**************************************************************************** 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/6x9k.pdb -o=6x9k.out --type=base File name: 6x9k.pdb no. of peptide chains: 1 [A=842] no. of DNA/RNA chains: 2 [C=12,D=12] no. of amino acids: 842 no. of nucleotides: 24 no. of atoms: 7255 no. of waters: 189 no. of metals: 2 [Zn=2] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 5CM-c 1 C.5CM6 2 PYO-u 1 D.PYO18 **************************************************************************** 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=12 strand-1 5'-GAGGCcGCCTGC-3' bp-type ||||||.||||| strand-2 3'-CTCCGGuGGACG-5' helix-form ..BBB..BBBB 1 C.DG1 D.DC24 G-C WC 19-XIX cWW cW-W 2 C.DA2 D.DT23 A-T WC 20-XX cWW cW-W 3 C.DG3 D.DC22 G-C WC 19-XIX cWW cW-W 4 C.DG4 D.DC21 G-C WC 19-XIX cWW cW-W 5 C.DC5 D.DG20 C-G WC 19-XIX cWW cW-W 6 C.5CM6 D.DG19 c-G WC 19-XIX cWW cW-W 7 C.DG7 D.PYO18 G-u -- -- cWW cW-W 8 C.DC8 D.DG17 C-G WC 19-XIX cWW cW-W 9 C.DC9 D.DG16 C-G WC 19-XIX cWW cW-W 10 C.DT10 D.DA15 T-A WC 20-XX cWW cW-W 11 C.DG11 D.DC14 G-C WC 19-XIX cWW cW-W 12 C.DC12 D.DG13 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 13 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6x9k G-met C.DG4 A.MET1533 10.01 140.06 4.24 -2.75 8.64 -30.20 58.28 132.05 2 6x9k C-cys C.DC5 A.CYS1499 11.53 -92.41 -8.23 8.08 -0.01 -20.95 51.54 -77.01 3 6x9k C-met C.DC5 A.MET1533 8.40 114.41 5.14 -2.39 6.21 -16.67 65.97 98.39 4 6x9k C-cys C.5CM6 A.CYS1499 -10.87 -118.01 -4.44 9.09 -3.97 -9.41 46.40 -111.57 5 6x9k C-leu C.5CM6 A.LEU1500 10.92 -91.28 3.02 7.70 -7.13 83.78 -30.12 -22.67 6 6x9k C-trp C.5CM6 A.TRP1510 10.62 88.47 0.05 5.36 9.16 -2.74 87.82 11.56 7 6x9k C-met C.5CM6 A.MET1533 -6.73 90.77 5.22 -2.92 3.08 -5.82 71.39 59.98 8 6x9k C-gly C.5CM6 A.GLY1534 4.16 -95.30 3.43 1.59 1.73 -7.61 23.16 -92.86 9 6x9k G-his C.DG7 A.HIS1507 9.35 -178.62 -5.02 7.22 -3.18 86.07 2.03 -178.11 10 6x9k A-asn D.DA15 A.ASN1508 9.48 -169.70 -6.68 5.67 3.61 9.71 -23.99 -169.43 11 6x9k G-met D.DG19 A.MET1533 7.81 -94.19 6.04 3.61 -3.40 -0.02 -64.67 -72.63 12 6x9k G-gly D.DG19 A.GLY1534 -5.24 89.36 4.36 -2.34 -1.72 -0.57 -31.74 84.67 13 6x9k G-lys D.DG19 A.LYS1535 -5.78 150.62 0.37 -0.90 -5.70 -36.44 -76.01 139.99 **************************************************************************** List of 11 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6x9k AT-asn D.DA15 C.DT10 A.ASN1508 9.49 -168.88 -6.65 5.62 3.77 10.71 -24.54 -168.57 2 6x9k GC-cys D.DG20 C.DC5 A.CYS1499 -11.46 92.60 -8.12 -8.09 -0.04 -21.06 -52.53 76.62 3 6x9k GC-cys D.DG19 C.5CM6 A.CYS1499 10.98 114.97 -4.53 -9.45 3.29 -7.32 -51.15 106.66 4 6x9k GC-gly D.DG19 C.5CM6 A.GLY1534 -4.70 92.12 3.90 -1.95 -1.73 -3.99 -27.37 88.78 5 6x9k GC-leu D.DG19 C.5CM6 A.LEU1500 -11.12 90.80 2.17 -6.61 -8.67 -83.91 -17.00 33.72 6 6x9k GC-lys D.DG19 C.5CM6 A.LYS1535 -5.47 154.39 -0.10 -0.56 -5.44 -35.59 -71.30 146.45 7 6x9k GC-met C.DG4 D.DC21 A.MET1533 9.82 141.47 4.40 -2.53 8.40 -31.54 60.12 133.13 8 6x9k GC-met D.DG20 C.DC5 A.MET1533 -8.42 -114.97 5.22 2.52 -6.10 -15.86 -65.95 -99.25 9 6x9k GC-met D.DG19 C.5CM6 A.MET1533 7.27 -92.17 5.62 3.27 -3.25 -2.98 -67.99 -66.38 10 6x9k GC-trp D.DG19 C.5CM6 A.TRP1510 -10.83 -88.77 0.17 -4.48 -9.86 -0.08 -86.90 -20.27 11 6x9k GU-his C.DG7 D.PYO18 A.HIS1507 9.36 -177.92 -4.56 7.25 -3.76 88.18 -8.32 -177.10 **************************************************************************** List of 15 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6x9k OP1@C.DG3 N@A.SER1418 3.36 po4:backbone 2 6x9k OP1@C.DG4 NH1@A.ARG1424 2.72 po4:sidechain:salt-bridge 3 6x9k OP1@C.DC5 NE@A.ARG1490 2.91 po4:sidechain:salt-bridge 4 6x9k OP1@C.DC5 NH2@A.ARG1490 3.13 po4:sidechain:salt-bridge 5 6x9k OP2@C.DC5 N@A.CYS1499 3.47 po4:backbone 6 6x9k O3'@C.DG4 NH2@A.ARG1490 3.22 po4:sidechain 7 6x9k OP2@C.5CM6 ND1@A.HIS1502 2.90 po4:sidechain:salt-bridge 8 6x9k OP1@C.DG7 NH2@A.ARG1506 3.39 po4:sidechain:salt-bridge 9 6x9k OP2@C.DG7 NE@A.ARG1506 3.02 po4:sidechain:salt-bridge 10 6x9k OP2@C.DG7 NE2@A.HIS1507 2.81 po4:sidechain:salt-bridge 11 6x9k OP1@D.DC14 OH@A.TYR976 3.55 po4:sidechain 12 6x9k OP1@D.DA15 OG@A.SER977 2.57 po4:sidechain 13 6x9k OP2@D.DA15 ND2@A.ASN1508 2.82 po4:sidechain 14 6x9k OP1@D.DG16 OH@A.TYR979 2.36 po4:sidechain 15 6x9k OP2@D.DG16 NZ@A.LYS981 3.37 po4:sidechain:salt-bridge **************************************************************************** List of 1 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6x9k N4@C.5CM6 O@A.MET1533 2.64 base:backbone **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6x9k C-trp C.5CM6 A.TRP1510 3.48 25 **************************************************************************** List of 2 additional files 1 -- 6x9k-baseAA-stacks.pdb 2 -- 6x9k-pairs.pdb