**************************************************************************** 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/2uyc.pdb -o=2uyc.out --type=base File name: 2uyc.pdb no. of peptide chains: 1 [A=328] no. of DNA/RNA chains: 2 [C=13,D=12] no. of amino acids: 328 no. of nucleotides: 26 no. of atoms: 3434 no. of waters: 234 no. of metals: 0 **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 5CM-c 1 C.5CM407 2 SAH-a 1 A.SAH1328 **************************************************************************** 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'-GGATGcCTGAC-3' bp-type ||||||||||| strand-2 3'-CCTACGGACTG-5' helix-form .B...xBBB. 1 C.DG402 D.DC433 G-C WC 19-XIX cWW cW-W 2 C.DG403 D.DC432 G-C WC 19-XIX cWW cW-W 3 C.DA404 D.DT431 A-T WC 20-XX cWW cW-W 4 C.DT405 D.DA430 T-A 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.DG411 D.DC424 G-C WC 19-XIX cWW cW-W 10 C.DA412 D.DT423 A-T WC 20-XX cWW cW-W 11 C.DC413 D.DG422 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 69 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 2uyc T-trp C.DT401 A.TRP41 -5.31 95.75 -2.11 2.94 -3.89 -85.46 -2.70 48.04 2 2uyc T-asp C.DT401 A.ASP42 -5.18 164.75 -0.90 5.00 -1.03 -44.40 -64.20 160.33 3 2uyc T-lys C.DT401 A.LYS43 4.70 133.52 -2.65 3.03 -2.43 89.68 5.66 112.26 4 2uyc T-gly C.DT405 A.GLY255 8.64 85.39 7.47 1.18 4.16 34.13 -8.92 79.07 5 2uyc T-gly C.DT405 A.GLY256 6.43 -127.39 -2.33 4.54 3.92 15.66 -30.07 -124.81 6 2uyc T-gly C.DT405 A.GLY257 8.46 79.12 3.52 7.59 1.24 24.64 -61.87 45.43 7 2uyc T-ala C.DT405 A.ALA260 10.23 -131.52 -6.24 7.92 -1.75 64.18 12.47 -121.60 8 2uyc T-lys C.DT405 A.LYS261 12.15 -99.13 1.15 11.89 -2.25 70.18 41.36 -62.28 9 2uyc G-gly C.DG406 A.GLY256 4.58 -171.88 -1.16 4.34 0.88 13.67 -30.93 -171.52 10 2uyc G-gly C.DG406 A.GLY257 6.67 -76.95 3.81 5.41 -0.90 3.26 -76.88 -0.51 11 2uyc C-gly C.5CM407 A.GLY236 7.40 166.87 4.86 -3.96 3.93 -39.94 17.75 165.84 12 2uyc C-gln C.5CM407 A.GLN237 5.50 -127.28 -0.07 4.56 3.06 2.15 16.03 -126.71 13 2uyc C-glu C.5CM407 A.GLU239 9.74 141.39 7.79 -5.64 1.54 -2.53 -4.21 141.35 14 2uyc C-gly C.5CM407 A.GLY256 -4.51 153.88 1.70 -3.29 -2.58 3.91 34.16 152.63 15 2uyc C-gly C.5CM407 A.GLY257 -6.61 -78.31 2.16 5.32 -3.26 -22.52 -66.98 -36.21 16 2uyc G-ser C.DG408 A.SER87 7.11 -58.83 -4.27 -5.64 -0.76 -26.28 38.19 -37.27 17 2uyc G-gly C.DG408 A.GLY236 4.89 132.96 2.93 -3.90 0.37 -38.10 32.36 127.75 18 2uyc G-gln C.DG408 A.GLN237 -4.18 -163.30 2.81 3.09 -0.20 10.58 8.92 -163.17 19 2uyc G-arg C.DG408 A.ARG240 10.51 -147.85 7.20 7.65 -0.07 -28.05 -68.96 -139.31 20 2uyc T-ile C.DT410 A.ILE86 -8.02 -84.43 -7.68 -2.17 0.80 -17.99 -50.37 -67.93 21 2uyc G-ile C.DG411 A.ILE86 -9.63 -117.53 -9.20 0.97 -2.67 -33.48 -48.97 -106.73 22 2uyc A-ile D.DA425 A.ILE86 8.06 89.20 -7.76 2.13 -0.50 -11.15 53.78 73.27 23 2uyc A-arg D.DA425 A.ARG228 -14.61 -86.54 -7.45 12.02 -3.69 39.35 -20.54 -76.29 24 2uyc A-arg D.DA425 A.ARG240 12.67 -166.40 -8.21 7.93 5.49 48.84 -41.58 -163.93 25 2uyc G-ile D.DG426 A.ILE86 -7.86 61.39 -5.21 4.55 -3.74 1.33 53.09 31.98 26 2uyc G-ser D.DG426 A.SER87 5.91 69.16 -2.46 3.82 3.78 -16.16 -42.45 53.61 27 2uyc G-gln D.DG426 A.GLN237 6.65 -178.50 -3.67 3.68 4.15 -13.01 11.05 -178.49 28 2uyc G-arg D.DG426 A.ARG240 11.71 161.39 6.90 -8.97 3.03 -36.52 60.16 157.18 29 2uyc C-gly D.DC427 A.GLY78 5.03 -167.32 2.13 3.98 2.22 -28.85 -62.52 -164.62 30 2uyc C-phe D.DC427 A.PHE79 6.96 -38.37 5.91 3.07 2.03 3.70 36.11 -12.65 31 2uyc C-pro D.DC427 A.PRO80 -7.91 55.24 7.28 3.03 -0.73 -20.97 -2.96 51.32 32 2uyc C-cys D.DC427 A.CYS81 -7.30 -145.36 -5.79 4.39 -0.68 13.56 -81.50 -133.30 33 2uyc C-glu D.DC427 A.GLU119 -4.47 -148.05 3.02 2.31 -2.34 -46.55 -67.56 -137.21 34 2uyc C-asn D.DC427 A.ASN120 -3.84 49.18 2.78 -0.13 -2.64 -22.84 38.55 20.82 35 2uyc C-val D.DC427 A.VAL121 -5.35 107.03 -0.58 2.40 -4.75 -20.66 -11.55 105.18 36 2uyc C-arg D.DC427 A.ARG165 -6.00 113.97 -5.57 -1.89 -1.17 72.44 -46.39 83.66 37 2uyc C-gly D.DC427 A.GLY303 9.64 131.17 5.20 5.21 6.23 -66.81 -55.15 110.76 38 2uyc C-asn D.DC427 A.ASN304 7.00 55.76 0.56 6.84 1.39 37.81 -12.64 39.82 39 2uyc C-ser D.DC427 A.SER305 6.41 -167.76 -2.03 -4.46 4.14 -58.87 -16.55 -165.77 40 2uyc G-ser D.DG428 A.SER87 -7.89 40.63 -3.50 6.69 -2.30 -26.23 -31.03 0.01 41 2uyc G-gln D.DG428 A.GLN237 -5.36 131.05 0.36 -4.28 -3.20 9.90 -21.91 129.88 42 2uyc G-ser D.DG428 A.SER252 9.71 -119.70 -4.28 8.66 -0.98 4.85 35.43 -116.30 43 2uyc G-tyr D.DG428 A.TYR254 7.74 172.31 4.88 -0.94 5.93 3.01 24.37 172.13 44 2uyc G-gly D.DG428 A.GLY255 5.32 45.35 2.66 3.89 2.46 25.47 36.87 7.18 45 2uyc G-gly D.DG428 A.GLY256 4.61 -149.28 1.71 3.41 2.58 3.49 -24.78 -148.51 46 2uyc C-tyr D.DC429 A.TYR254 8.06 144.30 6.70 -3.58 2.69 17.63 20.12 143.27 47 2uyc C-gly D.DC429 A.GLY255 -6.70 -58.17 5.59 3.43 -1.34 38.09 36.66 -25.20 48 2uyc C-gly D.DC429 A.GLY256 -4.46 -177.64 0.55 4.32 -0.96 -10.11 -19.54 -177.59 49 2uyc A-phe A.SAH1328 A.PHE18 -7.00 62.90 -2.16 3.02 -5.93 40.39 43.69 21.43 50 2uyc A-ala A.SAH1328 A.ALA19 -9.92 -128.16 -8.17 -5.10 -2.40 -21.50 -19.28 -126.33 51 2uyc A-gly A.SAH1328 A.GLY20 -10.94 80.33 -3.27 9.22 -4.91 32.07 57.57 48.79 52 2uyc A-leu A.SAH1328 A.LEU21 14.63 101.01 -0.82 14.59 -0.59 4.41 11.84 100.43 53 2uyc A-gly A.SAH1328 A.GLY22 -14.83 -174.21 -3.25 -9.79 -10.66 -41.74 69.76 -172.37 54 2uyc A-gly A.SAH1328 A.GLY23 -17.10 67.03 -8.13 14.97 1.46 -44.69 -15.76 48.85 55 2uyc A-phe A.SAH1328 A.PHE24 -16.65 -72.47 -14.91 -1.55 -7.24 60.72 -10.98 -40.04 56 2uyc A-asn A.SAH1328 A.ASN39 -7.15 -88.52 -5.67 -4.31 0.60 73.04 10.75 -52.79 57 2uyc A-glu A.SAH1328 A.GLU40 6.16 141.68 -0.23 6.02 1.30 -3.32 -31.53 140.11 58 2uyc A-trp A.SAH1328 A.TRP41 5.30 -75.82 -4.00 -1.47 3.16 -73.95 16.13 -4.74 59 2uyc A-asp A.SAH1328 A.ASP60 3.04 -81.69 0.67 -2.96 0.17 -66.62 -19.75 -45.98 60 2uyc A-ile A.SAH1328 A.ILE61 -3.60 152.19 -3.50 0.42 -0.71 -75.75 -40.53 141.66 61 2uyc A-thr A.SAH1328 A.THR62 -5.42 51.30 1.45 -5.16 -0.82 29.15 -14.65 40.14 62 2uyc A-gly A.SAH1328 A.GLY78 -12.02 135.74 4.80 5.61 -9.49 18.08 -13.39 134.83 63 2uyc A-pro A.SAH1328 A.PRO80 -9.68 -53.16 -2.46 8.13 -4.64 17.84 -41.51 -28.79 64 2uyc A-leu A.SAH1328 A.LEU100 -7.75 141.79 2.62 -4.32 -5.89 24.52 -23.32 139.99 65 2uyc A-tyr A.SAH1328 A.TYR285 -23.93 -71.90 -20.61 8.12 9.05 -35.62 -51.06 -37.93 66 2uyc A-gln A.SAH1328 A.GLN301 15.46 -168.30 -12.81 -5.44 -6.75 -38.84 64.54 -165.21 67 2uyc A-asn A.SAH1328 A.ASN304 -14.73 -122.88 -13.71 5.28 -0.95 -72.64 25.00 -104.81 68 2uyc A-ser A.SAH1328 A.SER305 -16.01 158.86 7.78 9.90 -9.88 15.21 -62.64 154.95 69 2uyc A-val A.SAH1328 A.VAL306 -18.06 -139.96 -17.64 -3.78 0.80 72.29 -35.91 -126.61 **************************************************************************** List of 26 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 2uyc AT-ala D.DA430 C.DT405 A.ALA260 -10.13 141.66 -5.86 -8.14 1.43 68.98 -11.17 132.77 2 2uyc AT-arg D.DA425 C.DT410 A.ARG228 -14.60 -86.94 -7.26 12.06 -3.88 40.00 -24.86 -75.32 3 2uyc AT-arg D.DA425 C.DT410 A.ARG240 12.69 -167.25 -8.26 7.87 5.57 52.11 -44.45 -164.57 4 2uyc AT-gly D.DA430 C.DT405 A.GLY255 -8.31 -80.47 7.20 -0.72 -4.09 36.63 16.10 -71.33 5 2uyc AT-gly D.DA430 C.DT405 A.GLY256 -6.25 137.03 -2.15 -4.35 -3.93 17.03 27.06 135.21 6 2uyc AT-gly D.DA430 C.DT405 A.GLY257 -8.43 -78.20 3.75 -7.41 -1.47 23.94 67.19 -34.43 7 2uyc AT-ile D.DA425 C.DT410 A.ILE86 8.04 86.74 -7.72 2.15 -0.64 -14.57 52.09 70.59 8 2uyc AT-lys D.DA430 C.DT405 A.LYS261 -11.94 107.23 1.77 -11.63 2.04 78.56 -37.53 70.18 9 2uyc GC-arg D.DG426 C.DC409 A.ARG240 11.62 161.08 6.88 -8.82 3.14 -37.65 60.03 156.73 10 2uyc GC-gln D.DG428 C.5CM407 A.GLN237 -5.43 129.13 0.15 -4.43 -3.14 5.97 -19.04 128.29 11 2uyc GC-gln D.DG426 C.DC409 A.GLN237 6.57 -178.16 -3.69 3.52 4.14 -11.94 10.90 -178.14 12 2uyc GC-glu D.DG428 C.5CM407 A.GLU239 -9.68 -139.37 7.54 5.79 -1.79 -2.88 8.83 -139.23 13 2uyc GC-gly C.DG406 D.DC429 A.GLY255 6.72 56.87 5.82 -3.03 1.43 33.60 -33.93 31.84 14 2uyc GC-gly C.DG406 D.DC429 A.GLY256 4.52 -177.06 -0.85 4.34 0.93 11.64 -25.29 -176.97 15 2uyc GC-gly C.DG406 D.DC429 A.GLY257 6.61 -76.51 4.10 5.15 -0.54 5.13 -75.74 -10.32 16 2uyc GC-gly D.DG428 C.5CM407 A.GLY236 -7.30 -163.24 4.54 4.00 -4.09 -40.76 -14.14 -161.97 17 2uyc GC-gly D.DG428 C.5CM407 A.GLY255 5.25 41.16 2.74 3.85 2.29 21.86 34.64 4.11 18 2uyc GC-gly D.DG428 C.5CM407 A.GLY256 4.56 -151.57 1.71 3.35 2.58 3.78 -29.46 -150.57 19 2uyc GC-gly D.DG428 C.5CM407 A.GLY257 6.59 79.57 2.30 -5.36 3.07 -19.58 66.70 41.42 20 2uyc GC-ile D.DG426 C.DC409 A.ILE86 -7.98 60.55 -5.27 4.56 -3.88 0.84 52.06 32.05 21 2uyc GC-ile C.DG411 D.DC424 A.ILE86 -9.73 -117.38 -9.29 0.86 -2.77 -31.95 -48.47 -107.07 22 2uyc GC-ser D.DG428 C.5CM407 A.SER87 -7.90 -44.96 -3.38 6.61 -2.70 -30.97 -32.56 -1.30 23 2uyc GC-ser D.DG428 C.5CM407 A.SER252 9.66 -120.76 -4.01 8.70 -1.25 4.89 30.69 -118.28 24 2uyc GC-ser D.DG426 C.DC409 A.SER87 6.00 70.07 -2.60 3.90 3.76 -16.65 -43.42 53.95 25 2uyc GC-tyr C.DG406 D.DC429 A.TYR254 -8.07 -138.66 6.62 3.93 -2.41 17.09 -25.36 -137.07 26 2uyc GC-tyr D.DG428 C.5CM407 A.TYR254 7.65 169.82 5.03 -0.93 5.68 1.23 28.41 169.49 **************************************************************************** List of 20 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 2uyc O5'@C.DT401 OH@A.TYR254 3.85 po4:sidechain 2 2uyc O5'@C.DT401 NZ@A.LYS300 2.98 po4:sidechain 3 2uyc OP1@C.DG403 OG@A.SER294 2.61 po4:sidechain 4 2uyc OP2@C.DG403 OG@A.SER296 3.12 po4:sidechain 5 2uyc OP2@C.DG403 NE2@A.GLN297 2.68 po4:sidechain 6 2uyc OP2@C.DG406 NH1@A.ARG209 2.57 po4:sidechain:salt-bridge 7 2uyc O3'@C.DT410 NE2@A.GLN90 2.91 po4:sidechain 8 2uyc OP1@C.DA412 OG@A.SER126 2.71 po4:sidechain 9 2uyc OP2@D.DA425 NE@A.ARG228 2.79 po4:sidechain:salt-bridge 10 2uyc OP2@D.DA425 NH2@A.ARG228 2.58 po4:sidechain:salt-bridge 11 2uyc OP2@D.DA425 OH@A.TYR242 2.72 po4:sidechain 12 2uyc OP1@D.DG426 N@A.THR250 2.73 po4:backbone 13 2uyc OP1@D.DG426 OG1@A.THR250 2.67 po4:sidechain 14 2uyc OP1@D.DC427 OG@A.SER85 2.75 po4:sidechain 15 2uyc OP2@D.DC427 NH1@A.ARG165 2.94 po4:sidechain:salt-bridge 16 2uyc OP2@D.DG428 N@A.TYR254 2.61 po4:backbone 17 2uyc O3'@D.DC427 N@A.ALA253 3.24 po4:backbone 18 2uyc OP1@D.DC429 NH2@A.ARG97 2.76 po4:sidechain:salt-bridge 19 2uyc OP2@D.DC429 NH1@A.ARG97 3.22 po4:sidechain:salt-bridge 20 2uyc OP1@D.DA430 NZ@A.LYS89 2.89 po4:sidechain:salt-bridge **************************************************************************** List of 3 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 2uyc O4'@C.DT401 OD2@A.ASP42 2.95 sugar:sidechain 2 2uyc O4'@D.DC427 NH2@A.ARG165 3.00 sugar:sidechain 3 2uyc O2'@A.SAH1328 OE2@A.GLU40 2.68 sugar:sidechain **************************************************************************** List of 25 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 2uyc O2@C.DT401 N@A.LYS43 2.72 base:backbone 2 2uyc N3@C.DT401 O@A.TRP41 3.96 base:backbone 3 2uyc N7@C.DG406 N@A.GLY257 2.87 base:backbone 4 2uyc N4@C.5CM407 O@A.GLN237 2.80 base:backbone 5 2uyc O6@C.DG408 N@A.GLN237 2.72 base:backbone 6 2uyc N1@C.DG408 OE1@A.GLN237 2.74 base:sidechain 7 2uyc N2@C.DG408 O@A.SER87 3.96 base:backbone 8 2uyc N2@C.DG408 OE1@A.GLN237 2.96 base:sidechain 9 2uyc N7@D.DG426 NH1@A.ARG240 2.84 base:sidechain 10 2uyc O6@D.DG426 NH2@A.ARG240 2.89 base:sidechain 11 2uyc N2@D.DG426 O@A.ILE86 2.97 base:backbone 12 2uyc O2@D.DC427 NE@A.ARG165 2.78 base:sidechain 13 2uyc O2@D.DC427 NH2@A.ARG165 2.81 base:sidechain 14 2uyc N3@D.DC427 OE2@A.GLU119 2.85 base:sidechain 15 2uyc N4@D.DC427 O@A.PHE79 2.91 base:backbone 16 2uyc N4@D.DC427 OE1@A.GLU119 2.69 base:sidechain 17 2uyc O6@D.DG428 N@A.GLY256 2.90 base:backbone 18 2uyc N4@D.DC429 O@A.TYR254 2.97 base:backbone 19 2uyc O@A.SAH1328 N@A.GLY23 3.12 base:backbone 20 2uyc O@A.SAH1328 OG@A.SER305 3.00 base:sidechain 21 2uyc OXT@A.SAH1328 N@A.LEU21 3.03 base:backbone 22 2uyc OXT@A.SAH1328 OG@A.SER305 2.95 base:sidechain 23 2uyc N6@A.SAH1328 OD1@A.ASP60 3.22 base:sidechain 24 2uyc N1@A.SAH1328 N@A.ILE61 3.01 base:backbone 25 2uyc N3@A.SAH1328 N@A.TRP41 3.24 base:backbone **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 2uyc G-gln C.DG408 A.GLN237 0.23 19 2 2uyc G-arg D.DG426 A.ARG240 0.07 5 3 2uyc C-glu D.DC427 A.GLU119 0.34 28 4 2uyc C-arg D.DC427 A.ARG165 0.70 64 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 2uyc A-arg D.DA425 A.ARG240 3.31 9 2 2uyc G-gln D.DG426 A.GLN237 3.48 16 3 2uyc G-gln D.DG428 A.GLN237 3.34 17 4 2uyc A-trp A.SAH1328 A.TRP41 3.39 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 -- 2uyc-baseAA-pairs.pdb 2 -- 2uyc-baseAA-stacks.pdb 3 -- 2uyc-pairs.pdb