**************************************************************************** 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/4mht.pdb -o=4mht.out --type=base File name: 4mht.pdb no. of peptide chains: 1 [A=328] no. of DNA/RNA chains: 2 [C=12,D=13] no. of amino acids: 328 no. of nucleotides: 26 no. of atoms: 3254 no. of waters: 111 no. of metals: 0 **************************************************************************** List of 2 types of 3 modified nucleotides nt count list 1 5CM-c 2 C.5CM407,D.5CM427 2 SAH-a 1 A.SAH328 **************************************************************************** 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'-GATAGcCTATC-3' bp-type ||||||||||| strand-2 3'-CTATCGGATAG-5' helix-form BBBB.xBBBB 1 C.DG402 D.DC433 G-C WC 19-XIX cWW cW-W 2 C.DA403 D.DT432 A-T WC 20-XX cWW cW-W 3 C.DT404 D.DA431 T-A WC 20-XX cWW cW-W 4 C.DA405 D.DT430 A-T WC 20-XX cWW cW-W 5 C.DG406 D.DC429 G-C WC 19-XIX cWW cW-W 6 C.5CM407 D.DG428 c-G WC 19-XIX cWW cW-W 7 C.DC409 D.DG426 C-G WC 19-XIX cWW cW-W 8 C.DT410 D.DA425 T-A WC 20-XX cWW cW-W 9 C.DA411 D.DT424 A-T WC 20-XX cWW cW-W 10 C.DT412 D.DA423 T-A WC 20-XX cWW cW-W 11 C.DC413 D.DG422 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 64 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4mht T-ser C.DT404 A.SER296 12.04 -151.43 -8.96 7.89 -1.50 49.71 -25.74 -147.55 2 4mht A-tyr C.DA405 A.TYR254 7.20 -102.77 5.10 5.05 0.64 12.30 -26.19 -99.74 3 4mht A-gly C.DA405 A.GLY255 7.16 70.77 6.13 0.46 3.67 34.54 -16.45 60.71 4 4mht A-gly C.DA405 A.GLY256 5.40 -145.04 -2.12 3.42 3.60 13.46 -27.06 -143.75 5 4mht A-gly C.DA405 A.GLY257 8.10 64.69 3.03 7.26 1.92 21.00 -56.49 24.71 6 4mht G-gly C.DG406 A.GLY256 4.64 -179.00 -1.32 4.41 0.63 18.36 -32.25 -178.95 7 4mht G-gly C.DG406 A.GLY257 6.86 -73.61 4.00 5.48 -1.02 3.60 -73.34 -5.64 8 4mht C-gln C.5CM407 A.GLN237 5.45 -133.31 0.09 4.47 3.12 2.60 18.54 -132.64 9 4mht C-glu C.5CM407 A.GLU239 9.83 126.70 7.99 -5.62 1.13 -13.80 1.12 126.28 10 4mht C-gly C.5CM407 A.GLY256 -4.91 148.19 1.63 -3.52 -3.00 0.37 34.99 146.60 11 4mht C-gly C.5CM407 A.GLY257 -6.79 -76.43 2.56 5.04 -3.77 -18.77 -62.86 -41.64 12 4mht G-ser C.DG408 A.SER87 7.30 -60.32 -4.23 -5.89 -0.77 -27.06 39.29 -38.06 13 4mht G-gly C.DG408 A.GLY236 4.89 134.54 3.04 -3.82 0.30 -35.07 32.22 130.04 14 4mht G-gln C.DG408 A.GLN237 -4.05 -164.03 2.63 3.07 -0.22 10.16 9.39 -163.91 15 4mht G-arg C.DG408 A.ARG240 10.56 -151.40 6.88 8.01 0.37 -35.93 -73.67 -141.80 16 4mht T-ile C.DT410 A.ILE86 -7.70 -79.15 -7.29 -1.92 1.61 -26.95 -53.93 -53.92 17 4mht A-ile C.DA411 A.ILE86 -9.82 -118.82 -9.22 1.49 -3.03 -36.25 -51.80 -106.61 18 4mht A-ile D.DA425 A.ILE86 8.12 83.85 -7.72 2.41 -0.75 -9.67 53.74 66.30 19 4mht A-arg D.DA425 A.ARG240 12.82 -169.76 -7.67 9.01 4.92 56.66 -42.20 -167.44 20 4mht G-ile D.DG426 A.ILE86 -7.81 66.04 -5.29 4.48 -3.60 1.10 58.95 31.19 21 4mht G-ser D.DG426 A.SER87 5.96 68.28 -2.28 3.89 3.91 -12.92 -39.75 55.26 22 4mht G-gln D.DG426 A.GLN237 6.62 -176.56 -3.51 3.93 4.01 -17.96 12.58 -176.50 23 4mht G-arg D.DG426 A.ARG240 11.93 167.55 6.88 -9.59 1.75 -41.21 62.35 164.32 24 4mht C-gly D.5CM427 A.GLY78 4.78 -165.45 2.31 3.49 2.31 -39.35 -63.36 -161.68 25 4mht C-phe D.5CM427 A.PHE79 -6.64 -47.29 5.60 2.86 2.13 0.52 45.01 -14.89 26 4mht C-pro D.5CM427 A.PRO80 -7.48 53.42 6.81 2.98 -0.85 -16.29 -1.84 51.02 27 4mht C-cys D.5CM427 A.CYS81 -7.17 -142.42 -5.91 3.93 -1.06 17.77 -75.03 -131.35 28 4mht C-glu D.5CM427 A.GLU119 -4.08 -147.04 2.84 1.56 -2.48 -51.12 -65.89 -135.34 29 4mht C-asn D.5CM427 A.ASN120 -3.29 52.59 1.88 -0.06 -2.70 -22.34 43.56 19.83 30 4mht C-val D.5CM427 A.VAL121 -5.54 103.34 -1.19 2.92 -4.55 -16.67 -8.24 102.13 31 4mht C-arg D.5CM427 A.ARG163 -9.60 -98.82 -8.55 -4.31 0.74 -71.56 -53.70 -47.32 32 4mht C-arg D.5CM427 A.ARG165 -6.23 108.39 -6.11 -0.95 -0.77 73.70 -44.80 73.44 33 4mht C-asn D.5CM427 A.ASN304 6.95 48.46 -1.20 6.56 1.96 25.29 29.21 29.82 34 4mht C-ser D.5CM427 A.SER305 6.84 -166.54 -1.82 -4.58 4.74 -62.77 -23.52 -163.84 35 4mht G-ser D.DG428 A.SER87 -7.93 44.04 -3.54 6.71 -2.32 -26.31 -35.19 3.02 36 4mht G-gln D.DG428 A.GLN237 -5.27 135.30 0.20 -4.31 -3.02 7.64 -23.28 134.20 37 4mht G-tyr D.DG428 A.TYR254 7.78 172.04 4.72 -0.91 6.12 -0.75 28.59 171.78 38 4mht G-gly D.DG428 A.GLY255 5.34 43.51 2.48 3.80 2.83 19.26 37.87 9.60 39 4mht G-gly D.DG428 A.GLY256 5.03 -145.42 1.90 3.47 3.11 0.58 -28.27 -144.31 40 4mht C-tyr D.DC429 A.TYR254 7.62 141.59 6.35 -3.46 2.41 20.33 28.43 139.65 41 4mht C-gly D.DC429 A.GLY255 -6.20 -59.59 5.30 2.94 -1.32 30.94 42.65 -28.89 42 4mht C-gly D.DC429 A.GLY256 -4.25 -176.43 1.07 4.05 -0.72 -19.80 -23.28 -176.30 43 4mht T-tyr D.DT430 A.TYR254 -7.31 108.11 5.47 -4.75 -0.97 21.49 27.63 104.02 44 4mht A-phe A.SAH328 A.PHE18 -6.95 62.15 -1.93 2.71 -6.10 40.54 38.65 28.09 45 4mht A-ala A.SAH328 A.ALA19 -9.79 -128.41 -7.94 -5.07 -2.68 -21.42 -23.26 -126.22 46 4mht A-gly A.SAH328 A.GLY20 -10.87 77.32 -3.21 9.10 -4.99 25.72 56.23 48.94 47 4mht A-leu A.SAH328 A.LEU21 -14.49 102.75 -0.80 14.42 -1.19 2.85 10.16 102.36 48 4mht A-gly A.SAH328 A.GLY22 -14.84 -175.04 -2.78 -10.11 -10.49 -35.30 66.78 -173.73 49 4mht A-gly A.SAH328 A.GLY23 -17.07 71.15 -8.22 14.90 1.30 -50.37 -18.13 48.73 50 4mht A-phe A.SAH328 A.PHE24 -16.53 -72.02 -14.54 -1.74 -7.66 61.52 -14.79 -36.35 51 4mht A-asn A.SAH328 A.ASN39 -7.25 -89.61 -5.44 -4.77 0.49 76.10 6.18 -51.01 52 4mht A-glu A.SAH328 A.GLU40 5.92 140.43 -0.74 5.74 1.23 -10.93 -31.92 138.57 53 4mht A-trp A.SAH328 A.TRP41 5.23 -72.85 -4.00 -1.67 2.92 -72.06 8.27 -7.24 54 4mht A-asp A.SAH328 A.ASP60 3.33 -76.20 0.98 -3.18 -0.01 -59.67 -24.05 -43.24 55 4mht A-ile A.SAH328 A.ILE61 -3.87 104.55 -0.17 -3.24 -2.10 27.43 85.11 61.15 56 4mht A-thr A.SAH328 A.THR62 -5.53 64.44 1.37 -5.34 -0.42 34.53 -26.22 48.88 57 4mht A-gly A.SAH328 A.GLY78 -11.85 141.39 5.04 4.66 -9.66 18.32 -13.96 140.56 58 4mht A-pro A.SAH328 A.PRO80 -9.70 -59.32 -2.55 8.16 -4.58 18.43 -49.89 -27.29 59 4mht A-leu A.SAH328 A.LEU100 -8.08 137.99 2.80 -4.38 -6.19 16.39 -24.05 136.53 60 4mht A-tyr A.SAH328 A.TYR285 -23.94 -69.30 -20.95 8.54 7.82 -26.97 -53.76 -36.18 61 4mht A-gln A.SAH328 A.GLN301 15.35 -169.47 -12.35 -6.16 -6.73 -34.91 62.75 -166.99 62 4mht A-asn A.SAH328 A.ASN304 -15.00 -88.27 -8.53 10.21 -6.93 75.26 -43.46 -17.23 63 4mht A-ser A.SAH328 A.SER305 -15.72 161.02 8.18 9.35 -9.64 14.68 -54.35 158.45 64 4mht A-val A.SAH328 A.VAL306 -17.97 -95.87 -7.82 12.97 -9.67 -46.28 73.73 -44.95 **************************************************************************** List of 23 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4mht AT-arg D.DA425 C.DT410 A.ARG240 12.60 -168.60 -7.89 8.90 4.17 60.92 -51.15 -165.16 2 4mht AT-gly C.DA405 D.DT430 A.GLY255 7.14 72.47 5.95 0.29 3.94 34.72 -21.55 61.19 3 4mht AT-gly C.DA405 D.DT430 A.GLY256 5.31 -147.40 -1.90 3.31 3.69 17.88 -25.89 -146.10 4 4mht AT-gly C.DA405 D.DT430 A.GLY257 7.97 68.91 3.03 7.06 2.12 22.27 -61.29 23.61 5 4mht AT-ile D.DA425 C.DT410 A.ILE86 7.90 80.96 -7.50 2.20 -1.19 -18.32 53.91 60.18 6 4mht AT-ile C.DA411 D.DT424 A.ILE86 -9.69 -118.70 -9.08 1.55 -3.00 -31.89 -51.89 -107.49 7 4mht AT-ser D.DA431 C.DT404 A.SER296 -12.03 151.05 -8.69 -8.16 1.61 53.99 30.25 146.11 8 4mht AT-tyr C.DA405 D.DT430 A.TYR254 7.26 -105.38 5.29 4.91 0.81 16.90 -26.89 -101.87 9 4mht GC-arg D.DG426 C.DC409 A.ARG240 11.65 165.25 6.67 -9.17 2.68 -50.11 61.64 160.79 10 4mht GC-gln D.DG428 C.5CM407 A.GLN237 -5.36 134.29 0.15 -4.39 -3.07 5.10 -20.94 133.42 11 4mht GC-gln D.DG426 C.DC409 A.GLN237 6.39 -173.59 -3.52 3.29 4.20 -9.69 11.09 -173.54 12 4mht GC-glu D.DG428 C.5CM407 A.GLU239 -9.80 -125.20 7.92 5.64 -1.22 -13.39 2.07 -124.78 13 4mht GC-gly C.DG406 D.DC429 A.GLY255 6.37 56.94 5.56 -2.80 1.33 27.26 -39.83 31.16 14 4mht GC-gly C.DG406 D.DC429 A.GLY256 4.45 178.72 1.19 -4.23 0.68 -19.04 27.76 178.66 15 4mht GC-gly C.DG406 D.DC429 A.GLY257 6.70 -75.18 3.96 5.36 -0.65 6.92 -74.23 -10.51 16 4mht GC-gly D.DG428 C.5CM407 A.GLY255 5.35 40.89 2.59 3.88 2.62 16.51 36.67 7.56 17 4mht GC-gly D.DG428 C.5CM407 A.GLY256 4.97 -146.80 1.76 3.49 3.06 0.50 -31.63 -145.45 18 4mht GC-gly D.DG428 C.5CM407 A.GLY257 6.83 77.22 2.54 -5.17 3.66 -16.36 62.51 44.79 19 4mht GC-ile D.DG426 C.DC409 A.ILE86 -8.02 59.48 -5.31 4.25 -4.25 -2.82 50.91 31.71 20 4mht GC-ser D.DG428 C.5CM407 A.SER87 -8.04 46.86 -3.47 6.75 -2.65 -29.74 -36.12 2.66 21 4mht GC-ser D.DG426 C.DC409 A.SER87 6.14 75.51 -2.88 4.00 3.67 -16.77 -47.23 58.42 22 4mht GC-tyr C.DG406 D.DC429 A.TYR254 7.74 -139.21 6.41 3.70 -2.24 17.96 -32.12 -136.91 23 4mht GC-tyr D.DG428 C.5CM407 A.TYR254 7.76 170.69 4.96 -0.92 5.90 -1.89 31.63 170.32 **************************************************************************** List of 21 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4mht OP1@C.DA403 OG@A.SER294 2.93 po4:sidechain 2 4mht OP2@C.DA403 NE2@A.GLN297 2.97 po4:sidechain 3 4mht OP2@C.DG406 NH1@A.ARG209 3.20 po4:sidechain:salt-bridge 4 4mht OP1@C.DA411 NE2@A.GLN90 3.98 po4:sidechain 5 4mht OP1@C.DT412 OG@A.SER126 3.22 po4:sidechain 6 4mht OP1@D.DA425 OG1@A.THR226 2.75 po4:sidechain 7 4mht OP2@D.DA425 NE@A.ARG228 3.10 po4:sidechain:salt-bridge 8 4mht OP2@D.DA425 NH2@A.ARG228 2.91 po4:sidechain:salt-bridge 9 4mht OP2@D.DA425 OH@A.TYR242 2.70 po4:sidechain 10 4mht OP1@D.DG426 NZ@A.LYS162 2.97 po4:sidechain:salt-bridge 11 4mht OP1@D.DG426 N@A.THR250 2.71 po4:backbone 12 4mht OP1@D.DG426 OG1@A.THR250 2.82 po4:sidechain 13 4mht O3'@D.DA425 NZ@A.LYS162 2.94 po4:sidechain 14 4mht OP1@D.5CM427 OG@A.SER85 2.46 po4:sidechain 15 4mht OP2@D.5CM427 NH1@A.ARG165 2.91 po4:sidechain:salt-bridge 16 4mht O5'@D.5CM427 NH2@A.ARG165 3.25 po4:sidechain 17 4mht OP2@D.DG428 N@A.ALA253 3.07 po4:backbone 18 4mht OP2@D.DG428 N@A.TYR254 2.79 po4:backbone 19 4mht OP1@D.DC429 NH2@A.ARG97 3.17 po4:sidechain:salt-bridge 20 4mht OP2@D.DC429 NH2@A.ARG97 3.08 po4:sidechain:salt-bridge 21 4mht OP1@D.DT430 NZ@A.LYS89 2.72 po4:sidechain:salt-bridge **************************************************************************** List of 1 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 4mht O2'@A.SAH328 OE2@A.GLU40 2.86 sugar:sidechain **************************************************************************** List of 21 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4mht N7@C.DG406 N@A.GLY257 3.18 base:backbone 2 4mht N4@C.5CM407 O@A.GLN237 2.83 base:backbone 3 4mht O6@C.DG408 N@A.GLN237 2.55 base:backbone 4 4mht N1@C.DG408 OE1@A.GLN237 2.58 base:sidechain 5 4mht N2@C.DG408 OE1@A.GLN237 2.87 base:sidechain 6 4mht N7@D.DG426 NH2@A.ARG240 2.80 base:sidechain 7 4mht O6@D.DG426 NH2@A.ARG240 3.24 base:sidechain 8 4mht N2@D.DG426 O@A.ILE86 2.86 base:backbone 9 4mht N3@D.5CM427 OE2@A.GLU119 2.97 base:sidechain 10 4mht O2@D.5CM427 NE@A.ARG165 2.75 base:sidechain 11 4mht N4@D.5CM427 O@A.PHE79 2.47 base:backbone 12 4mht N4@D.5CM427 OE1@A.GLU119 3.02 base:sidechain 13 4mht O6@D.DG428 N@A.GLY256 3.30 base:backbone 14 4mht N4@D.DC429 O@A.TYR254 2.69 base:backbone 15 4mht O@A.SAH328 N@A.GLY23 3.25 base:backbone 16 4mht O@A.SAH328 OG@A.SER305 2.87 base:sidechain 17 4mht OXT@A.SAH328 N@A.LEU21 2.81 base:backbone 18 4mht OXT@A.SAH328 OG@A.SER305 2.82 base:sidechain 19 4mht N6@A.SAH328 OD1@A.ASP60 3.60 base:sidechain 20 4mht N1@A.SAH328 N@A.ILE61 3.41 base:backbone 21 4mht N3@A.SAH328 N@A.TRP41 3.16 base:backbone **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4mht G-gln C.DG408 A.GLN237 0.21 19 2 4mht G-arg D.DG426 A.ARG240 0.11 8 3 4mht C-glu D.5CM427 A.GLU119 0.65 29 4 4mht C-arg D.5CM427 A.ARG165 0.66 53 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4mht G-gln D.DG426 A.GLN237 3.45 18 2 4mht C-asn D.5CM427 A.ASN120 5.08 34 3 4mht G-gln D.DG428 A.GLN237 3.36 14 4 4mht A-trp A.SAH328 A.TRP41 3.43 9 **************************************************************************** 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 GQG D.DG426,A.GLN237,D.DG428 **************************************************************************** List of 3 additional files 1 -- 4mht-baseAA-pairs.pdb 2 -- 4mht-baseAA-stacks.pdb 3 -- 4mht-pairs.pdb