**************************************************************************** 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/6x9j.pdb -o=6x9j.out --type=base File name: 6x9j.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: 7461 no. of waters: 390 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 .BB...BBBBB 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 15 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6x9j C-cys C.DC5 A.CYS1499 11.51 -102.07 -7.95 8.26 -1.00 -19.30 58.56 -85.84 2 6x9j C-met C.DC5 A.MET1533 7.63 119.52 4.92 -2.53 5.25 -9.78 74.60 101.04 3 6x9j C-gly C.DC5 A.GLY1534 5.91 -80.68 2.42 2.70 4.67 -24.29 39.51 -67.96 4 6x9j C-cys C.5CM6 A.CYS1499 -11.44 -116.90 -4.68 9.50 -4.32 -6.99 50.20 -109.25 5 6x9j C-leu C.5CM6 A.LEU1500 11.33 -92.67 1.92 7.40 8.36 -85.56 17.36 -34.80 6 6x9j C-trp C.5CM6 A.TRP1510 10.79 87.33 0.94 5.51 9.23 4.45 85.61 18.57 7 6x9j C-met C.5CM6 A.MET1533 -7.12 98.91 5.78 -2.87 3.02 -4.25 75.07 69.75 8 6x9j C-gly C.5CM6 A.GLY1534 4.49 -98.38 3.31 2.30 1.97 -17.15 32.68 -92.90 9 6x9j C-lys C.5CM6 A.LYS1535 5.42 177.70 2.32 -2.21 4.37 28.78 -74.38 177.01 10 6x9j G-his C.DG7 A.HIS1507 9.21 178.50 4.90 -6.90 -3.63 -82.75 -8.21 177.99 11 6x9j A-asn D.DA15 A.ASN1508 9.52 -168.13 -6.58 5.12 4.60 9.78 -23.06 -167.84 12 6x9j U-lys D.PYO18 A.LYS1535 9.09 -153.59 -4.77 7.71 0.63 19.90 84.15 -143.46 13 6x9j G-gly D.DG19 A.GLY1534 5.38 101.44 4.33 -3.03 -0.96 -10.54 -50.76 90.52 14 6x9j G-lys D.DG19 A.LYS1535 -5.48 148.41 4.10 -3.65 0.15 -5.25 81.14 137.95 15 6x9j G-gly D.DG20 A.GLY1534 -5.66 83.00 2.97 -2.87 -3.88 -26.69 -40.32 69.64 **************************************************************************** List of 12 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6x9j AT-asn D.DA15 C.DT10 A.ASN1508 9.56 -166.95 -6.49 5.11 4.81 9.91 -23.16 -166.63 2 6x9j GC-cys D.DG20 C.DC5 A.CYS1499 -11.36 103.21 -7.59 -8.34 1.42 -20.38 -58.74 87.02 3 6x9j GC-cys D.DG19 C.5CM6 A.CYS1499 11.72 119.58 -4.58 -10.01 4.03 -4.97 -59.62 109.03 4 6x9j GC-gly D.DG20 C.DC5 A.GLY1534 -5.77 81.83 2.69 -2.79 -4.27 -25.49 -39.91 68.80 5 6x9j GC-gly D.DG19 C.5CM6 A.GLY1534 4.91 99.63 3.85 -2.66 -1.48 -14.00 -41.77 91.77 6 6x9j GC-leu D.DG19 C.5CM6 A.LEU1500 -11.57 85.94 2.95 -7.24 -8.53 -78.54 -23.06 28.87 7 6x9j GC-lys D.DG19 C.5CM6 A.LYS1535 -5.42 -176.36 1.78 2.97 -4.17 32.17 83.22 -174.89 8 6x9j GC-met D.DG20 C.DC5 A.MET1533 -7.58 -120.05 5.21 2.64 -4.83 -9.42 -76.03 -100.91 9 6x9j GC-met D.DG19 C.5CM6 A.MET1533 7.65 -101.41 6.36 3.30 -2.69 4.52 -73.26 -75.65 10 6x9j GC-trp D.DG19 C.5CM6 A.TRP1510 -10.84 -91.90 1.63 -4.43 -9.75 12.78 -88.04 -25.94 11 6x9j GU-his C.DG7 D.PYO18 A.HIS1507 9.13 179.90 4.25 -6.80 -4.37 -81.06 3.49 179.87 12 6x9j GU-lys C.DG7 D.PYO18 A.LYS1535 -8.94 -157.84 0.79 6.64 -5.93 -20.54 -82.12 -149.87 **************************************************************************** List of 16 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6x9j OP1@C.DG3 N@A.SER1418 2.82 po4:backbone 2 6x9j OP2@C.DG3 OE2@A.GLU1531 3.07 po4:sidechain 3 6x9j OP1@C.DG4 NH1@A.ARG1424 2.88 po4:sidechain:salt-bridge 4 6x9j OP2@C.DC5 N@A.CYS1499 3.66 po4:backbone 5 6x9j OP2@C.5CM6 ND1@A.HIS1502 2.81 po4:sidechain:salt-bridge 6 6x9j OP1@C.DG7 NH1@A.ARG1506 3.01 po4:sidechain:salt-bridge 7 6x9j OP2@C.DG7 NH1@A.ARG1506 2.51 po4:sidechain:salt-bridge 8 6x9j OP2@C.DG7 NE2@A.HIS1507 2.77 po4:sidechain:salt-bridge 9 6x9j OP1@D.DC14 OH@A.TYR976 3.18 po4:sidechain 10 6x9j OP1@D.DA15 OG@A.SER977 2.52 po4:sidechain 11 6x9j OP2@D.DA15 ND2@A.ASN1508 2.86 po4:sidechain 12 6x9j OP1@D.DG16 OH@A.TYR979 3.04 po4:sidechain 13 6x9j OP2@D.DG16 NZ@A.LYS981 3.41 po4:sidechain:salt-bridge 14 6x9j OP1@D.PYO18 N@A.ASN1270 2.45 po4:backbone 15 6x9j OP2@D.DG19 NZ.A@A.LYS1535 3.29 po4:sidechain:salt-bridge 16 6x9j O5'@D.DG19 NZ.A@A.LYS1535 3.13 po4:sidechain **************************************************************************** List of 2 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6x9j N4@C.5CM6 O@A.MET1533 2.74 base:backbone 2 6x9j O6@D.DG19 N@A.LYS1535 3.10 base:backbone **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6x9j C-trp C.5CM6 A.TRP1510 3.41 23 **************************************************************************** List of 2 additional files 1 -- 6x9j-baseAA-stacks.pdb 2 -- 6x9j-pairs.pdb