**************************************************************************** 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/5vmw.pdb -o=5vmw.out --type=base File name: 5vmw.pdb no. of peptide chains: 1 [A=121] no. of DNA/RNA chains: 2 [D=18,E=18] no. of amino acids: 121 no. of nucleotides: 36 no. of atoms: 1806 no. of waters: 40 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5CM-c 4 D.5CM8,D.5CM10,E.5CM26,E.5CM28 **************************************************************************** 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'-TGCTTCCcGcGAATAACG-3' bp-type |||||||||||||||||| strand-2 3'-ACGAAGGGcGcTTATTGC-5' helix-form BBBBBBBBBBBBBBBBB 1 D.DT1 E.DA36 T-A WC 20-XX cWW cW-W 2 D.DG2 E.DC35 G-C WC 19-XIX cWW cW-W 3 D.DC3 E.DG34 C-G WC 19-XIX cWW cW-W 4 D.DT4 E.DA33 T-A WC 20-XX cWW cW-W 5 D.DT5 E.DA32 T-A WC 20-XX cWW cW-W 6 D.DC6 E.DG31 C-G WC 19-XIX cWW cW-W 7 D.DC7 E.DG30 C-G WC 19-XIX cWW cW-W 8 D.5CM8 E.DG29 c-G WC 19-XIX cWW cW-W 9 D.DG9 E.5CM28 G-c WC 19-XIX cWW cW-W 10 D.5CM10 E.DG27 c-G WC 19-XIX cWW cW-W 11 D.DG11 E.5CM26 G-c WC 19-XIX cWW cW-W 12 D.DA12 E.DT25 A-T WC 20-XX cWW cW-W 13 D.DA13 E.DT24 A-T WC 20-XX cWW cW-W 14 D.DT14 E.DA23 T-A WC 20-XX cWW cW-W 15 D.DA15 E.DT22 A-T WC 20-XX cWW cW-W 16 D.DA16 E.DT21 A-T WC 20-XX cWW cW-W 17 D.DC17 E.DG20 C-G WC 19-XIX cWW cW-W 18 D.DG18 E.DC19 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 35 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5vmw T-gln D.DT4 A.GLN563 9.48 -148.93 -5.73 7.52 0.74 8.39 68.55 -142.06 2 5vmw T-asn D.DT5 A.ASN561 11.78 176.80 6.32 -8.64 4.92 -14.63 48.99 176.45 3 5vmw T-gln D.DT5 A.GLN563 8.20 -176.21 -2.05 7.67 -2.07 22.64 50.41 -175.73 4 5vmw C-gln D.DC6 A.GLN563 -8.44 146.88 -1.23 -5.85 -5.96 -37.55 -50.00 141.05 5 5vmw C-glu D.DC7 A.GLU535 10.07 -157.40 -4.47 7.90 4.38 -10.04 37.30 -156.03 6 5vmw C-tyr D.DC7 A.TYR536 10.51 117.60 7.67 -1.11 7.10 27.11 62.97 102.35 7 5vmw C-arg D.5CM8 A.ARG511 12.35 -118.28 -7.81 8.69 4.02 -20.47 20.58 -116.01 8 5vmw C-leu D.5CM8 A.LEU533 12.04 -178.55 -6.12 10.16 2.07 35.98 -66.03 -178.17 9 5vmw C-glu D.5CM8 A.GLU535 9.29 -176.55 -2.12 8.84 1.90 1.27 21.45 -176.49 10 5vmw G-ser D.DG9 A.SER508 9.00 -178.58 -5.66 5.05 -4.85 34.71 66.66 -178.21 11 5vmw G-arg D.DG9 A.ARG511 10.98 -155.55 -2.42 10.67 0.94 -10.80 23.71 -154.89 12 5vmw C-cys D.5CM10 A.CYS505 -10.91 -141.06 -5.04 9.59 1.29 7.98 -65.88 -133.06 13 5vmw C-thr D.5CM10 A.THR507 9.40 -172.21 -3.29 7.98 3.72 -35.23 4.25 -171.82 14 5vmw C-ser D.5CM10 A.SER508 -8.63 158.04 2.97 -4.14 -6.96 -55.62 -51.07 152.12 15 5vmw C-arg D.5CM10 A.ARG511 -10.15 172.34 -0.79 -9.91 -2.04 0.56 -21.89 172.20 16 5vmw G-thr D.DG11 A.THR507 7.82 155.26 0.43 -7.69 1.37 19.19 -2.96 154.90 17 5vmw G-arg D.DG11 A.ARG595 11.95 32.90 -11.05 -2.94 3.46 21.72 5.29 24.30 18 5vmw G-tyr D.DG11 A.TYR597 12.38 68.80 -10.93 1.08 -5.71 13.19 66.72 11.09 19 5vmw A-arg D.DA12 A.ARG595 10.88 -30.19 -10.84 -0.72 0.55 25.93 0.81 -15.57 20 5vmw A-tyr D.DA12 A.TYR597 -11.43 -77.06 -7.95 3.06 -7.61 38.01 62.04 -27.37 21 5vmw T-thr E.DT25 A.THR507 9.49 -121.46 -2.70 8.95 1.64 14.93 20.26 -119.88 22 5vmw T-arg E.DT25 A.ARG595 10.88 34.78 -10.83 0.98 0.21 31.72 8.73 11.44 23 5vmw C-thr E.5CM26 A.THR507 -7.57 -153.06 -0.06 7.44 -1.40 13.35 1.58 -152.87 24 5vmw C-arg E.5CM26 A.ARG511 10.05 -143.73 -5.22 8.00 3.12 -26.08 10.68 -142.57 25 5vmw C-arg E.5CM26 A.ARG595 -12.28 -29.10 -11.58 2.98 -2.81 17.82 -0.43 -23.09 26 5vmw G-arg E.DG27 A.ARG511 10.32 -176.33 -0.63 10.27 0.84 -10.62 23.46 -176.23 27 5vmw G-glu E.DG27 A.GLU535 9.39 -117.54 -5.44 6.85 3.41 -29.45 20.19 -114.00 28 5vmw G-arg E.DG27 A.ARG595 -12.25 -65.56 -8.84 5.49 -6.47 26.96 -12.67 -59.09 29 5vmw G-tyr E.DG27 A.TYR597 -12.11 -84.05 -11.75 1.83 2.28 -0.33 -69.52 -50.57 30 5vmw C-arg E.5CM28 A.ARG511 -10.69 153.06 -2.43 -10.13 -2.39 4.11 -23.21 152.47 31 5vmw C-glu E.5CM28 A.GLU535 -9.45 -147.52 -3.06 8.95 0.12 -24.21 25.58 -145.88 32 5vmw G-glu E.DG29 A.GLU535 -9.41 176.99 -1.88 -8.95 -2.24 7.60 -19.78 176.94 33 5vmw G-tyr E.DG30 A.TYR562 9.05 -146.30 -5.13 7.32 -1.42 20.73 11.42 -145.55 34 5vmw G-gln E.DG30 A.GLN563 9.49 -128.72 -4.73 4.42 6.94 -66.96 21.73 -116.05 35 5vmw G-gln E.DG31 A.GLN563 8.44 -155.29 -1.63 6.93 4.54 -52.46 39.44 -150.51 **************************************************************************** List of 28 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5vmw AT-arg D.DA12 E.DT25 A.ARG595 -10.88 -32.01 -10.84 -0.85 0.17 28.81 -3.98 -13.52 2 5vmw AT-asn E.DA32 D.DT5 A.ASN561 -11.64 -173.09 5.97 8.35 -5.51 -21.88 -45.58 -172.36 3 5vmw AT-gln E.DA33 D.DT4 A.GLN563 -9.39 144.21 -5.90 -7.17 -1.35 14.70 -66.49 136.46 4 5vmw AT-gln E.DA32 D.DT5 A.GLN563 -8.15 173.50 -1.97 -7.75 1.58 30.29 -53.46 172.43 5 5vmw AT-thr D.DA12 E.DT25 A.THR507 -9.54 119.29 -2.88 -8.88 -1.93 18.19 -15.76 117.77 6 5vmw AT-tyr D.DA12 E.DT25 A.TYR597 -11.40 -73.63 -7.72 3.21 -7.75 40.26 57.93 -22.61 7 5vmw GC-arg E.DG29 D.5CM8 A.ARG511 -12.30 118.59 -7.69 -8.72 -4.00 -18.08 -18.50 116.81 8 5vmw GC-arg D.DG9 E.5CM28 A.ARG511 10.83 -154.25 -2.42 10.42 1.68 -3.34 23.51 -153.67 9 5vmw GC-arg E.DG27 D.5CM10 A.ARG511 10.23 -174.33 -0.71 10.11 1.45 -5.04 22.65 -174.21 10 5vmw GC-arg E.DG27 D.5CM10 A.ARG595 -12.18 -66.01 -8.62 5.43 -6.67 29.55 -17.73 -57.18 11 5vmw GC-arg D.DG11 E.5CM26 A.ARG511 -10.00 144.06 -4.94 -8.08 -3.23 -23.04 -11.42 143.10 12 5vmw GC-arg D.DG11 E.5CM26 A.ARG595 12.11 30.91 -11.32 -2.96 3.14 19.79 2.84 23.70 13 5vmw GC-cys E.DG27 D.5CM10 A.CYS505 10.91 143.80 -4.88 -9.59 -1.76 13.44 67.82 135.67 14 5vmw GC-gln E.DG31 D.DC6 A.GLN563 8.44 -151.01 -1.44 6.43 5.27 -45.16 44.93 -145.73 15 5vmw GC-gln E.DG30 D.DC7 A.GLN563 9.60 -121.46 -4.31 3.64 7.76 -60.06 27.86 -108.58 16 5vmw GC-glu E.DG30 D.DC7 A.GLU535 -10.17 157.11 -4.91 -7.91 -4.09 -10.56 -26.55 156.37 17 5vmw GC-glu E.DG29 D.5CM8 A.GLU535 -9.35 176.77 -2.00 -8.90 -2.07 4.44 -20.64 176.72 18 5vmw GC-glu D.DG9 E.5CM28 A.GLU535 9.52 146.55 -2.96 -9.02 -0.61 -17.59 -22.05 145.48 19 5vmw GC-glu E.DG27 D.5CM10 A.GLU535 9.31 -115.76 -5.59 6.54 3.56 -24.94 16.38 -113.24 20 5vmw GC-leu E.DG29 D.5CM8 A.LEU533 -12.06 -179.36 5.96 10.25 -2.24 -38.27 -67.18 -179.18 21 5vmw GC-ser D.DG9 E.5CM28 A.SER508 8.86 -175.30 -5.73 5.21 -4.32 41.51 68.23 -173.87 22 5vmw GC-ser E.DG27 D.5CM10 A.SER508 8.66 -161.05 3.07 4.59 6.67 -60.57 53.53 -155.02 23 5vmw GC-thr E.DG27 D.5CM10 A.THR507 -9.47 171.06 -3.28 -7.82 -4.22 -29.38 -3.93 170.75 24 5vmw GC-thr D.DG11 E.5CM26 A.THR507 7.69 154.16 0.19 -7.56 1.39 16.26 -2.29 153.88 25 5vmw GC-tyr E.DG30 D.DC7 A.TYR536 -10.54 -114.61 8.00 0.64 -6.82 19.66 -69.57 -96.03 26 5vmw GC-tyr E.DG30 D.DC7 A.TYR562 9.09 -147.47 -5.27 7.39 -0.47 25.65 20.99 -146.02 27 5vmw GC-tyr E.DG27 D.5CM10 A.TYR597 -12.11 -88.65 -11.85 1.66 1.85 2.03 -75.01 -51.17 28 5vmw GC-tyr D.DG11 E.5CM26 A.TYR597 12.52 65.82 -10.85 0.95 -6.17 12.19 64.07 9.37 **************************************************************************** List of 17 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmw OP2@D.DC7 OH@A.TYR536 2.86 po4:sidechain 2 5vmw OP1@D.5CM8 NH1@A.ARG501 2.62 po4:sidechain:salt-bridge 3 5vmw OP2@D.5CM8 OH@A.TYR503 2.78 po4:sidechain 4 5vmw OP1@D.DG9 N@A.VAL504 3.12 po4:backbone 5 5vmw OP2@D.DG9 N@A.CYS505 3.67 po4:backbone 6 5vmw OP2@D.DG9 OG@A.SER508 2.65 po4:sidechain 7 5vmw OP1@D.DA13 N@A.ALA598 2.75 po4:backbone 8 5vmw OP1@E.DT25 NZ@A.LYS520 3.29 po4:sidechain:salt-bridge 9 5vmw OP2@E.5CM26 OH@A.TYR522 3.30 po4:sidechain 10 5vmw OP2@E.DG27 OG1@A.THR538 2.68 po4:sidechain 11 5vmw OP1@E.5CM28 NH2@A.ARG549 2.75 po4:sidechain:salt-bridge 12 5vmw OP2@E.5CM28 NH1@A.ARG549 2.79 po4:sidechain:salt-bridge 13 5vmw OP1@E.DG29 OH@A.TYR584 2.54 po4:sidechain 14 5vmw OP2@E.DG29 OH@A.TYR550 2.76 po4:sidechain 15 5vmw OP1@E.DG30 O.A@A.SER578 3.23 po4:backbone 16 5vmw OP2@E.DG30 OH@A.TYR562 2.54 po4:sidechain 17 5vmw OP1@E.DG31 OG.A@A.SER578 3.28 po4:sidechain **************************************************************************** List of 2 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmw O4'@E.5CM26 NH2@A.ARG595 2.71 sugar:sidechain 2 5vmw O4'@E.DG27 NH1@A.ARG595 3.04 sugar:sidechain **************************************************************************** List of 15 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5vmw N4@D.DC6 NE2@A.GLN563 3.18 base:sidechain 2 5vmw N4@D.DC7 OE2@A.GLU535 3.69 base:sidechain 3 5vmw N4@D.5CM8 OE1@A.GLU535 3.11 base:sidechain 4 5vmw N4@D.5CM8 OE2@A.GLU535 2.77 base:sidechain 5 5vmw N7@D.DG9 NH2@A.ARG511 3.10 base:sidechain 6 5vmw O6@D.DG9 NH1@A.ARG511 3.01 base:sidechain 7 5vmw O6@D.DG9 NH2@A.ARG511 3.19 base:sidechain 8 5vmw N2@D.DG11 OH@A.TYR597 3.27 base:sidechain 9 5vmw O2@E.DT25 NH2@A.ARG595 2.67 base:sidechain 10 5vmw O2@E.5CM26 NH1@A.ARG595 2.91 base:sidechain 11 5vmw O2@E.5CM26 NH2@A.ARG595 3.29 base:sidechain 12 5vmw N4@E.5CM26 OG1@A.THR507 3.89 base:sidechain 13 5vmw O6@E.DG27 NH1@A.ARG511 2.69 base:sidechain 14 5vmw N4@E.5CM28 OE1@A.GLU535 2.78 base:sidechain 15 5vmw O6@E.DG31 NE2@A.GLN563 3.02 base:sidechain **************************************************************************** List of 5 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5vmw G-arg D.DG9 A.ARG511 0.12 34 2 5vmw G-tyr D.DG11 A.TYR597 0.43 30 3 5vmw T-arg E.DT25 A.ARG595 2.27 65 4 5vmw G-arg E.DG27 A.ARG511 0.55 31 5 5vmw G-gln E.DG31 A.GLN563 0.95 47 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5vmw C-arg D.5CM8 A.ARG511 3.71 33 2 5vmw C-arg E.5CM26 A.ARG511 3.73 35 **************************************************************************** List of 3 additional files 1 -- 5vmw-baseAA-pairs.pdb 2 -- 5vmw-baseAA-stacks.pdb 3 -- 5vmw-pairs.pdb