**************************************************************************** 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/5ego.pdb -o=5ego.out --type=base File name: 5ego.pdb no. of peptide chains: 2 [A=57,B=63] no. of DNA/RNA chains: 2 [D=18,E=18] no. of amino acids: 120 no. of nucleotides: 36 no. of atoms: 1770 no. of waters: 20 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 D.5CM33,E.5CM4 **************************************************************************** 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=18 strand-1 5'-GTTGACAGTTTTAcGAGG-3' bp-type |||||||||||||||||| strand-2 3'-CAACTGTCAAAATGcTCC-5' helix-form .B.B..BBBBBBBBBB. 1 D.DG20 E.DC18 G-C WC 19-XIX cWW cW-W 2 D.DT21 E.DA17 T-A WC 20-XX cWW cW-W 3 D.DT22 E.DA16 T-A WC 20-XX cWW cW-W 4 D.DG23 E.DC15 G-C WC 19-XIX cWW cW-W 5 D.DA24 E.DT14 A-T WC 20-XX cWW cW-W 6 D.DC25 E.DG13 C-G WC 19-XIX cWW cW-W 7 D.DA26 E.DT12 A-T WC 20-XX cWW cW-W 8 D.DG27 E.DC11 G-C WC 19-XIX cWW cW-W 9 D.DT28 E.DA10 T-A WC 20-XX cWW cW-W 10 D.DT29 E.DA9 T-A WC 20-XX cWW cW-W 11 D.DT30 E.DA8 T-A WC 20-XX cWW cW-W 12 D.DT31 E.DA7 T-A WC 20-XX cWW cW-W 13 D.DA32 E.DT6 A-T WC 20-XX cWW cW-W 14 D.5CM33 E.DG5 c-G WC 19-XIX cWW cW-W 15 D.DG34 E.5CM4 G-c WC 19-XIX cWW cW-W 16 D.DA35 E.DT3 A-T WC 20-XX cWW cW-W 17 D.DG36 E.DC2 G-C WC 19-XIX cWW cW-W 18 D.DG37 E.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 33 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5ego T-arg D.DT22 A.ARG329 13.05 -138.99 -9.31 8.94 -1.91 -7.98 88.70 -121.13 2 5ego G-asn D.DG23 A.ASN325 8.99 -159.41 -5.77 6.82 -1.01 31.07 58.78 -155.32 3 5ego G-arg D.DG23 A.ARG329 11.40 -169.16 -2.68 10.24 -4.22 20.14 82.46 -165.29 4 5ego A-asn D.DA24 A.ASN321 9.17 178.73 7.97 -4.51 0.41 -24.71 -21.09 178.68 5 5ego A-asn D.DA24 A.ASN325 7.63 174.96 2.63 -6.28 -3.44 -50.44 -39.92 174.04 6 5ego A-arg D.DA24 A.ARG328 10.94 -165.52 2.40 9.83 4.15 -23.87 16.24 -165.04 7 5ego A-arg D.DA24 A.ARG329 -10.91 169.02 -2.14 -8.95 -5.85 -47.31 -66.20 165.50 8 5ego C-asn D.DC25 A.ASN321 -9.21 164.13 6.87 -5.53 -2.66 -36.42 -6.78 163.25 9 5ego C-asn D.DC25 A.ASN325 -8.34 166.01 0.69 -6.08 -5.67 -64.70 -22.19 163.07 10 5ego C-arg D.DC25 A.ARG328 11.14 174.94 -4.07 -10.06 2.50 13.44 -8.84 174.89 11 5ego T-arg D.DT30 B.ARG220 9.38 24.86 -9.28 0.72 1.20 14.71 18.31 8.20 12 5ego T-arg D.DT31 B.ARG217 11.64 -15.53 -11.25 -1.77 2.42 10.81 9.43 -5.96 13 5ego T-arg D.DT31 B.ARG220 -8.90 -26.09 -8.00 3.01 -2.47 10.82 8.37 -22.27 14 5ego T-asn D.DT31 B.ASN266 9.18 -160.30 -5.98 6.92 -0.80 26.38 64.39 -155.96 15 5ego A-arg D.DA32 B.ARG217 -12.42 -42.26 -12.23 1.96 -1.00 7.39 4.96 -41.36 16 5ego A-ile D.DA32 B.ILE262 9.39 179.47 8.03 -4.70 1.29 -15.35 -26.20 179.45 17 5ego A-asn D.DA32 B.ASN266 7.85 172.35 3.00 -6.28 -3.62 -43.51 -47.88 170.95 18 5ego C-arg D.5CM33 B.ARG217 -13.38 -67.20 -11.46 5.00 -4.75 -2.41 1.73 -67.14 19 5ego C-arg D.5CM33 B.ARG258 14.05 157.75 12.95 -5.27 1.36 8.20 3.60 157.68 20 5ego C-ile D.5CM33 B.ILE262 -9.56 155.77 7.00 -5.94 -2.67 -18.26 -11.70 155.32 21 5ego C-gln E.DC2 B.GLN265 10.90 -65.09 -4.52 8.34 5.36 2.61 31.72 -57.54 22 5ego T-gln E.DT3 B.GLN265 9.96 -88.77 -2.01 9.60 1.73 1.53 15.12 -87.73 23 5ego C-val E.5CM4 B.VAL269 10.95 -128.77 -4.99 8.80 4.18 -38.60 16.41 -124.83 24 5ego A-arg E.DA7 B.ARG217 -11.80 4.05 -11.50 1.97 -1.79 0.24 -0.75 3.98 25 5ego A-arg E.DA8 B.ARG220 -9.31 -15.12 -9.28 -0.49 -0.54 -6.54 -9.68 -9.62 26 5ego A-arg E.DA9 B.ARG220 -10.03 -51.19 -8.84 2.49 -4.03 -3.53 -6.21 -50.72 27 5ego C-ile E.DC11 A.ILE324 9.79 -86.79 -3.32 8.85 2.55 7.66 14.05 -85.59 28 5ego T-ile E.DT12 A.ILE324 -10.41 -117.21 -0.93 10.30 -1.17 9.10 10.59 -116.69 29 5ego T-arg E.DT12 A.ARG328 13.01 -137.08 -9.20 9.15 0.91 -5.32 31.74 -135.24 30 5ego G-arg E.DG13 A.ARG328 -11.66 -175.98 -4.71 10.42 -2.27 7.07 24.74 -175.88 31 5ego T-arg E.DT14 A.ARG328 -10.98 154.43 1.60 -9.77 -4.75 -18.39 -14.84 153.86 32 5ego T-arg E.DT14 A.ARG329 10.95 -179.58 -1.20 9.55 5.22 -47.07 73.01 -179.42 33 5ego C-arg E.DC15 A.ARG329 10.83 158.06 -1.98 -9.70 4.39 24.30 -59.57 154.01 **************************************************************************** List of 27 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5ego AT-arg E.DA16 D.DT22 A.ARG329 -12.95 134.29 -9.13 -8.75 2.80 -6.98 -76.14 120.73 2 5ego AT-arg D.DA24 E.DT14 A.ARG328 10.96 -159.99 2.00 9.82 4.45 -21.14 15.41 -159.45 3 5ego AT-arg D.DA24 E.DT14 A.ARG329 -10.93 174.37 -1.68 -9.26 -5.55 -47.29 -69.56 172.42 4 5ego AT-arg D.DA26 E.DT12 A.ARG328 -12.83 135.81 -9.30 -8.83 -0.58 -0.10 -21.00 135.02 5 5ego AT-arg E.DA9 D.DT29 B.ARG220 -9.99 -52.86 -8.66 2.74 -4.14 3.41 -11.92 -51.48 6 5ego AT-arg E.DA8 D.DT30 B.ARG220 -9.34 -17.22 -9.28 -0.62 -0.87 4.00 -14.20 -8.90 7 5ego AT-arg E.DA7 D.DT31 B.ARG217 -11.72 9.01 -11.38 1.86 -2.10 5.48 -5.14 4.97 8 5ego AT-arg E.DA7 D.DT31 B.ARG220 8.90 22.24 -7.95 -2.73 2.90 6.17 -3.39 21.11 9 5ego AT-arg D.DA32 E.DT6 B.ARG217 -12.39 -38.73 -12.14 1.62 -1.86 7.23 -3.92 -37.88 10 5ego AT-asn D.DA24 E.DT14 A.ASN321 9.14 -175.95 -8.13 4.13 0.59 27.10 22.96 -175.75 11 5ego AT-asn D.DA24 E.DT14 A.ASN325 7.63 -179.94 -2.91 6.27 -3.23 51.86 43.13 -179.93 12 5ego AT-asn E.DA7 D.DT31 B.ASN266 -9.09 156.10 -6.04 -6.74 0.85 28.05 -58.62 151.58 13 5ego AT-asn D.DA32 E.DT6 B.ASN266 7.87 179.33 3.21 -6.48 -3.10 -50.26 -46.89 179.19 14 5ego AT-gln D.DA35 E.DT3 B.GLN265 -10.02 89.13 -2.01 -9.59 -2.09 8.69 -7.22 88.56 15 5ego AT-ile D.DA26 E.DT12 A.ILE324 -10.12 116.61 -0.89 -10.05 0.80 12.43 0.88 116.19 16 5ego AT-ile D.DA32 E.DT6 B.ILE262 9.43 -175.39 -8.24 4.34 1.48 22.97 23.45 -175.20 17 5ego GC-arg D.DG23 E.DC15 A.ARG329 -11.10 -163.56 -2.37 9.97 -4.27 22.31 71.08 -159.30 18 5ego GC-arg E.DG13 D.DC25 A.ARG328 -11.40 -175.45 -4.40 10.24 -2.39 10.33 16.82 -175.38 19 5ego GC-arg E.DG5 D.5CM33 B.ARG217 13.46 66.57 -11.31 -5.17 5.15 3.45 5.85 66.26 20 5ego GC-arg E.DG5 D.5CM33 B.ARG258 -14.07 -158.52 13.01 4.90 -2.14 -1.05 -1.11 -158.52 21 5ego GC-asn D.DG23 E.DC15 A.ASN325 8.71 -153.59 -5.77 6.30 -1.70 32.68 47.32 -149.79 22 5ego GC-asn E.DG13 D.DC25 A.ASN321 -9.29 -161.25 6.84 5.89 2.24 -38.68 14.53 -159.95 23 5ego GC-asn E.DG13 D.DC25 A.ASN325 8.59 -161.91 0.87 6.32 5.75 -67.20 29.22 -157.41 24 5ego GC-gln D.DG36 E.DC2 B.GLN265 -10.96 62.57 -4.85 -8.34 -5.21 2.61 -21.33 59.12 25 5ego GC-ile D.DG27 E.DC11 A.ILE324 -9.78 84.64 -3.49 -8.72 -2.71 10.09 -7.01 83.91 26 5ego GC-ile E.DG5 D.5CM33 B.ILE262 -9.52 -157.66 7.18 5.95 1.92 -27.32 14.60 -156.80 27 5ego GC-val D.DG34 E.5CM4 B.VAL269 -11.04 124.04 -5.67 -8.35 -4.48 -30.16 -5.59 121.78 **************************************************************************** List of 20 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ego OP1@D.DA24 NE2@A.GLN318 3.00 po4:sidechain 2 5ego OP1@D.DT30 NZ@B.LYS270 2.95 po4:sidechain:salt-bridge 3 5ego OP2@D.DT30 NZ@B.LYS270 3.30 po4:sidechain:salt-bridge 4 5ego OP1@D.DT31 N@B.TYR223 3.03 po4:backbone 5 5ego OP2@D.DT31 NE1@B.TRP263 3.97 po4:sidechain 6 5ego O3'@D.DT30 NH2@B.ARG220 3.29 po4:sidechain 7 5ego O5'@D.DT31 NH2@B.ARG220 3.06 po4:sidechain 8 5ego OP1@D.DA32 N@B.ILE221 3.44 po4:backbone 9 5ego OP2@D.DA32 OH@B.TYR223 2.38 po4:sidechain 10 5ego OP2@D.DA32 NE2@B.GLN259 2.98 po4:sidechain 11 5ego O3'@D.DT31 N@B.ILE221 3.54 po4:backbone 12 5ego OP2@E.DC2 NE2@B.GLN265 2.80 po4:sidechain 13 5ego OP2@E.DT3 NE@B.ARG268 3.08 po4:sidechain:salt-bridge 14 5ego OP2@E.DT3 NH2@B.ARG268 2.83 po4:sidechain:salt-bridge 15 5ego OP2@E.5CM4 NZ@B.LYS272 3.01 po4:sidechain:salt-bridge 16 5ego OP1@E.DA10 NZ@B.LYS219 2.79 po4:sidechain:salt-bridge 17 5ego OP2@E.DA10 NZ@A.LYS305 2.64 po4:sidechain:salt-bridge 18 5ego OP1@E.DC11 OH@A.TYR299 2.83 po4:sidechain 19 5ego OP2@E.DC11 NE@A.ARG327 2.60 po4:sidechain:salt-bridge 20 5ego OP2@E.DC11 NH2@A.ARG327 2.92 po4:sidechain:salt-bridge **************************************************************************** List of 2 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ego O4'@D.DT31 NE@B.ARG220 2.97 sugar:sidechain 2 5ego O4'@E.DA10 NH1@B.ARG220 3.05 sugar:sidechain **************************************************************************** List of 12 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ego N7@D.DG23 NH1@A.ARG329 2.63 base:sidechain 2 5ego O6@D.DG23 NH2@A.ARG329 2.53 base:sidechain 3 5ego N7@D.DA24 OD1@A.ASN325 3.10 base:sidechain 4 5ego N6@D.DA24 ND2@A.ASN325 2.99 base:sidechain 5 5ego N6@D.DA24 NH2@A.ARG328 3.02 base:sidechain 6 5ego N7@D.DA32 OD1@B.ASN266 3.12 base:sidechain 7 5ego N6@D.DA32 ND2@B.ASN266 3.23 base:sidechain 8 5ego N3@D.DA32 NH2@B.ARG217 2.94 base:sidechain 9 5ego N3@E.DA9 NH1@B.ARG220 2.79 base:sidechain 10 5ego N7@E.DG13 NH1@A.ARG328 2.86 base:sidechain 11 5ego O6@E.DG13 NH2@A.ARG328 2.61 base:sidechain 12 5ego O4@E.DT14 NH2@A.ARG329 3.59 base:sidechain **************************************************************************** List of 7 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5ego G-arg D.DG23 A.ARG329 0.37 17 2 5ego A-asn D.DA24 A.ASN325 1.02 28 3 5ego A-arg D.DA24 A.ARG328 1.61 22 4 5ego A-arg D.DA32 B.ARG217 1.44 26 5 5ego A-asn D.DA32 B.ASN266 1.38 28 6 5ego G-arg E.DG13 A.ARG328 0.15 13 7 5ego T-arg E.DT14 A.ARG329 1.37 18 **************************************************************************** List of 3 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5ego T-arg D.DT22 A.ARG329 4.05 13 2 5ego T-asn D.DT31 B.ASN266 4.32 24 3 5ego T-arg E.DT12 A.ARG328 3.53 6 **************************************************************************** List of 3 additional files 1 -- 5ego-baseAA-pairs.pdb 2 -- 5ego-baseAA-stacks.pdb 3 -- 5ego-pairs.pdb