**************************************************************************** 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/2zo1.pdb -o=2zo1.out --type=base File name: 2zo1.pdb no. of peptide chains: 1 [B=206] no. of DNA/RNA chains: 2 [D=9,E=12] no. of amino acids: 206 no. of nucleotides: 21 no. of atoms: 2132 no. of waters: 97 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 5CM-c 1 E.5CM426 **************************************************************************** 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=8 strand-1 5'-TGCCTGAC-3' bp-type |||||||| strand-2 3'-ACGGACTG-5' helix-form x.xBBBB 1 D.DT405 E.DA430 T-A WC 20-XX cWW cW-W 2 D.DG406 E.DC428 G-C WC 19-XIX cWW cW-W 3 D.DC407 E.DG427 C-G WC 19-XIX cWW cW-W 4 D.DC409 E.DG425 C-G WC 19-XIX cWW cW-W 5 D.DT410 E.DA424 T-A WC 20-XX cWW cW-W 6 D.DG411 E.DC423 G-C WC 19-XIX cWW cW-W 7 D.DA412 E.DT422 A-T WC 20-XX cWW cW-W 8 D.DC413 E.DG421 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 34 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 2zo1 G-gly D.DG406 B.GLY493 11.11 -93.75 -2.82 9.86 -4.28 66.96 45.65 -51.88 2 2zo1 G-asn D.DG406 B.ASN494 9.19 173.84 6.50 -0.15 6.50 -6.02 23.10 173.70 3 2zo1 G-lys D.DG406 B.LYS495 6.91 38.95 2.19 5.01 4.22 10.92 34.06 15.67 4 2zo1 C-asn D.DC407 B.ASN494 8.28 138.20 7.12 -3.06 2.92 2.97 30.75 136.56 5 2zo1 C-lys D.DC407 B.LYS495 -6.42 -41.76 5.29 3.50 1.00 14.83 31.19 -23.84 6 2zo1 C-arg D.DC407 B.ARG496 5.62 -166.90 2.19 5.08 1.02 2.17 -46.96 -165.71 7 2zo1 G-his D.DG408 B.HIS450 7.68 140.28 -3.99 -1.43 6.41 -41.06 -51.45 132.26 8 2zo1 G-arg D.DG408 B.ARG496 -7.13 178.60 -1.79 -6.40 -2.56 0.23 47.40 178.47 9 2zo1 C-his D.DC409 B.HIS450 -9.19 108.50 -6.18 4.86 4.75 -68.77 -34.49 83.47 10 2zo1 C-arg D.DC409 B.ARG496 -7.16 129.30 -2.97 -3.06 -5.76 9.29 42.28 125.14 11 2zo1 T-his D.DT410 B.HIS450 -9.85 97.51 -5.05 8.36 1.31 -82.37 -19.29 53.91 12 2zo1 G-his E.DG425 B.HIS450 9.18 -109.63 -6.25 -5.24 -4.22 -74.00 37.07 -79.66 13 2zo1 G-val E.DG425 B.VAL451 7.65 -34.65 -7.00 2.71 1.50 33.29 5.56 -7.97 14 2zo1 G-leu E.DG425 B.LEU491 10.87 -159.38 -7.18 7.72 2.66 38.30 -34.40 -157.09 15 2zo1 G-lys E.DG425 B.LYS495 8.59 89.73 6.52 2.81 4.84 35.25 0.38 83.91 16 2zo1 G-arg E.DG425 B.ARG496 7.22 -124.80 -2.89 3.29 5.74 4.72 -39.67 -120.93 17 2zo1 C-gly E.5CM426 B.GLY453 7.67 -89.51 -4.49 5.67 2.54 -30.73 72.01 -47.41 18 2zo1 C-val E.5CM426 B.VAL466 7.39 127.89 2.49 3.00 6.28 -10.77 -3.59 127.61 19 2zo1 C-leu E.5CM426 B.LEU467 5.16 -103.59 -0.31 0.30 5.14 41.68 -65.81 -74.64 20 2zo1 C-ala E.5CM426 B.ALA468 6.41 95.82 -2.01 5.41 2.80 -15.74 -23.14 92.61 21 2zo1 C-gly E.5CM426 B.GLY469 -5.53 -155.36 -0.29 -4.97 -2.40 -3.59 71.47 -149.50 22 2zo1 C-gly E.5CM426 B.GLY470 -5.88 95.97 -3.06 4.94 0.89 -56.28 -69.18 39.96 23 2zo1 C-tyr E.5CM426 B.TYR471 -4.84 68.85 -1.23 -1.05 -4.57 61.18 -20.66 25.29 24 2zo1 C-asp E.5CM426 B.ASP474 -3.92 158.66 -2.25 -2.23 -2.31 45.13 56.61 153.48 25 2zo1 C-tyr E.5CM426 B.TYR483 4.79 86.74 3.20 -3.52 -0.56 -12.63 -74.58 46.09 26 2zo1 C-thr E.5CM426 B.THR484 -5.01 150.09 2.36 -3.95 -1.98 -47.06 55.20 142.67 27 2zo1 C-gly E.5CM426 B.GLY485 -7.65 21.10 7.12 2.75 -0.50 16.24 12.18 5.77 28 2zo1 C-ser E.5CM426 B.SER486 -8.70 110.20 5.17 1.75 -6.77 -14.40 -78.01 83.98 29 2zo1 G-arg E.DG427 B.ARG496 -5.93 -177.11 -3.30 4.63 -1.68 -15.83 -37.06 -176.92 30 2zo1 C-lys E.DC428 B.LYS544 14.80 -116.29 -7.95 12.24 -2.44 35.77 -20.73 -111.33 31 2zo1 A-phe E.DA429 B.PHE437 -7.03 161.10 1.29 -6.03 -3.36 61.82 -51.62 155.14 32 2zo1 A-val E.DA429 B.VAL439 -7.72 -167.82 0.60 7.50 1.72 -46.25 -34.52 -166.08 33 2zo1 A-pro E.DA429 B.PRO612 -4.97 94.35 -3.91 -2.42 -1.89 -35.61 -80.95 36.92 34 2zo1 A-tyr E.DA429 B.TYR615 -6.51 28.04 -4.99 -0.62 -4.13 -5.13 24.58 12.58 **************************************************************************** List of 13 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 2zo1 AT-his E.DA424 D.DT410 B.HIS450 9.80 -96.73 -4.96 -8.39 -1.01 -82.57 23.34 -49.81 2 2zo1 GC-arg E.DG427 D.DC407 B.ARG496 -5.77 174.82 2.74 -4.89 -1.38 8.84 41.80 174.44 3 2zo1 GC-arg E.DG425 D.DC409 B.ARG496 7.19 -127.04 -2.93 3.17 5.75 7.01 -40.96 -123.03 4 2zo1 GC-asn D.DG406 E.DC428 B.ASN494 9.20 166.53 6.75 -0.70 6.22 -5.24 26.27 166.15 5 2zo1 GC-asn E.DG427 D.DC407 B.ASN494 -8.25 -131.55 6.56 3.35 -3.71 -1.22 -21.65 -130.61 6 2zo1 GC-gly D.DG406 E.DC428 B.GLY493 11.19 -95.03 -1.93 9.99 -4.67 67.47 39.44 -59.08 7 2zo1 GC-his E.DG425 D.DC409 B.HIS450 9.19 -109.01 -6.22 -5.06 -4.49 -71.37 35.80 -81.58 8 2zo1 GC-leu E.DG425 D.DC409 B.LEU491 10.86 -161.40 -7.10 7.72 2.82 40.92 -35.17 -159.11 9 2zo1 GC-lys D.DG406 E.DC428 B.LYS495 6.97 35.34 2.74 5.00 4.00 10.29 33.03 7.31 10 2zo1 GC-lys D.DG406 E.DC428 B.LYS544 -14.75 124.22 -7.28 -12.65 2.15 36.08 20.84 119.93 11 2zo1 GC-lys E.DG427 D.DC407 B.LYS495 -6.45 41.75 5.37 -3.13 -1.75 23.61 -23.57 25.46 12 2zo1 GC-lys E.DG425 D.DC409 B.LYS495 8.55 88.86 6.42 2.84 4.89 33.43 -2.35 83.55 13 2zo1 GC-val E.DG425 D.DC409 B.VAL451 7.64 -34.85 -7.03 2.73 1.27 33.83 2.30 -8.18 **************************************************************************** List of 15 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 2zo1 OP1@D.DT405 NZ@B.LYS495 3.46 po4:sidechain:salt-bridge 2 2zo1 OP2@D.DG406 NZ@B.LYS495 3.10 po4:sidechain:salt-bridge 3 2zo1 OP2@D.DC407 ND2@B.ASN494 3.09 po4:sidechain 4 2zo1 OP1@D.DA412 NE2@B.HIS455 2.92 po4:sidechain:salt-bridge 5 2zo1 OP1@D.DA412 NE@B.ARG457 2.84 po4:sidechain:salt-bridge 6 2zo1 OP2@D.DA412 NH2@B.ARG457 3.19 po4:sidechain:salt-bridge 7 2zo1 OP1@D.DC413 N@B.SER458 2.91 po4:backbone 8 2zo1 OP1@D.DC413 OG@B.SER458 2.62 po4:sidechain 9 2zo1 OP1@E.DG425 OG@B.SER486 2.66 po4:sidechain 10 2zo1 OP1@E.5CM426 N@B.GLY453 2.82 po4:backbone 11 2zo1 OP2@E.5CM426 OH@B.TYR471 2.72 po4:sidechain 12 2zo1 OP1@E.DG427 NH1@B.ARG438 3.20 po4:sidechain:salt-bridge 13 2zo1 OP1@E.DC428 N@B.ARG438 2.97 po4:backbone 14 2zo1 OP2@E.DC428 NZ@B.LYS544 3.57 po4:sidechain:salt-bridge 15 2zo1 OP1@E.DA429 NH2@B.ARG436 3.41 po4:sidechain:salt-bridge **************************************************************************** List of 11 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 2zo1 N4@D.DC407 O@B.ASN494 3.35 base:backbone 2 2zo1 N7@D.DG408 NH2@B.ARG496 3.32 base:sidechain 3 2zo1 O6@D.DG408 NE@B.ARG496 2.37 base:sidechain 4 2zo1 O6@D.DG408 NH2@B.ARG496 3.16 base:sidechain 5 2zo1 O2@D.DC409 NE2@B.HIS450 2.69 base:sidechain 6 2zo1 N3@E.5CM426 OD1@B.ASP474 2.65 base:sidechain 7 2zo1 O2@E.5CM426 N@B.ALA468 3.06 base:backbone 8 2zo1 O2@E.5CM426 N@B.GLY469 3.32 base:backbone 9 2zo1 O2@E.5CM426 N@B.GLY470 2.77 base:backbone 10 2zo1 N4@E.5CM426 OD2@B.ASP474 3.05 base:sidechain 11 2zo1 N4@E.5CM426 O@B.THR484 2.70 base:backbone **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 2zo1 G-arg D.DG408 B.ARG496 0.51 21 2 2zo1 C-asp E.5CM426 B.ASP474 0.06 18 **************************************************************************** List of 5 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 2zo1 C-arg D.DC407 B.ARG496 3.67 24 2 2zo1 G-arg E.DG425 B.ARG496 3.22 7 3 2zo1 C-tyr E.5CM426 B.TYR471 3.28 35 4 2zo1 C-tyr E.5CM426 B.TYR483 3.14 2 5 2zo1 A-phe E.DA429 B.PHE437 3.54 3 **************************************************************************** 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 B.TYR471,E.5CM426,B.TYR483 **************************************************************************** List of 3 additional files 1 -- 2zo1-baseAA-pairs.pdb 2 -- 2zo1-baseAA-stacks.pdb 3 -- 2zo1-pairs.pdb