**************************************************************************** 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/4r2e.pdb -o=4r2e.out --type=base File name: 4r2e.pdb no. of peptide chains: 1 [A=88] no. of DNA/RNA chains: 2 [B=11,C=11] no. of amino acids: 88 no. of nucleotides: 22 no. of atoms: 1335 no. of waters: 144 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 B.5CM9,C.5CM3 **************************************************************************** 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=10 strand-1 5'-GCGTGGGcGT-3' bp-type |||||||||| strand-2 3'-CGCACCCGcA-5' helix-form BBBB...BB 1 B.DG2 C.DC11 G-C WC 19-XIX cWW cW-W 2 B.DC3 C.DG10 C-G WC 19-XIX cWW cW-W 3 B.DG4 C.DC9 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA8 T-A WC 20-XX cWW cW-W 5 B.DG6 C.DC7 G-C WC 19-XIX cWW cW-W 6 B.DG7 C.DC6 G-C WC 19-XIX cWW cW-W 7 B.DG8 C.DC5 G-C WC 19-XIX cWW cW-W 8 B.5CM9 C.DG4 c-G WC 19-XIX cWW cW-W 9 B.DG10 C.5CM3 G-c WC 19-XIX cWW cW-W 10 B.DT11 C.DA2 T-A WC 20-XX cWW cW-W **************************************************************************** List of 44 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4r2e A-arg B.DA1 A.ARG430 -8.21 76.57 -7.08 0.78 -4.06 -59.86 -35.80 33.82 2 4r2e G-glu B.DG2 A.GLU427 9.67 146.29 3.74 -1.16 8.84 3.91 78.67 135.93 3 4r2e G-arg B.DG2 A.ARG430 11.10 -147.61 -3.38 10.45 1.65 1.09 57.20 -142.95 4 4r2e C-arg B.DC3 A.ARG424 11.28 -137.72 -4.05 9.22 5.08 15.26 -58.89 -130.56 5 4r2e C-asp B.DC3 A.ASP426 9.54 -154.96 -3.41 6.95 5.57 -28.61 21.07 -153.69 6 4r2e C-glu B.DC3 A.GLU427 8.66 127.04 5.74 -1.79 6.23 19.94 83.38 105.05 7 4r2e C-arg B.DC3 A.ARG430 -10.30 -171.10 0.16 10.21 -1.39 11.22 47.54 -170.22 8 4r2e G-arg B.DG4 A.ARG424 10.96 -173.84 -1.98 10.37 2.96 7.66 -56.19 -173.00 9 4r2e T-his B.DT5 A.HIS397 9.18 -172.96 -7.21 4.62 -3.30 16.02 87.17 -170.15 10 4r2e T-thr B.DT5 A.THR400 10.85 -135.27 -2.74 10.21 2.44 -22.52 49.41 -129.36 11 4r2e T-arg B.DT5 A.ARG424 9.74 157.69 1.20 -9.62 0.98 1.33 61.57 153.97 12 4r2e G-arg B.DG6 A.ARG394 11.06 -145.25 -3.40 10.10 2.97 22.53 -37.80 -142.42 13 4r2e G-his B.DG6 A.HIS397 -9.11 145.02 4.86 -5.50 5.40 25.43 81.73 131.65 14 4r2e G-arg B.DG7 A.ARG372 11.99 -129.17 -6.64 8.76 4.79 -36.86 65.19 -114.55 15 4r2e G-arg B.DG7 A.ARG394 11.12 -176.37 -3.28 10.61 0.62 11.68 -44.92 -176.05 16 4r2e G-asp B.DG7 A.ASP396 -9.30 175.13 -0.77 -9.05 2.00 20.90 -40.31 174.72 17 4r2e G-gln B.DG8 A.GLN369 9.74 157.98 3.78 -2.97 8.47 15.59 77.29 151.37 18 4r2e G-arg B.DG8 A.ARG372 11.21 -153.92 -3.11 10.68 1.39 -16.49 61.89 -149.13 19 4r2e G-arg B.DG8 A.ARG394 -10.86 152.21 1.94 -10.59 -1.35 -4.00 55.87 148.43 20 4r2e C-arg B.5CM9 A.ARG366 10.90 -147.15 -3.46 9.63 3.76 23.73 -34.02 -144.80 21 4r2e C-gln B.5CM9 A.GLN369 8.87 133.15 5.68 -3.45 5.88 37.76 72.87 116.39 22 4r2e C-arg B.5CM9 A.ARG372 -10.51 176.56 -0.62 -10.22 -2.36 -0.43 -61.03 176.01 23 4r2e G-arg B.DG10 A.ARG366 11.14 -172.04 -2.99 10.67 1.13 19.61 -44.40 -171.27 24 4r2e T-arg B.DT11 A.ARG366 -10.16 158.66 1.83 -9.93 -1.12 -8.76 53.51 155.99 25 4r2e T-ser C.DT1 A.SER367 10.69 179.03 7.60 -5.87 -4.69 -55.61 -32.32 178.86 26 4r2e T-asp C.DT1 A.ASP368 9.18 -135.26 -5.76 6.41 3.16 -30.28 52.74 -127.63 27 4r2e A-arg C.DA2 A.ARG366 10.21 -158.77 2.16 9.96 0.70 -15.10 -41.65 -157.06 28 4r2e A-asp C.DA2 A.ASP368 8.72 -160.31 -3.38 8.03 0.34 -0.94 52.23 -158.05 29 4r2e C-arg C.5CM3 A.ARG366 -10.79 175.08 -2.63 -10.37 -1.33 21.54 45.25 174.57 30 4r2e C-asp C.5CM3 A.ASP368 -9.34 178.52 0.89 -8.86 -2.81 -13.03 -43.02 178.40 31 4r2e G-arg C.DG4 A.ARG372 10.60 -178.82 -0.77 10.48 1.44 -7.88 55.39 -178.67 32 4r2e G-asp C.DG4 A.ASP396 8.61 -114.86 -6.11 5.33 2.90 -17.32 30.29 -111.30 33 4r2e C-arg C.DC5 A.ARG372 -11.02 149.21 -3.17 -10.25 -2.51 -5.15 -56.44 144.89 34 4r2e C-arg C.DC5 A.ARG394 -10.76 -144.89 1.29 10.69 0.09 -14.65 -54.22 -140.02 35 4r2e C-asp C.DC5 A.ASP396 -8.87 -148.09 -3.82 7.99 -0.57 -10.17 37.30 -146.12 36 4r2e C-arg C.DC6 A.ARG394 -10.80 -179.32 2.92 10.29 -1.50 -23.28 -57.59 -179.20 37 4r2e C-asp C.DC6 A.ASP396 -9.10 -176.68 -0.68 8.49 -3.20 7.82 28.58 -176.57 38 4r2e C-ser C.DC6 A.SER425 11.03 -139.98 -9.07 5.84 -2.30 50.15 51.32 -130.04 39 4r2e C-asp C.DC7 A.ASP426 8.87 -118.82 -5.45 6.25 3.15 -18.98 39.47 -113.48 40 4r2e A-arg C.DA8 A.ARG424 -9.61 -156.17 1.03 9.51 -0.94 1.25 -54.79 -153.11 41 4r2e A-asp C.DA8 A.ASP426 7.68 -148.60 -3.11 7.02 -0.37 -5.96 38.32 -146.65 42 4r2e C-arg C.DC9 A.ARG424 -10.67 177.06 -1.74 -10.03 -3.21 10.25 59.15 176.61 43 4r2e C-asp C.DC9 A.ASP426 -8.93 -174.48 -0.46 8.23 -3.46 5.43 32.69 -174.24 44 4r2e G-arg C.DG10 A.ARG430 -10.49 168.71 0.18 -10.45 0.88 17.93 -53.78 167.17 **************************************************************************** List of 31 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4r2e AT-arg C.DA8 B.DT5 A.ARG424 -9.68 -156.93 1.11 9.56 -0.96 1.30 -58.18 -153.54 2 4r2e AT-arg C.DA2 B.DT11 A.ARG366 10.19 -158.65 2.00 9.95 0.91 -12.07 -47.65 -156.49 3 4r2e AT-asp C.DA8 B.DT5 A.ASP426 7.70 -148.76 -2.99 7.08 -0.49 -5.78 34.94 -147.16 4 4r2e AT-asp C.DA2 B.DT11 A.ASP368 8.64 -156.80 -3.48 7.91 0.25 0.28 46.42 -154.72 5 4r2e AT-his C.DA8 B.DT5 A.HIS397 -9.09 -164.34 3.31 2.85 -7.97 -7.81 -87.70 -158.16 6 4r2e AT-thr C.DA8 B.DT5 A.THR400 -10.76 134.48 -2.68 -10.07 -2.68 -20.29 -51.87 128.10 7 4r2e GC-arg B.DG2 C.DC11 A.ARG430 10.94 -146.72 -3.44 10.24 1.74 1.98 55.66 -142.21 8 4r2e GC-arg C.DG10 B.DC3 A.ARG424 -11.23 139.78 -3.86 -9.06 -5.39 19.35 57.26 133.11 9 4r2e GC-arg C.DG10 B.DC3 A.ARG430 -10.40 169.89 0.17 -10.33 1.14 14.57 -50.67 168.72 10 4r2e GC-arg B.DG4 C.DC9 A.ARG424 10.82 -175.46 -1.86 10.20 3.08 8.96 -57.66 -174.80 11 4r2e GC-arg B.DG6 C.DC7 A.ARG394 10.99 -146.66 -3.42 9.86 3.46 27.89 -41.32 -143.11 12 4r2e GC-arg B.DG7 C.DC6 A.ARG372 11.84 -127.89 -6.88 8.59 4.38 -34.26 56.94 -116.65 13 4r2e GC-arg B.DG7 C.DC6 A.ARG394 10.96 -178.54 -3.09 10.46 1.05 17.47 -51.27 -178.36 14 4r2e GC-arg B.DG8 C.DC5 A.ARG372 11.12 -151.52 -3.14 10.48 1.97 -10.78 59.26 -146.95 15 4r2e GC-arg B.DG8 C.DC5 A.ARG394 -10.81 148.51 1.62 -10.66 -0.72 -9.33 55.07 144.23 16 4r2e GC-arg C.DG4 B.5CM9 A.ARG366 -10.90 148.42 -3.43 -9.60 -3.86 26.06 38.02 145.60 17 4r2e GC-arg C.DG4 B.5CM9 A.ARG372 10.56 -177.70 -0.70 10.36 1.90 -4.19 58.26 -177.37 18 4r2e GC-arg B.DG10 C.5CM3 A.ARG366 10.96 -173.57 -2.81 10.52 1.23 20.58 -44.82 -172.92 19 4r2e GC-asp C.DG10 B.DC3 A.ASP426 -9.53 153.31 -3.23 -6.83 -5.81 -24.72 -23.42 152.07 20 4r2e GC-asp B.DG4 C.DC9 A.ASP426 9.05 174.85 -0.37 -8.41 3.32 7.64 -33.87 174.60 21 4r2e GC-asp B.DG6 C.DC7 A.ASP426 -8.90 115.79 -5.51 -6.04 -3.52 -13.28 -37.21 111.24 22 4r2e GC-asp B.DG7 C.DC6 A.ASP396 9.20 175.90 -0.74 -8.79 2.62 14.32 -34.49 175.68 23 4r2e GC-asp B.DG8 C.DC5 A.ASP396 -8.85 146.78 -3.72 -8.03 0.09 -3.84 -36.46 144.95 24 4r2e GC-asp C.DG4 B.5CM9 A.ASP396 8.56 -114.07 -6.07 5.13 3.18 -12.63 30.74 -110.80 25 4r2e GC-asp B.DG10 C.5CM3 A.ASP368 9.48 -178.05 0.74 9.05 2.72 -14.83 43.05 -177.88 26 4r2e GC-gln B.DG8 C.DC5 A.GLN369 9.64 153.26 3.58 -2.44 8.61 10.84 76.24 145.63 27 4r2e GC-gln C.DG4 B.5CM9 A.GLN369 -8.89 -129.36 5.61 3.34 -6.03 34.37 -72.74 -111.88 28 4r2e GC-glu B.DG2 C.DC11 A.GLU427 9.55 145.38 3.66 -0.87 8.78 2.29 79.14 134.58 29 4r2e GC-glu C.DG10 B.DC3 A.GLU427 -8.69 -125.36 5.57 1.88 -6.40 19.10 -78.74 -105.73 30 4r2e GC-his B.DG6 C.DC7 A.HIS397 9.00 140.81 4.61 -5.11 5.81 19.86 80.37 126.89 31 4r2e GC-ser B.DG7 C.DC6 A.SER425 -10.95 140.24 -9.01 -6.01 1.61 58.25 -54.35 127.43 **************************************************************************** List of 7 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4r2e OP1@B.DG4 ND1@A.HIS401 2.78 po4:sidechain:salt-bridge 2 4r2e OP1@B.DG7 ND1@A.HIS373 2.69 po4:sidechain:salt-bridge 3 4r2e OP1@B.DG8 NH2@A.ARG362 3.01 po4:sidechain:salt-bridge 4 4r2e OP2@B.DG8 NE2@A.GLN369 3.36 po4:sidechain 5 4r2e O3'@B.DG7 NH2@A.ARG362 3.51 po4:sidechain 6 4r2e OP2@C.DC5 NZ@A.LYS399 2.77 po4:sidechain:salt-bridge 7 4r2e OP2@C.DC6 OG@A.SER425 2.85 po4:sidechain **************************************************************************** List of 13 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4r2e N7@B.DG2 NH2@A.ARG430 2.93 base:sidechain 2 4r2e O6@B.DG2 NH1@A.ARG430 3.00 base:sidechain 3 4r2e N7@B.DG4 NH1@A.ARG424 2.94 base:sidechain 4 4r2e O6@B.DG4 NH2@A.ARG424 2.86 base:sidechain 5 4r2e N7@B.DG6 NE2@A.HIS397 2.86 base:sidechain 6 4r2e N7@B.DG7 NH1@A.ARG394 3.10 base:sidechain 7 4r2e O6@B.DG7 NH2@A.ARG394 2.83 base:sidechain 8 4r2e N7@B.DG8 NH2@A.ARG372 2.81 base:sidechain 9 4r2e O6@B.DG8 NH1@A.ARG372 2.87 base:sidechain 10 4r2e N7@B.DG10 NH1@A.ARG366 2.84 base:sidechain 11 4r2e O6@B.DG10 NH2@A.ARG366 2.82 base:sidechain 12 4r2e N6@C.DA2 OD2@A.ASP368 3.47 base:sidechain 13 4r2e N4@C.DC5 OD2@A.ASP396 2.84 base:sidechain **************************************************************************** List of 8 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4r2e G-arg B.DG2 A.ARG430 0.00 22 2 4r2e G-arg B.DG4 A.ARG424 0.11 29 3 4r2e G-his B.DG6 A.HIS397 0.52 11 4 4r2e G-arg B.DG7 A.ARG394 0.00 10 5 4r2e G-arg B.DG8 A.ARG372 0.02 11 6 4r2e G-arg B.DG10 A.ARG366 0.19 13 7 4r2e A-asp C.DA2 A.ASP368 2.13 16 8 4r2e C-asp C.DC5 A.ASP396 1.08 23 **************************************************************************** List of 5 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4r2e A-arg B.DA1 A.ARG430 3.50 8 2 4r2e C-arg B.DC3 A.ARG424 3.37 16 3 4r2e T-his B.DT5 A.HIS397 3.52 13 4 4r2e G-arg B.DG6 A.ARG394 3.28 8 5 4r2e C-arg B.5CM9 A.ARG366 3.68 7 **************************************************************************** List of 3 additional files 1 -- 4r2e-baseAA-pairs.pdb 2 -- 4r2e-baseAA-stacks.pdb 3 -- 4r2e-pairs.pdb