**************************************************************************** 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/4qeo.pdb -o=4qeo.out --type=base File name: 4qeo.pdb no. of peptide chains: 2 [A=473,P=7] no. of DNA/RNA chains: 2 [C=11,D=13] no. of amino acids: 480 no. of nucleotides: 25 no. of atoms: 4570 no. of waters: 285 no. of metals: 4 [Zn=4] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 5CM-c 1 C.5CM7 2 SAH-a 1 A.SAH801 **************************************************************************** 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=9 strand-1 5'-GGTACTATC-3' bp-type ||||||||| strand-2 3'-CCATGATAG-5' helix-form BBBBBxBB 1 C.DG1 D.DC13 G-C WC 19-XIX cWW cW-W 2 C.DG2 D.DC12 G-C WC 19-XIX cWW cW-W 3 C.DT3 D.DA11 T-A WC 20-XX cWW cW-W 4 C.DA4 D.DT10 A-T WC 20-XX cWW cW-W 5 C.DC5 D.DG9 C-G WC 19-XIX cWW cW-W 6 C.DT6 D.DA8 T-A WC 20-XX cWW cW-W 7 C.DA8 D.DT6 A-T WC 20-XX cWW cW-W 8 C.DT9 D.DA5 T-A WC 20-XX cWW cW-W 9 C.DC10 D.DG4 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 45 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4qeo T-leu C.DT6 A.LEU176 8.28 -26.69 -7.17 3.41 2.36 16.16 16.47 -13.50 2 4qeo T-asn C.DT6 A.ASN177 9.61 -159.25 -7.33 -4.11 4.67 73.90 -6.74 -153.90 3 4qeo T-leu C.DT6 A.LEU227 10.96 -90.55 -6.84 7.30 4.49 -22.71 47.19 -76.72 4 4qeo C-gly C.5CM7 A.GLY178 8.10 -90.19 -4.47 6.07 2.98 -36.66 70.49 -46.77 5 4qeo C-val C.5CM7 A.VAL202 7.72 125.63 3.18 2.86 6.42 -13.49 -0.59 125.22 6 4qeo C-met C.5CM7 A.MET203 5.05 -93.26 -0.79 1.53 4.74 45.13 -56.01 -63.91 7 4qeo C-ser C.5CM7 A.SER204 6.35 102.04 -1.84 5.38 2.85 -16.83 -8.82 100.74 8 4qeo C-gly C.5CM7 A.GLY205 -5.25 -157.04 -0.10 -4.91 -1.84 -15.95 56.44 -153.61 9 4qeo C-gln C.5CM7 A.GLN206 -5.87 126.77 1.30 1.83 -5.43 70.81 51.65 103.23 10 4qeo C-tyr C.5CM7 A.TYR207 -4.61 74.15 -1.37 -1.36 -4.18 63.53 -22.71 32.77 11 4qeo C-asp C.5CM7 A.ASP210 -3.83 158.50 -2.23 -2.35 -2.05 44.08 60.72 152.79 12 4qeo C-tyr C.5CM7 A.TYR219 4.93 90.45 3.53 -3.41 -0.46 -9.16 -78.01 49.04 13 4qeo C-thr C.5CM7 A.THR220 -5.16 149.12 2.41 -4.07 -2.06 -49.34 53.26 141.42 14 4qeo C-gly C.5CM7 A.GLY221 -7.76 22.67 7.25 2.78 -0.09 14.76 16.24 5.72 15 4qeo C-gln C.5CM7 A.GLN222 -8.80 97.10 6.05 2.49 -5.89 -18.77 -65.70 73.73 16 4qeo A-arg C.DA8 A.ARG126 10.50 -57.40 -10.30 -0.21 -2.05 -25.31 51.48 -1.93 17 4qeo A-trp C.DA8 A.TRP175 -10.50 -162.58 -2.55 -0.68 -10.16 -58.46 57.54 -156.85 18 4qeo A-leu C.DA8 A.LEU176 -8.42 -71.36 -5.59 2.22 -5.89 12.37 -9.68 -69.83 19 4qeo A-leu C.DA8 A.LEU227 -6.90 -136.94 0.80 6.40 -2.45 3.65 33.32 -134.93 20 4qeo A-thr C.DA8 A.THR228 7.20 -117.77 3.08 5.76 -3.03 34.78 -75.50 -92.64 21 4qeo T-arg C.DT9 A.ARG126 -10.24 -57.16 -8.25 2.17 -5.67 -13.66 48.36 -28.18 22 4qeo A-thr D.DA5 A.THR228 7.09 141.90 2.40 -4.30 5.10 21.48 85.76 125.84 23 4qeo T-thr D.DT6 A.THR228 -7.24 132.60 -0.78 -3.92 -6.04 -52.00 -60.41 116.85 24 4qeo G-trp D.DG7 A.TRP175 12.19 101.10 -4.71 4.99 10.07 -69.29 -3.31 78.80 25 4qeo G-leu D.DG7 A.LEU176 10.16 -27.26 -9.46 0.70 3.62 22.18 10.58 -11.90 26 4qeo G-leu D.DG7 A.LEU227 -8.61 57.38 -7.94 -3.29 0.43 -7.32 -21.79 52.94 27 4qeo A-trp D.DA8 A.TRP175 -9.45 91.08 -4.41 -0.20 -8.36 65.70 47.55 45.61 28 4qeo A-arg A.SAH801 A.ARG452 -13.03 168.73 9.80 5.53 -6.56 -20.81 56.04 166.99 29 4qeo A-lys A.SAH801 A.LYS455 -7.44 -127.94 -1.14 -1.62 -7.17 -50.33 29.74 -119.62 30 4qeo A-lys A.SAH801 A.LYS456 -5.61 -41.36 -3.04 1.16 -4.57 40.91 -0.13 -6.22 31 4qeo A-gly A.SAH801 A.GLY457 -9.27 162.54 6.92 1.46 -6.00 76.80 45.08 155.41 32 4qeo A-trp A.SAH801 A.TRP458 -11.04 101.42 6.29 5.04 -7.54 28.68 26.73 95.53 33 4qeo A-tyr A.SAH801 A.TYR493 14.40 121.78 8.91 6.62 9.17 -37.93 39.78 113.49 34 4qeo A-arg A.SAH801 A.ARG548 -14.62 140.87 14.37 2.65 0.49 18.52 23.10 139.47 35 4qeo A-phe A.SAH801 A.PHE549 -12.84 155.20 11.91 4.33 -2.07 -80.33 4.43 147.33 36 4qeo A-ile A.SAH801 A.ILE550 -11.24 21.89 5.70 8.60 -4.45 1.22 -9.65 19.63 37 4qeo A-asn A.SAH801 A.ASN551 -7.49 -118.28 -0.40 7.31 -1.56 -23.64 86.42 -87.42 38 4qeo A-his A.SAH801 A.HIS552 6.49 -145.30 -1.24 5.00 3.94 -48.70 -49.57 -137.44 39 4qeo A-tyr A.SAH801 A.TYR593 10.74 -172.65 -7.62 6.87 3.19 2.16 41.58 -172.14 40 4qeo A-ala A.SAH801 A.ALA611 6.40 -132.57 -0.65 -3.46 5.35 17.03 29.47 -130.26 41 4qeo A-cys A.SAH801 A.CYS612 3.45 -76.07 0.45 -3.26 1.05 -69.62 -24.00 -20.58 42 4qeo A-tyr A.SAH801 A.TYR613 -3.00 -177.52 2.91 -0.09 0.70 32.23 55.68 -177.07 43 4qeo A-cys A.SAH801 A.CYS614 -4.39 100.03 2.15 -3.75 0.78 85.56 -10.89 56.61 44 4qeo A-leu A.SAH801 A.LEU623 7.01 140.20 1.52 -2.31 6.45 -33.48 -5.54 138.30 45 4qeo A-lys A.SAH801 P.LYS9 13.01 96.87 4.17 3.57 11.79 -20.42 66.60 72.14 **************************************************************************** List of 11 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4qeo AT-arg C.DA8 D.DT6 A.ARG126 10.43 -48.01 -9.98 -0.37 -2.99 -24.25 41.41 -1.36 2 4qeo AT-arg D.DA5 C.DT9 A.ARG126 10.36 57.12 -8.33 -2.27 5.72 -12.01 -48.37 28.85 3 4qeo AT-asn D.DA8 C.DT6 A.ASN177 -9.55 160.20 -7.01 4.19 -4.95 72.09 1.39 155.45 4 4qeo AT-leu D.DA8 C.DT6 A.LEU176 -8.16 30.37 -7.12 -3.10 -2.49 19.77 -20.06 11.47 5 4qeo AT-leu D.DA8 C.DT6 A.LEU227 -10.80 89.62 -6.69 -7.03 -4.74 -22.12 -51.55 73.00 6 4qeo AT-leu C.DA8 D.DT6 A.LEU176 -8.41 -71.65 -5.17 2.43 -6.18 19.42 -16.54 -67.53 7 4qeo AT-leu C.DA8 D.DT6 A.LEU227 -6.94 -132.15 0.77 6.63 -1.92 12.35 31.04 -129.90 8 4qeo AT-thr C.DA8 D.DT6 A.THR228 7.22 -140.18 -0.65 4.44 5.65 -59.53 65.20 -123.35 9 4qeo AT-thr D.DA5 C.DT9 A.THR228 7.21 140.59 2.43 -4.39 5.17 21.69 86.30 123.58 10 4qeo AT-trp D.DA8 C.DT6 A.TRP175 -9.54 90.52 -4.75 -0.62 -8.25 62.68 52.26 43.15 11 4qeo AT-trp C.DA8 D.DT6 A.TRP175 -10.47 -155.78 -2.48 0.28 -10.17 -50.41 55.07 -149.41 **************************************************************************** List of 15 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4qeo OP1@C.DT6 NE2@A.GLN222 2.82 po4:sidechain 2 4qeo OP1@C.5CM7 N@A.GLY178 2.87 po4:backbone 3 4qeo OP2@C.5CM7 OH@A.TYR207 2.69 po4:sidechain 4 4qeo OP1@C.DA8 NH1@A.ARG163 3.04 po4:sidechain:salt-bridge 5 4qeo OP1@C.DA8 OG@A.SER204 2.68 po4:sidechain 6 4qeo OP2@C.DA8 NH2@A.ARG271 2.50 po4:sidechain:salt-bridge 7 4qeo O5'@C.DA8 NH1@A.ARG163 3.21 po4:sidechain 8 4qeo OP1@C.DT9 N@A.ARG163 2.96 po4:backbone 9 4qeo OP2@C.DT9 OH@A.TYR273 2.56 po4:sidechain 10 4qeo OP1@D.DG7 OG@A.SER125 2.89 po4:sidechain 11 4qeo OP1@D.DA8 NZ@A.LYS130 2.89 po4:sidechain:salt-bridge 12 4qeo OP1@D.DG9 OG1@A.THR133 2.72 po4:sidechain 13 4qeo OP1@D.DA11 NE2@A.HIS174 3.11 po4:sidechain:salt-bridge 14 4qeo OP1@D.DC12 OH@A.TYR181 3.62 po4:sidechain 15 4qeo OP2@D.DC12 N@A.MET184 3.56 po4:backbone **************************************************************************** List of 1 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 4qeo O4'@D.DA8 NE1@A.TRP175 3.31 sugar:sidechain **************************************************************************** List of 15 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4qeo N3@C.5CM7 OD2@A.ASP210 2.56 base:sidechain 2 4qeo O2@C.5CM7 N@A.SER204 3.07 base:backbone 3 4qeo O2@C.5CM7 N@A.GLY205 3.34 base:backbone 4 4qeo O2@C.5CM7 N@A.GLN206 3.11 base:backbone 5 4qeo N4@C.5CM7 OD1@A.ASP210 2.96 base:sidechain 6 4qeo N4@C.5CM7 O@A.THR220 2.77 base:backbone 7 4qeo N3@C.DA8 NH1@A.ARG126 3.14 base:sidechain 8 4qeo N@A.SAH801 O@A.LYS456 2.33 base:backbone 9 4qeo N@A.SAH801 O@A.TRP458 2.55 base:backbone 10 4qeo N@A.SAH801 OD1@A.ASN551 2.74 base:sidechain 11 4qeo O@A.SAH801 OH@A.TYR493 2.25 base:sidechain 12 4qeo OXT@A.SAH801 N@A.TRP458 2.71 base:backbone 13 4qeo N7@A.SAH801 N@A.HIS552 3.35 base:backbone 14 4qeo N6@A.SAH801 O@A.HIS552 3.17 base:backbone 15 4qeo N1@A.SAH801 N@A.TYR613 2.85 base:backbone **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4qeo C-asp C.5CM7 A.ASP210 0.24 10 2 4qeo A-arg C.DA8 A.ARG126 0.26 45 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4qeo C-tyr C.5CM7 A.TYR207 3.34 23 2 4qeo C-tyr C.5CM7 A.TYR219 3.22 2 **************************************************************************** List of 1 interface stacks with 3+ planar moieties Note: an interface stack is an ordered list of three and more nucleobases and planar moieties of amino acids, assembled together via stacking interactions (nucleobases within to a stem are excluded by default). 1 size=3 YCY A.TYR207,C.5CM7,A.TYR219 **************************************************************************** List of 3 additional files 1 -- 4qeo-baseAA-pairs.pdb 2 -- 4qeo-baseAA-stacks.pdb 3 -- 4qeo-pairs.pdb