95 J.DT51 A-T WC 20-XX cWW cW-W 94 I.DA96 J.DT50 A-T WC 20-XX cWW cW-W 95 I.DT97 J.DA49 T-A WC 20-XX cWW cW-W 96 I.DG98 J.DC48 G-C WC 19-XIX cWW cW-W 97 I.DT99 J.DA47 T-A WC 20-XX cWW cW-W 98 I.DA100 J.DT46 A-T WC 20-XX cWW cW-W 99 I.DA101 J.DT45 A-T WC 20-XX cWW cW-W 100 I.DT102 J.DA44 T-A WC 20-XX cWW cW-W 101 I.DC103 J.DG43 C-G WC 19-XIX cWW cW-W 102 I.DA104 J.DT42 A-T WC 20-XX cWW cW-W 103 I.DT105 J.DA41 T-A WC 20-XX cWW cW-W 104 I.DT106 J.DA40 T-A WC 20-XX cWW cW-W 105 I.5CM109 J.DG37 c-G WC 19-XIX cWW cW-W 106 I.DG110 J.5CM36 G-c WC 19-XIX cWW cW-W 107 I.DA111 J.DT34 A-T WC 20-XX cWW cW-W 108 I.DT113 J.DA33 T-A WC 20-XX cWW cW-W 109 I.DG114 J.DC32 G-C WC 19-XIX cWW cW-W 110 I.DG115 J.DC31 G-C WC 19-XIX cWW cW-W 111 I.DA116 J.DT30 A-T WC 20-XX cWW cW-W 112 I.DT117 J.DA29 T-A WC 20-XX cWW cW-W 113 I.DT118 J.DA28 T-A WC 20-XX cWW cW-W 114 I.5CM119 J.DG27 c-G WC 19-XIX cWW cW-W 115 I.DG120 J.5CM26 G-c WC 19-XIX cWW cW-W 116 I.DA121 J.DT25 A-T WC 20-XX cWW cW-W 117 I.DA122 J.DT24 A-T WC 20-XX cWW cW-W 118 I.DT123 J.DA23 T-A WC 20-XX cWW cW-W 119 I.DG124 J.DC22 G-C WC 19-XIX cWW cW-W 120 I.DG125 J.DC21 G-C WC 19-XIX cWW cW-W 121 I.DA126 J.DT20 A-T WC 20-XX cWW cW-W 122 I.DA127 J.DT19 A-T WC 20-XX cWW cW-W 123 I.DT128 J.DA18 T-A WC 20-XX cWW cW-W 124 I.DC129 J.DG17 C-G WC 19-XIX cWW cW-W 125 I.DT130 J.DA16 T-A WC 20-XX cWW cW-W 126 I.DT131 J.DA15 T-A WC 20-XX cWW cW-W 127 I.5CM132 J.DG14 c-G WC 19-XIX cWW cW-W 128 I.DG133 J.5CM13 G-c WC 19-XIX cWW cW-W 129 I.DA134 J.DT12 A-T WC 20-XX cWW cW-W 130 I.DA135 J.DT11 A-T WC 20-XX cWW cW-W 131 I.DT136 J.DA10 T-A WC 20-XX cWW cW-W 132 I.DG137 J.DC9 G-C WC 19-XIX cWW cW-W 133 I.DG138 J.DC8 G-C WC 19-XIX cWW cW-W 134 I.DA139 J.DT7 A-T WC 20-XX cWW cW-W 135 I.DA140 J.DT6 A-T WC 20-XX cWW cW-W 136 I.DA141 J.DT5 A-T WC 20-XX cWW cW-W 137 I.DT142 J.DA4 T-A WC 20-XX cWW cW-W 138 I.DG143 J.DC3 G-C WC 19-XIX cWW cW-W 139 I.DA144 J.DT2 A-T -- -- cWW cW-W 140 I.DT145 J.DA1 T-A WC 20-XX cWW cW-W **************************************************************************** List of 14 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5cpk T-his I.DT5 E.HIS39 -11.47 -39.39 -9.92 5.75 -0.29 9.55 -34.88 -15.88 2 5cpk A-arg I.DA49 A.ARG83 -13.29 -81.24 -12.80 3.31 -1.42 44.01 -7.10 -69.76 3 5cpk A-arg I.DA50 A.ARG83 -13.89 -107.81 -11.87 5.66 -4.47 39.46 -20.26 -100.98 4 5cpk T-arg I.DT79 F.ARG45 13.15 -78.25 -12.70 -3.25 -1.05 39.62 50.04 -47.89 5 5cpk T-arg I.DT81 E.ARG40 11.58 -57.12 -10.82 -4.01 0.94 3.15 37.14 -44.08 6 5cpk T-arg I.DT82 E.ARG40 -11.42 -81.52 -11.03 -0.80 -2.83 11.63 28.06 -76.58 7 5cpk T-leu I.DT91 E.LEU65 -12.15 -94.20 -5.48 10.67 -1.96 20.00 -1.73 -92.54 8 5cpk G-arg I.DG110 G.ARG42 13.27 -62.71 -13.23 -0.21 1.06 43.17 22.96 -40.55 9 5cpk C-lys I.5CM132 G.LYS75 -11.35 117.93 7.02 -3.28 -8.29 -15.12 -42.16 112.22 10 5cpk A-arg J.DA65 E.ARG40 -12.03 59.89 -11.06 4.19 -2.20 6.98 -42.91 42.24 11 5cpk G-arg J.DG82 A.ARG40 -12.04 -70.71 -11.85 0.81 -1.95 10.94 16.06 -68.33 12 5cpk T-arg J.DT83 A.ARG40 -11.94 -107.12 -10.15 3.04 -5.51 -2.27 5.33 -107.01 13 5cpk T-leu J.DT91 A.LEU65 -11.85 -101.27 -5.59 10.18 -2.34 12.63 -0.42 -100.69 14 5cpk T-arg J.DT111 C.ARG42 12.43 -79.19 -12.00 2.22 -2.39 33.09 16.26 -71.36 **************************************************************************** List of 13 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5cpk AT-arg I.DA35 J.DT111 C.ARG42 12.53 76.10 -11.31 -2.36 4.84 42.30 4.31 64.66 2 5cpk AT-arg I.DA49 J.DT97 A.ARG83 -12.92 -83.80 -12.33 3.73 -1.02 48.77 -7.43 -70.03 3 5cpk AT-arg I.DA50 J.DT96 A.ARG83 -13.93 -106.17 -11.82 5.47 -4.94 46.58 -25.55 -95.63 4 5cpk AT-arg I.DA63 J.DT83 A.ARG40 12.26 103.36 -10.42 -3.35 5.52 6.56 -3.70 103.16 5 5cpk AT-arg J.DA67 I.DT79 F.ARG45 -13.23 74.00 -12.76 3.03 1.76 42.08 -40.17 47.90 6 5cpk AT-arg J.DA65 I.DT81 E.ARG40 -11.80 58.42 -10.95 4.09 -1.57 5.07 -40.02 43.17 7 5cpk AT-arg J.DA64 I.DT82 E.ARG40 -11.95 81.64 -11.55 1.33 2.76 10.39 -28.49 76.74 8 5cpk AT-his J.DA141 I.DT5 E.HIS39 11.58 42.50 -10.11 -5.63 0.05 9.91 38.66 14.92 9 5cpk AT-leu I.DA55 J.DT91 A.LEU65 11.84 96.76 -5.71 -10.17 2.07 21.73 12.27 94.28 10 5cpk AT-leu J.DA55 I.DT91 E.LEU65 12.15 92.65 -5.42 -10.68 2.00 25.31 11.41 89.31 11 5cpk GC-arg J.DG82 I.DC64 A.ARG40 -11.93 -68.24 -11.63 0.60 -2.58 9.08 9.00 -67.18 12 5cpk GC-arg I.DG110 J.5CM36 G.ARG42 -13.88 -43.98 -13.78 -0.94 -1.36 30.76 7.05 -31.04 13 5cpk GC-lys J.DG14 I.5CM132 G.LYS75 12.35 -126.94 7.87 4.22 8.53 -16.21 42.74 -122.01 **************************************************************************** List of 116 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5cpk O3'@I.DT5 ND1@E.HIS39 3.75 po4:sidechain 2 5cpk O3'@I.DG6 OH@E.TYR41 3.06 po4:sidechain 3 5cpk OP1@I.DA9 NZ@E.LYS56 3.33 po4:sidechain:salt-bridge 4 5cpk OP1@I.DG19 N@D.SER56 2.78 po4:backbone 5 5cpk OP1@I.DG19 OG@D.SER56 2.72 po4:sidechain 6 5cpk OP1@I.DG20 OH@D.TYR42 3.62 po4:sidechain 7 5cpk OP1@I.DG20 N@D.ILE54 3.66 po4:backbone 8 5cpk OP1@I.DG29 NH1@C.ARG32 2.74 po4:sidechain:salt-bridge 9 5cpk OP2@I.DG29 NH1@C.ARG32 3.17 po4:sidechain:salt-bridge 10 5cpk OP1@I.DG30 N@C.ARG17 3.27 po4:backbone 11 5cpk OP2@I.DG30 NE@C.ARG17 2.77 po4:sidechain:salt-bridge 12 5cpk OP2@I.DG30 NH2@C.ARG17 2.78 po4:sidechain:salt-bridge 13 5cpk OP1@I.DA31 N@C.LYS15 3.28 po4:backbone 14 5cpk OP1@I.DA31 NH2@C.ARG20 2.54 po4:sidechain:salt-bridge 15 5cpk OP1@I.DG39 N@D.SER87 3.10 po4:backbone 16 5cpk OP1@I.DG39 N@D.THR88 3.29 po4:backbone 17 5cpk OP1@I.DG39 OG1@D.THR88 2.14 po4:sidechain 18 5cpk O3'@I.DG38 OG@D.SER87 2.86 po4:sidechain 19 5cpk OP2@I.DT40 NH2@D.ARG86 3.39 po4:sidechain:salt-bridge 20 5cpk OP1@I.DA50 NH1@A.ARG72 3.09 po4:sidechain:salt-bridge 21 5cpk OP2@I.DA50 NH2@A.ARG72 3.16 po4:sidechain:salt-bridge 22 5cpk OP2@I.DA50 O@A.PHE84 2.86 po4:backbone 23 5cpk O3'@I.DA49 NH1@A.ARG83 2.96 po4:sidechain 24 5cpk OP1@I.DT51 NH2@A.ARG83 3.52 po4:sidechain:salt-bridge 25 5cpk O3'@I.DA50 NH2@A.ARG83 2.58 po4:sidechain 26 5cpk OP1@I.5CM60 OG1@B.THR30 2.99 po4:sidechain 27 5cpk OP1@I.5CM60 NH2@B.ARG36 3.60 po4:sidechain:salt-bridge 28 5cpk OP2@I.5CM60 NH1@B.ARG36 2.87 po4:sidechain:salt-bridge 29 5cpk OP2@I.DG61 N@B.LYS31 3.96 po4:backbone 30 5cpk OP1@I.DC68 NH2@A.ARG42 2.51 po4:sidechain:salt-bridge 31 5cpk OP2@I.DC68 NH2@A.ARG42 2.80 po4:sidechain:salt-bridge 32 5cpk OP1@I.DC70 N@A.VAL117 3.27 po4:backbone 33 5cpk OP1@I.DC70 N@A.THR118 3.21 po4:backbone 34 5cpk OP1@I.DC70 OG1@A.THR118 2.63 po4:sidechain 35 5cpk OP1@I.DC80 OG@F.SER47 3.50 po4:sidechain 36 5cpk OP1@I.DC80 N@F.GLY48 3.30 po4:backbone 37 5cpk OP1@I.DT81 N@F.ILE46 2.79 po4:backbone 38 5cpk OP1@I.DT82 N@E.GLY44 3.17 po4:backbone 39 5cpk OP1@I.DT82 N@E.VAL46 2.88 po4:backbone 40 5cpk OP1@I.DT82 N@E.ALA47 2.95 po4:backbone 41 5cpk O3'@I.DT81 N@E.GLY44 3.31 po4:backbone 42 5cpk OP1@I.5CM83 N@E.TYR41 2.95 po4:backbone 43 5cpk OP1@I.DA90 NH2@E.ARG69 2.70 po4:sidechain:salt-bridge 44 5cpk OP2@I.DA90 NH2@E.ARG69 3.02 po4:sidechain:salt-bridge 45 5cpk OP1@I.DT91 N@E.LYS64 2.45 po4:backbone 46 5cpk OP2@I.DT91 N@E.LEU65 3.53 po4:backbone 47 5cpk O3'@I.DA90 NE@E.ARG63 3.79 po4:sidechain 48 5cpk O3'@I.DT99 NH2@E.ARG83 2.75 po4:sidechain 49 5cpk OP1@I.DA101 N@F.LYS79 2.57 po4:backbone 50 5cpk OP1@I.DA101 N@F.THR80 2.80 po4:backbone 51 5cpk OP1@I.DA101 OG1@F.THR80 3.11 po4:sidechain 52 5cpk O3'@I.DA100 OG1@F.THR80 3.40 po4:sidechain 53 5cpk OP1@I.DC103 N@D.SER32 3.40 po4:backbone 54 5cpk OP1@I.DA111 N@G.ALA45 3.26 po4:backbone 55 5cpk OP1@I.DA112 N@G.VAL43 3.06 po4:backbone 56 5cpk OP1@I.DA121 OH@H.TYR40 3.12 po4:sidechain 57 5cpk OP1@I.DA122 NH2@G.ARG29 3.39 po4:sidechain:salt-bridge 58 5cpk OP1@I.DA122 N@H.SER36 3.17 po4:backbone 59 5cpk O3'@I.DA121 NH2@G.ARG29 3.32 po4:sidechain 60 5cpk OP1@I.DT131 N@G.THR76 2.94 po4:backbone 61 5cpk OP1@I.DT131 N@G.ARG77 2.74 po4:backbone 62 5cpk OP2@I.DT131 OG1@G.THR76 3.42 po4:sidechain 63 5cpk OP2@I.5CM132 NZ@G.LYS75 2.76 po4:sidechain:salt-bridge 64 5cpk OP1@I.DG143 N@A.ARG42 2.88 po4:backbone 65 5cpk OP1@I.DG143 OG1@A.THR45 2.93 po4:sidechain 66 5cpk OP2@I.DA144 NH1@A.ARG42 3.89 po4:sidechain:salt-bridge 67 5cpk O3'@J.DT6 OH@A.TYR41 2.93 po4:sidechain 68 5cpk OP1@J.DT19 N@H.SER56 2.35 po4:backbone 69 5cpk OP1@J.DT20 OH@H.TYR42 2.67 po4:sidechain 70 5cpk OP1@J.DA29 NE@G.ARG32 3.00 po4:sidechain:salt-bridge 71 5cpk OP1@J.DA29 NH2@G.ARG32 2.60 po4:sidechain:salt-bridge 72 5cpk OP1@J.DT30 N@G.ARG17 3.14 po4:backbone 73 5cpk OP2@J.DT30 NE@G.ARG17 3.26 po4:sidechain:salt-bridge 74 5cpk OP2@J.DT30 NH2@G.ARG17 3.25 po4:sidechain:salt-bridge 75 5cpk OP1@J.DC31 O@G.LYS15 3.09 po4:backbone 76 5cpk OP1@J.DC31 NH2@G.ARG20 2.68 po4:sidechain:salt-bridge 77 5cpk OP1@J.DA39 N@H.SER87 2.50 po4:backbone 78 5cpk OP1@J.DA39 OG@H.SER87 3.06 po4:sidechain 79 5cpk OP1@J.DA39 N@H.THR88 3.22 po4:backbone 80 5cpk O3'@J.DA38 OG@H.SER87 3.18 po4:sidechain 81 5cpk OP2@J.DA40 NH2@H.ARG86 3.31 po4:sidechain:salt-bridge 82 5cpk OP2@J.DA49 OG@E.SER86 3.35 po4:sidechain 83 5cpk OP1@J.DT50 NH1@E.ARG72 2.76 po4:sidechain:salt-bridge 84 5cpk OP1@J.DT50 N@E.PHE84 2.97 po4:backbone 85 5cpk OP2@J.DT50 NH2@E.ARG72 3.20 po4:sidechain:salt-bridge 86 5cpk OP1@J.DT60 OG1@F.THR30 3.22 po4:sidechain 87 5cpk OP1@J.DT60 NH2@F.ARG36 3.25 po4:sidechain:salt-bridge 88 5cpk OP2@J.DT60 NH1@F.ARG36 3.16 po4:sidechain:salt-bridge 89 5cpk OP1@J.DT68 NE@E.ARG42 3.05 po4:sidechain:salt-bridge 90 5cpk OP2@J.DT68 NH2@E.ARG42 2.45 po4:sidechain:salt-bridge 91 5cpk OP1@J.DC70 N@E.VAL117 2.85 po4:backbone 92 5cpk OP1@J.DC70 N@E.THR118 3.09 po4:backbone 93 5cpk OP1@J.DC70 OG1@E.THR118 2.75 po4:sidechain 94 5cpk OP1@J.DT81 N@B.ILE46 2.86 po4:backbone 95 5cpk OP2@J.DT81 NH2@B.ARG35 3.32 po4:sidechain:salt-bridge 96 5cpk OP1@J.DG82 N@A.GLY44 2.86 po4:backbone 97 5cpk OP1@J.DG82 N@A.VAL46 3.15 po4:backbone 98 5cpk OP1@J.DG82 N@A.ALA47 3.37 po4:backbone 99 5cpk OP1@J.DT83 N@A.TYR41 3.01 po4:backbone 100 5cpk OP1@J.DA90 NH2@A.ARG69 3.30 po4:sidechain:salt-bridge 101 5cpk OP2@J.DA90 NH2@A.ARG69 2.36 po4:sidechain:salt-bridge 102 5cpk OP1@J.DT91 N@A.LYS64 2.99 po4:backbone 103 5cpk OP2@J.DT91 N@A.LEU65 2.79 po4:backbone 104 5cpk OP1@J.DG101 N@B.LYS79 2.45 po4:backbone 105 5cpk OP1@J.DG101 N@B.THR80 2.97 po4:backbone 106 5cpk O3'@J.DA100 OG1@B.THR80 3.47 po4:sidechain 107 5cpk OP2@J.DT111 N@C.ALA45 3.35 po4:backbone 108 5cpk OP1@J.DG112 N@C.VAL43 3.00 po4:backbone 109 5cpk O5'@J.DC121 OH@D.TYR40 3.08 po4:sidechain 110 5cpk OP1@J.DA122 NH2@C.ARG29 3.03 po4:sidechain:salt-bridge 111 5cpk O3'@J.DC121 NH2@C.ARG29 3.37 po4:sidechain 112 5cpk OP1@J.DT123 N@D.LYS34 3.09 po4:backbone 113 5cpk O3'@J.DA122 O@D.LYS34 3.17 po4:backbone 114 5cpk OP1@J.DC131 N@C.ARG77 3.22 po4:backbone 115 5cpk OP1@J.DG143 N@E.ARG42 2.73 po4:backbone 116 5cpk OP1@J.DG143 OG1@E.THR45 2.93 po4:sidechain **************************************************************************** List of 3 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5cpk O4'@I.DT69 NH2@B.ARG45 3.29 sugar:sidechain 2 5cpk O4'@I.DA111 NH2@G.ARG42 2.85 sugar:sidechain 3 5cpk O4'@J.DT7 OH@A.TYR41 3.70 sugar:sidechain **************************************************************************** List of 4 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5cpk O2@I.DT82 NH1@E.ARG40 3.08 base:sidechain 2 5cpk O2@I.DT82 NH2@E.ARG40 2.91 base:sidechain 3 5cpk N2@J.DG82 NH2@A.ARG40 3.38 base:sidechain 4 5cpk O2@J.DT83 NH2@A.ARG40 2.93 base:sidechain **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5cpk T-arg I.DT82 E.ARG40 2.07 55 2 5cpk G-arg J.DG82 A.ARG40 0.09 32 **************************************************************************** List of 2 additional files 1 -- 5cpk-baseAA-pairs.pdb 2 -- 5cpk-pairs.pdb