**************************************************************************** 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/7r77.pdb -o=7r77.out --type=base File name: 7r77.pdb no. of peptide chains: 1 [A=1830] no. of DNA/RNA chains: 2 [B=12,D=13] no. of amino acids: 1830 no. of nucleotides: 25 no. of atoms: 14980 no. of waters: 0 no. of metals: 5 [Zn=5] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 5CM-c 1 B.5CM30 **************************************************************************** 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=11 strand-1 5'-GTCAGcCATGG-3' bp-type ||||||||||| strand-2 3'-CAGTCGGTACC-5' helix-form BBBBBxBBBB 1 B.DG25 D.DC12 G-C WC 19-XIX cWW cW-W 2 B.DT26 D.DA11 T-A WC 20-XX cWW cW-W 3 B.DC27 D.DG10 C-G WC 19-XIX cWW cW-W 4 B.DA28 D.DT9 A-T WC 20-XX cWW cW-W 5 B.DG29 D.DC8 G-C WC 19-XIX cWW cW-W 6 B.5CM30 D.DG7 c-G WC 19-XIX cWW cW-W 7 B.DC32 D.DG5 C-G WC 19-XIX cWW cW-W 8 B.DA33 D.DT4 A-T WC 20-XX cWW cW-W 9 B.DT34 D.DA3 T-A WC 20-XX cWW cW-W 10 B.DG35 D.DC2 G-C WC 19-XIX cWW cW-W 11 B.DG36 D.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 17 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7r77 C-cys B.5CM30 A.CYS593 11.85 -92.50 -5.92 9.43 -4.04 55.74 -11.52 -76.27 2 7r77 C-arg B.5CM30 A.ARG638 -12.77 -160.08 -8.09 9.87 0.58 22.16 -82.99 -152.67 3 7r77 C-ser B.5CM30 A.SER667 7.58 -105.83 4.17 5.97 -2.12 30.76 -20.76 -101.00 4 7r77 C-gln B.5CM30 A.GLN668 6.14 -125.99 1.47 3.66 4.70 -54.65 -21.56 -117.19 5 7r77 C-asn B.5CM30 A.ASN669 7.98 166.30 6.21 -2.59 4.30 21.40 -4.75 166.05 6 7r77 G-arg B.DG31 A.ARG596 13.16 -143.41 -5.09 12.09 1.10 23.42 -64.33 -135.37 7 7r77 G-gln B.DG31 A.GLN668 -4.68 -158.19 2.49 3.69 1.43 -57.76 -12.13 -154.89 8 7r77 G-asn B.DG31 A.ASN669 5.79 132.74 4.05 -4.03 0.94 13.69 -5.03 132.33 9 7r77 G-arg B.DG31 A.ARG672 7.79 176.71 -0.29 -5.39 5.62 -18.71 38.33 176.47 10 7r77 C-arg B.DC32 A.ARG672 -5.65 177.92 1.29 -4.92 -2.45 2.25 33.90 177.82 11 7r77 T-thr D.DT4 A.THR674 10.76 178.09 7.92 -7.02 1.91 -69.52 25.19 177.61 12 7r77 G-arg D.DG5 A.ARG672 5.91 -179.07 1.45 5.33 2.09 -6.51 -31.60 -179.03 13 7r77 C-gln D.DC6 A.GLN668 -5.84 98.25 -5.64 -1.21 -0.92 -84.32 -11.01 54.79 14 7r77 C-cys D.DC6 A.CYS684 6.88 103.91 0.29 0.43 6.86 -1.93 85.78 65.44 15 7r77 C-thr D.DC6 A.THR686 7.49 -144.34 -5.42 2.92 4.28 63.30 11.56 -137.59 16 7r77 G-ser D.DG7 A.SER667 -7.87 107.13 4.41 -6.15 2.19 33.96 25.34 100.87 17 7r77 G-gln D.DG7 A.GLN668 -6.25 128.27 1.46 -3.84 -4.70 -51.01 24.85 120.55 **************************************************************************** List of 7 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7r77 AT-thr B.DA33 D.DT4 A.THR674 -10.73 -179.89 8.12 6.57 -2.44 -74.82 -20.82 -179.86 2 7r77 GC-arg D.DG5 B.DC32 A.ARG672 5.78 -178.49 1.36 5.13 2.28 -2.16 -32.83 -178.43 3 7r77 GC-cys D.DG7 B.5CM30 A.CYS593 -11.86 92.64 -5.74 -9.45 4.30 56.87 14.00 75.29 4 7r77 GC-arg D.DG7 B.5CM30 A.ARG638 12.91 161.94 -8.09 -10.04 -0.60 24.05 84.43 154.85 5 7r77 GC-ser D.DG7 B.5CM30 A.SER667 -7.73 106.45 4.29 -6.05 2.16 32.36 23.04 100.94 6 7r77 GC-gln D.DG7 B.5CM30 A.GLN668 -6.19 127.11 1.46 -3.75 -4.70 -52.84 23.21 118.87 7 7r77 GC-asn D.DG7 B.5CM30 A.ASN669 -7.97 -166.04 6.22 2.68 -4.21 18.64 4.44 -165.84 **************************************************************************** List of 16 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 7r77 OP1@B.DG29 OG1@A.THR636 3.26 po4:sidechain 2 7r77 OP2@B.DG29 NE@A.ARG638 2.48 po4:sidechain:salt-bridge 3 7r77 OP1@B.5CM30 N@A.ARG592 3.42 po4:backbone 4 7r77 OP2@B.5CM30 N@A.CYS593 2.89 po4:backbone 5 7r77 OP1@B.DG31 NH1@A.ARG2036 2.82 po4:sidechain:salt-bridge 6 7r77 OP2@B.DG31 NH1@A.ARG596 2.47 po4:sidechain:salt-bridge 7 7r77 OP1@B.DC32 NH1@A.ARG2036 3.23 po4:sidechain:salt-bridge 8 7r77 OP1@B.DC32 NH2@A.ARG2036 2.74 po4:sidechain:salt-bridge 9 7r77 OP2@B.DC32 NH2@A.ARG596 3.12 po4:sidechain:salt-bridge 10 7r77 OP1@D.DT4 NZ@A.LYS510 3.41 po4:sidechain:salt-bridge 11 7r77 OP1@D.DG5 N@A.THR519 2.79 po4:backbone 12 7r77 OP1@D.DG5 OG1@A.THR519 3.10 po4:sidechain 13 7r77 OP1@D.DC6 N@A.ASN485 3.36 po4:backbone 14 7r77 OP1@D.DC6 ND2@A.ASN485 3.21 po4:sidechain 15 7r77 OP2@D.DC6 N@A.CYS484 3.33 po4:backbone 16 7r77 O3'@D.DG5 ND2@A.ASN485 3.26 po4:sidechain **************************************************************************** List of 3 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 7r77 N4@B.5CM30 O@A.SER667 3.27 base:backbone 2 7r77 O6@B.DG31 N@A.ASN669 3.24 base:backbone 3 7r77 N1@B.DG31 OE1@A.GLN668 3.20 base:sidechain **************************************************************************** List of 1 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 7r77 G-gln B.DG31 A.GLN668 2.20 49 **************************************************************************** List of 3 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 7r77 G-arg B.DG31 A.ARG672 3.76 10 2 7r77 C-arg B.DC32 A.ARG672 3.21 15 3 7r77 G-arg D.DG5 A.ARG672 3.82 13 **************************************************************************** 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=4 CGRC B.5CM30,B.DG31,A.ARG672,B.DC32 **************************************************************************** List of 3 additional files 1 -- 7r77-baseAA-pairs.pdb 2 -- 7r77-baseAA-stacks.pdb 3 -- 7r77-pairs.pdb