**************************************************************************** SNAP: a software tool for the characterization of 3D Structures of Nucleic Acid-Protein complexes v1.0.6-2019sep30, by xiangjun@x3dna.org SNAP has been made possible by the NIH grant R01GM096889 (to X.J.Lu). It is being actively maintained and developed. As always, I greatly appreciate your feedback. Please report all SNAP-related issues on the 3DNA Forum (forum.x3dna.org). I strive to respond promptly to any questions posted there. SNAP is free of charge for NON-COMMERCIAL purposes, and it comes with ABSOLUTELY NO WARRANTY. **************************************************************************** Note: By default, each nucleotide/amino-acid is identified by chainId.name#. So a common case would be B.DA1689, meaning adenosine #1689 on chain B. Use the --idstr=long option to get strictly delineated id strings. Command: x3dna-snap -i=5ef6.pdb -o=5ef6.out File name: 5ef6.pdb no. of peptide chains: 4 [A=61,B=61,G=62,J=62] no. of DNA/RNA chains: 8 [C=18,D=18,E=18,F=18,H=18,I=18,K=18,L=18] no. of amino acids: 246 no. of nucleotides: 144 no. of atoms: 5159 no. of waters: 101 no. of metals: 0 **************************************************************************** List of 1 type of 8 modified nucleotides nt count list 1 5CM-c 8 C.5CM11,F.5CM7,D.5CM11,E.5CM7,H.5CM11,I.5CM7,K.5CM11,L.5CM7 **************************************************************************** List of 4 helices 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=18 strand-1 5'-TTGTGTTTTAcGAGGTCC-3' bp-type |.|||||||||||||||| strand-2 3'-AACACAAAATGcTCCAGG-5' helix-form ..BBBBBBBBB....B. 1 C.DT1 F.DA18 T-A WC 20-XX cWW cW-W 2 C.DT2 F.DA17 T+A -- n/a cWH cW+M 3 C.DG3 F.DC16 G-C WC 19-XIX cWW cW-W 4 C.DT4 F.DA15 T-A WC 20-XX cWW cW-W 5 C.DG5 F.DC14 G-C WC 19-XIX cWW cW-W 6 C.DT6 F.DA13 T-A WC 20-XX cWW cW-W 7 C.DT7 F.DA12 T-A WC 20-XX cWW cW-W 8 C.DT8 F.DA11 T-A WC 20-XX cWW cW-W 9 C.DT9 F.DA10 T-A WC 20-XX cWW cW-W 10 C.DA10 F.DT9 A-T WC 20-XX cWW cW-W 11 C.5CM11 F.DG8 c-G WC 19-XIX cWW cW-W 12 C.DG12 F.5CM7 G-c WC 19-XIX cWW cW-W 13 C.DA13 F.DT6 A-T WC 20-XX cWW cW-W 14 C.DG14 F.DC5 G-C WC 19-XIX cWW cW-W 15 C.DG15 F.DC4 G-C WC 19-XIX cWW cW-W 16 C.DT16 F.DA3 T-A WC 20-XX cWW cW-W 17 C.DC17 F.DG2 C-G WC 19-XIX cWW cW-W 18 C.DC18 F.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=17 strand-1 5'-TTGTGTTTTAcGGGTCC-3' bp-type |.||||||||||||||| strand-2 3'-AACACAAAATGcCCAGG-5' helix-form ..BBBBBBBBBx..B. 1 D.DT1 E.DA18 T-A WC 20-XX cWW cW-W 2 D.DT2 E.DA17 T+A -- n/a cWH cW+M 3 D.DG3 E.DC16 G-C WC 19-XIX cWW cW-W 4 D.DT4 E.DA15 T-A WC 20-XX cWW cW-W 5 D.DG5 E.DC14 G-C WC 19-XIX cWW cW-W 6 D.DT6 E.DA13 T-A WC 20-XX cWW cW-W 7 D.DT7 E.DA12 T-A WC 20-XX cWW cW-W 8 D.DT8 E.DA11 T-A WC 20-XX cWW cW-W 9 D.DT9 E.DA10 T-A WC 20-XX cWW cW-W 10 D.DA10 E.DT9 A-T WC 20-XX cWW cW-W 11 D.5CM11 E.DG8 c-G WC 19-XIX cWW cW-W 12 D.DG12 E.5CM7 G-c WC 19-XIX cWW cW-W 13 D.DG14 E.DC5 G-C WC 19-XIX cWW cW-W 14 D.DG15 E.DC4 G-C WC 19-XIX cWW cW-W 15 D.DT16 E.DA3 T-A WC 20-XX cWW cW-W 16 D.DC17 E.DG2 C-G WC 19-XIX cWW cW-W 17 D.DC18 E.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[0] bps=17 strand-1 5'-TTGTGTTTTAcGGGTCC-3' bp-type |.||||||||||||||| strand-2 3'-AACACAAAATGcCCAGG-5' helix-form ..BBBBBBBBBx..B. 1 H.DT1 I.DA18 T-A WC 20-XX cWW cW-W 2 H.DT2 I.DA17 T+A -- n/a cWH cW+M 3 H.DG3 I.DC16 G-C WC 19-XIX cWW cW-W 4 H.DT4 I.DA15 T-A WC 20-XX cWW cW-W 5 H.DG5 I.DC14 G-C WC 19-XIX cWW cW-W 6 H.DT6 I.DA13 T-A WC 20-XX cWW cW-W 7 H.DT7 I.DA12 T-A WC 20-XX cWW cW-W 8 H.DT8 I.DA11 T-A WC 20-XX cWW cW-W 9 H.DT9 I.DA10 T-A WC 20-XX cWW cW-W 10 H.DA10 I.DT9 A-T WC 20-XX cWW cW-W 11 H.5CM11 I.DG8 c-G WC 19-XIX cWW cW-W 12 H.DG12 I.5CM7 G-c WC 19-XIX cWW cW-W 13 H.DG14 I.DC5 G-C WC 19-XIX cWW cW-W 14 H.DG15 I.DC4 G-C WC 19-XIX cWW cW-W 15 H.DT16 I.DA3 T-A WC 20-XX cWW cW-W 16 H.DC17 I.DG2 C-G WC 19-XIX cWW cW-W 17 H.DC18 I.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#4[0] bps=17 strand-1 5'-TTGTGTTTTAcGGGTCC-3' bp-type |.||||||||||||||| strand-2 3'-AACACAAAATGcCCAGG-5' helix-form ..BBBBBBBBBx..B. 1 K.DT1 L.DA18 T-A WC 20-XX cWW cW-W 2 K.DT2 L.DA17 T+A -- n/a cWH cW+M 3 K.DG3 L.DC16 G-C WC 19-XIX cWW cW-W 4 K.DT4 L.DA15 T-A WC 20-XX cWW cW-W 5 K.DG5 L.DC14 G-C WC 19-XIX cWW cW-W 6 K.DT6 L.DA13 T-A WC 20-XX cWW cW-W 7 K.DT7 L.DA12 T-A WC 20-XX cWW cW-W 8 K.DT8 L.DA11 T-A WC 20-XX cWW cW-W 9 K.DT9 L.DA10 T-A WC 20-XX cWW cW-W 10 K.DA10 L.DT9 A-T WC 20-XX cWW cW-W 11 K.5CM11 L.DG8 c-G WC 19-XIX cWW cW-W 12 K.DG12 L.5CM7 G-c WC 19-XIX cWW cW-W 13 K.DG14 L.DC5 G-C WC 19-XIX cWW cW-W 14 K.DG15 L.DC4 G-C WC 19-XIX cWW cW-W 15 K.DT16 L.DA3 T-A WC 20-XX cWW cW-W 16 K.DC17 L.DG2 C-G WC 19-XIX cWW cW-W 17 K.DC18 L.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 56 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5ef6 T-arg C.DT8 A.ARG220 8.84 47.26 -8.83 -0.25 -0.24 -5.27 46.97 0.07 2 5ef6 T-lys C.DT8 A.LYS273 14.75 -144.10 -4.74 13.74 -2.49 1.68 70.93 -135.53 3 5ef6 T-arg C.DT9 A.ARG217 10.42 -74.04 -7.75 -4.33 5.46 31.55 -17.91 -65.68 4 5ef6 T-arg C.DT9 A.ARG220 -8.65 -50.77 -7.23 2.36 -4.12 1.16 35.97 -36.42 5 5ef6 T-asn C.DT9 A.ASN266 9.07 -164.39 -6.10 6.63 -1.01 26.89 64.86 -160.89 6 5ef6 A-arg C.DA10 A.ARG217 -11.08 -101.79 -10.57 -2.39 2.33 17.58 -33.79 -96.29 7 5ef6 A-ile C.DA10 A.ILE262 9.41 177.10 8.19 -4.49 1.16 -19.21 -19.32 177.01 8 5ef6 A-asn C.DA10 A.ASN266 7.90 171.37 3.09 -6.24 -3.73 -44.53 -43.92 169.90 9 5ef6 C-arg C.5CM11 A.ARG217 -12.38 -124.64 -12.34 0.11 -0.94 6.03 -40.25 -120.60 10 5ef6 C-ile C.5CM11 A.ILE262 -9.34 152.80 7.19 -5.48 -2.36 -22.67 -9.56 152.15 11 5ef6 C-gln F.DC5 A.GLN265 11.25 -68.49 -4.86 8.62 5.35 1.13 33.65 -60.54 12 5ef6 T-gln F.DT6 A.GLN265 10.55 -83.86 -2.15 10.21 1.52 0.18 17.89 -82.28 13 5ef6 C-val F.5CM7 A.VAL269 11.14 -122.71 -5.85 8.23 4.71 -35.69 9.99 -119.26 14 5ef6 A-arg F.DA10 A.ARG217 -10.40 69.87 -7.77 4.46 -5.28 29.29 26.21 58.97 15 5ef6 A-arg F.DA11 A.ARG220 -8.94 36.37 -8.84 0.86 1.06 -18.79 -31.12 1.26 16 5ef6 A-arg F.DA12 A.ARG220 -9.54 -48.58 -8.53 3.73 -2.07 -26.94 -20.07 -35.61 17 5ef6 A-arg F.DA13 A.ARG220 -11.99 -85.43 -7.78 7.25 -5.53 -40.34 -11.98 -76.15 18 5ef6 T-arg D.DT8 B.ARG220 8.95 47.40 -8.94 -0.37 -0.04 -6.32 46.97 0.21 19 5ef6 T-lys D.DT8 B.LYS273 15.03 -141.23 -4.84 14.06 -2.17 1.89 64.86 -133.68 20 5ef6 T-arg D.DT9 B.ARG220 -8.52 -47.29 -7.03 2.37 -4.19 3.89 35.40 -31.63 21 5ef6 T-asn D.DT9 B.ASN266 9.43 -168.17 -6.67 6.49 -1.49 31.69 68.54 -165.02 22 5ef6 A-ile D.DA10 B.ILE262 9.49 178.29 8.12 -4.73 1.33 -19.16 -18.88 178.24 23 5ef6 A-asn D.DA10 B.ASN266 7.98 166.32 3.51 -5.94 -4.01 -50.80 -43.52 163.59 24 5ef6 C-ile D.5CM11 B.ILE262 -9.25 149.78 6.95 -5.69 -2.23 -20.03 -7.91 149.23 25 5ef6 C-gln E.DC5 B.GLN265 11.12 -69.57 -5.01 8.48 5.16 2.48 34.27 -61.44 26 5ef6 T-gln E.DT6 B.GLN265 10.11 -83.75 -2.13 9.68 2.02 17.26 20.22 -80.17 27 5ef6 C-val E.5CM7 B.VAL269 11.20 -121.80 -5.68 8.40 4.76 -36.06 10.81 -118.16 28 5ef6 A-arg E.DA11 B.ARG220 -9.07 -34.28 -8.94 1.05 1.10 -15.75 -30.41 -1.46 29 5ef6 A-arg E.DA12 B.ARG220 -9.49 -49.07 -8.48 3.74 -2.04 -26.38 -18.93 -37.30 30 5ef6 A-arg E.DA13 B.ARG220 -11.83 -84.67 -7.68 7.13 -5.49 -40.61 -12.67 -75.02 31 5ef6 T-arg H.DT8 G.ARG220 8.61 49.98 -8.58 0.17 -0.74 -1.04 49.82 4.02 32 5ef6 T-lys H.DT8 G.LYS273 14.97 -142.73 -4.29 14.12 -2.52 4.71 71.26 -133.65 33 5ef6 T-arg H.DT9 G.ARG220 -8.23 -49.00 -6.66 2.47 -4.17 1.72 38.19 -31.25 34 5ef6 T-asn H.DT9 G.ASN266 9.22 -156.70 -5.69 7.24 -0.48 23.60 62.46 -152.01 35 5ef6 A-ile H.DA10 G.ILE262 9.40 176.39 8.12 -4.64 0.97 -17.12 -20.82 176.29 36 5ef6 A-asn H.DA10 G.ASN266 7.86 175.84 2.58 -6.54 -3.51 -39.07 -44.01 175.23 37 5ef6 C-ile H.5CM11 G.ILE262 -9.37 150.24 6.96 -5.66 -2.68 -19.60 -5.99 149.75 38 5ef6 C-gln I.DC5 G.GLN265 11.07 -67.48 -4.93 8.35 5.34 6.19 35.21 -58.21 39 5ef6 T-gln I.DT6 G.GLN265 10.14 -85.76 -2.04 9.83 1.37 2.68 21.06 -83.59 40 5ef6 C-val I.5CM7 G.VAL269 11.00 -122.38 -5.55 8.17 4.86 -34.03 10.60 -119.18 41 5ef6 A-arg I.DA11 G.ARG220 -8.80 -37.69 -8.70 0.53 1.23 -15.61 -33.98 -4.86 42 5ef6 A-arg I.DA12 G.ARG220 -9.24 -52.55 -8.42 3.29 -1.90 -26.45 -23.52 -39.48 43 5ef6 A-arg I.DA13 G.ARG220 -11.61 -89.49 -7.85 6.67 -5.35 -43.36 -17.16 -78.67 44 5ef6 T-arg K.DT8 J.ARG220 8.92 -48.09 -8.91 -0.27 -0.32 -5.71 47.73 -1.29 45 5ef6 T-lys K.DT8 J.LYS273 14.73 -142.80 -4.65 13.76 -2.42 3.35 68.45 -134.59 46 5ef6 T-arg K.DT9 J.ARG220 -8.30 -50.60 -6.97 2.23 -3.92 -0.76 37.41 -34.69 47 5ef6 T-asn K.DT9 J.ASN266 9.42 -161.78 -6.24 6.97 -1.02 26.71 62.24 -158.02 48 5ef6 A-ile K.DA10 J.ILE262 9.47 175.92 8.15 -4.72 0.96 -18.94 -18.50 175.81 49 5ef6 A-asn K.DA10 J.ASN266 7.85 170.83 2.94 -6.26 -3.71 -44.66 -40.61 169.39 50 5ef6 C-ile K.5CM11 J.ILE262 -9.40 149.61 7.09 -5.59 -2.63 -20.30 -6.88 149.06 51 5ef6 C-gln L.DC5 J.GLN265 11.33 -66.69 -4.90 8.65 5.43 1.62 33.32 -58.60 52 5ef6 T-gln L.DT6 J.GLN265 10.27 -85.48 -2.02 10.00 1.20 -2.78 19.50 -83.61 53 5ef6 C-val L.5CM7 J.VAL269 10.99 -120.47 -5.47 8.18 4.89 -32.91 15.01 -117.03 54 5ef6 A-arg L.DA11 J.ARG220 -9.03 -35.59 -8.91 1.04 1.09 -16.31 -31.63 -0.71 55 5ef6 A-arg L.DA12 J.ARG220 -9.39 -49.33 -8.36 3.77 -2.01 -26.86 -21.33 -36.00 56 5ef6 A-arg L.DA13 J.ARG220 -11.81 -86.51 -7.77 6.94 -5.55 -45.04 -13.25 -74.87 **************************************************************************** List of 48 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5ef6 AT-arg F.DA13 C.DT6 A.ARG220 -11.92 -85.45 -7.29 7.85 -5.24 -32.62 -16.24 -78.68 2 5ef6 AT-arg F.DA12 C.DT7 A.ARG220 -9.46 -51.53 -8.29 4.01 -2.15 -20.79 -26.54 -39.55 3 5ef6 AT-arg F.DA11 C.DT8 A.ARG220 -8.89 41.12 -8.85 0.55 0.65 -12.27 -39.24 0.65 4 5ef6 AT-arg F.DA10 C.DT9 A.ARG217 -10.41 71.77 -7.76 4.40 -5.37 30.38 22.05 62.33 5 5ef6 AT-arg F.DA10 C.DT9 A.ARG220 8.51 47.32 -7.07 -2.12 4.23 -1.95 -31.74 35.51 6 5ef6 AT-arg C.DA10 F.DT9 A.ARG217 -11.01 -100.99 -10.45 -2.87 1.91 24.22 -37.91 -92.97 7 5ef6 AT-arg E.DA13 D.DT6 B.ARG220 -11.82 -84.97 -7.28 7.80 -5.08 -31.47 -16.56 -78.48 8 5ef6 AT-arg E.DA12 D.DT7 B.ARG220 -9.38 -52.06 -8.17 4.11 -2.08 -19.65 -25.53 -41.45 9 5ef6 AT-arg E.DA11 D.DT8 B.ARG220 -9.01 -40.44 -8.96 0.70 0.56 -11.29 -38.83 -0.79 10 5ef6 AT-arg E.DA10 D.DT9 B.ARG220 8.54 43.08 -6.90 -2.07 4.59 -1.02 -28.08 32.99 11 5ef6 AT-arg I.DA13 H.DT6 G.ARG220 -11.49 -89.13 -7.43 7.38 -4.73 -32.73 -20.07 -82.05 12 5ef6 AT-arg I.DA12 H.DT7 G.ARG220 -9.16 -55.50 -8.25 3.55 -1.79 -19.17 -29.94 -43.33 13 5ef6 AT-arg I.DA11 H.DT8 G.ARG220 -8.70 -43.25 -8.64 0.18 0.98 -8.63 -42.16 -4.38 14 5ef6 AT-arg I.DA10 H.DT9 G.ARG220 8.14 44.19 -6.44 -2.31 4.42 -0.20 -32.04 30.84 15 5ef6 AT-arg L.DA13 K.DT6 J.ARG220 -11.75 -85.32 -7.31 7.66 -5.09 -34.04 -17.92 -77.69 16 5ef6 AT-arg L.DA12 K.DT7 J.ARG220 -9.29 -51.82 -8.14 4.04 -1.90 -19.51 -27.76 -39.76 17 5ef6 AT-arg L.DA11 K.DT8 J.ARG220 -8.97 41.42 -8.92 0.65 0.70 -11.29 -39.85 0.34 18 5ef6 AT-arg L.DA10 K.DT9 J.ARG220 8.38 46.43 -6.94 -2.04 4.23 -2.16 -31.97 34.06 19 5ef6 AT-asn F.DA10 C.DT9 A.ASN266 -9.13 160.41 -6.25 -6.60 0.88 27.91 -61.10 156.44 20 5ef6 AT-asn C.DA10 F.DT9 A.ASN266 7.88 177.56 3.37 -6.40 -3.13 -49.77 -46.55 177.05 21 5ef6 AT-asn E.DA10 D.DT9 B.ASN266 -9.35 163.29 -6.74 -6.32 1.41 35.26 -61.35 159.47 22 5ef6 AT-asn D.DA10 E.DT9 B.ASN266 7.89 173.10 3.88 -5.96 -3.40 -55.98 -45.93 171.45 23 5ef6 AT-asn I.DA10 H.DT9 G.ASN266 -9.24 152.45 -5.84 -7.16 0.25 26.95 -58.32 147.34 24 5ef6 AT-asn H.DA10 I.DT9 G.ASN266 7.82 -176.15 -2.96 6.70 -2.73 46.32 45.28 -175.44 25 5ef6 AT-asn L.DA10 K.DT9 J.ASN266 -9.33 157.81 -6.41 -6.73 0.81 29.77 -59.11 153.44 26 5ef6 AT-asn K.DA10 L.DT9 J.ASN266 7.83 178.67 3.31 -6.38 -3.12 -51.74 -42.87 178.40 27 5ef6 AT-gln C.DA13 F.DT6 A.GLN265 -10.54 85.43 -2.88 -9.99 -1.74 8.59 -8.74 84.72 28 5ef6 AT-ile C.DA10 F.DT9 A.ILE262 9.40 -177.65 -8.31 4.09 1.61 25.68 20.36 -177.55 29 5ef6 AT-ile D.DA10 E.DT9 B.ILE262 9.52 -175.99 -8.39 4.15 1.75 25.61 18.82 -175.84 30 5ef6 AT-ile H.DA10 I.DT9 G.ILE262 9.41 -177.11 -8.33 4.12 1.48 25.79 20.83 -176.98 31 5ef6 AT-ile K.DA10 L.DT9 J.ILE262 9.49 -177.55 -8.41 4.18 1.34 27.36 18.83 -177.44 32 5ef6 AT-lys F.DA11 C.DT8 A.LYS273 -14.64 137.53 -4.99 -13.63 1.98 4.08 -62.04 129.96 33 5ef6 AT-lys E.DA11 D.DT8 B.LYS273 -14.91 134.32 -5.20 -13.89 1.52 5.31 -57.88 127.27 34 5ef6 AT-lys I.DA11 H.DT8 G.LYS273 -14.93 135.02 -4.82 -14.01 1.84 6.47 -62.48 126.74 35 5ef6 AT-lys L.DA11 K.DT8 J.LYS273 -14.65 135.45 -5.10 -13.62 1.73 5.86 -61.24 127.65 36 5ef6 GC-arg F.DG8 C.5CM11 A.ARG217 12.19 129.15 -12.09 -0.66 1.41 13.54 45.28 124.10 37 5ef6 GC-gln C.DG14 F.DC5 A.GLN265 -11.35 65.68 -5.10 -8.33 -5.78 5.62 -28.31 59.65 38 5ef6 GC-gln D.DG14 E.DC5 B.GLN265 -11.32 64.44 -5.51 -8.29 -5.39 5.85 -26.51 59.01 39 5ef6 GC-gln H.DG14 I.DC5 G.GLN265 -11.30 62.96 -5.52 -8.15 -5.55 8.51 -26.51 57.04 40 5ef6 GC-gln K.DG14 L.DC5 J.GLN265 -11.38 62.66 -5.30 -8.38 -5.58 6.05 -24.88 57.68 41 5ef6 GC-ile F.DG8 C.5CM11 A.ILE262 -9.56 -153.04 7.23 5.99 1.75 -32.00 11.35 -151.79 42 5ef6 GC-ile E.DG8 D.5CM11 B.ILE262 -9.51 -153.51 7.26 5.96 1.46 -30.65 10.63 -152.39 43 5ef6 GC-ile I.DG8 H.5CM11 G.ILE262 -9.54 -153.18 7.21 5.97 1.83 -31.87 9.73 -151.98 44 5ef6 GC-ile L.DG8 K.5CM11 J.ILE262 -9.64 -152.84 7.34 5.95 1.89 -32.52 9.88 -151.58 45 5ef6 GC-val C.DG12 F.5CM7 A.VAL269 -11.21 121.96 -6.12 -8.14 -4.69 -29.92 -3.78 119.68 46 5ef6 GC-val D.DG12 E.5CM7 B.VAL269 -11.25 122.15 -5.95 -8.33 -4.66 -30.29 -2.70 119.84 47 5ef6 GC-val H.DG12 I.5CM7 G.VAL269 -11.19 121.74 -5.86 -8.15 -4.93 -28.87 -4.22 119.60 48 5ef6 GC-val K.DG12 L.5CM7 J.VAL269 -11.15 121.79 -5.64 -8.27 -4.91 -28.73 -6.64 119.61 **************************************************************************** List of 57 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ef6 OP1@C.DT8 NZ@A.LYS270 2.79 po4:sidechain:salt-bridge 2 5ef6 OP1@C.DT9 N@A.TYR223 2.89 po4:backbone 3 5ef6 OP2@C.DT9 NE1@A.TRP263 3.59 po4:sidechain 4 5ef6 O3'@C.DT8 NH1@A.ARG220 3.78 po4:sidechain 5 5ef6 OP1@C.DA10 N@A.ILE221 3.56 po4:backbone 6 5ef6 OP2@C.DA10 OH@A.TYR223 2.66 po4:sidechain 7 5ef6 OP2@C.DA10 NE2@A.GLN259 2.97 po4:sidechain 8 5ef6 OP1@C.DC17 N@J.LYS243 2.76 po4:backbone 9 5ef6 OP1@F.DC4 NZ@A.LYS243 2.74 po4:sidechain:salt-bridge 10 5ef6 OP1@F.DC4 NH2@A.ARG246 2.68 po4:sidechain:salt-bridge 11 5ef6 OP1@F.DC5 NH2@A.ARG268 3.53 po4:sidechain:salt-bridge 12 5ef6 OP2@F.DC5 NE2@A.GLN265 2.82 po4:sidechain 13 5ef6 OP1@F.DT6 NE@A.ARG268 2.75 po4:sidechain:salt-bridge 14 5ef6 OP2@F.DT6 NH2@A.ARG268 2.70 po4:sidechain:salt-bridge 15 5ef6 OP1@D.DT8 NZ@B.LYS270 2.58 po4:sidechain:salt-bridge 16 5ef6 OP1@D.DT9 N@B.TYR223 2.94 po4:backbone 17 5ef6 OP2@D.DT9 NE1@B.TRP263 3.60 po4:sidechain 18 5ef6 O3'@D.DT8 NH1@B.ARG220 3.93 po4:sidechain 19 5ef6 OP1@D.DA10 N@B.ILE221 3.65 po4:backbone 20 5ef6 OP2@D.DA10 OH@B.TYR223 2.49 po4:sidechain 21 5ef6 OP2@D.DA10 NE2@B.GLN259 2.93 po4:sidechain 22 5ef6 OP1@D.DC17 N@G.LYS243 2.80 po4:backbone 23 5ef6 OP1@E.DC4 NZ@B.LYS243 2.82 po4:sidechain:salt-bridge 24 5ef6 OP1@E.DC4 NH2@B.ARG246 2.69 po4:sidechain:salt-bridge 25 5ef6 OP2@E.DC5 NE2@B.GLN265 2.94 po4:sidechain 26 5ef6 OP1@E.DT6 NE@B.ARG268 2.77 po4:sidechain:salt-bridge 27 5ef6 OP2@E.DT6 NH2@B.ARG268 2.83 po4:sidechain:salt-bridge 28 5ef6 OP1@E.5CM7 NZ@B.LYS272 3.40 po4:sidechain:salt-bridge 29 5ef6 OP1@H.DT8 NZ@G.LYS270 2.79 po4:sidechain:salt-bridge 30 5ef6 OP1@H.DT9 N@G.TYR223 2.80 po4:backbone 31 5ef6 OP2@H.DT9 NE1@G.TRP263 3.65 po4:sidechain 32 5ef6 O3'@H.DT8 NH1@G.ARG220 3.46 po4:sidechain 33 5ef6 OP1@H.DA10 N@G.ILE221 3.72 po4:backbone 34 5ef6 OP2@H.DA10 OH@G.TYR223 2.49 po4:sidechain 35 5ef6 OP2@H.DA10 NE2@G.GLN259 2.90 po4:sidechain 36 5ef6 OP2@H.5CM11 NH2@G.ARG258 2.22 po4:sidechain:salt-bridge 37 5ef6 OP1@H.DC17 N@B.LYS243 2.94 po4:backbone 38 5ef6 OP1@I.DC4 NZ@G.LYS243 2.57 po4:sidechain:salt-bridge 39 5ef6 OP1@I.DC4 NH2@G.ARG246 2.68 po4:sidechain:salt-bridge 40 5ef6 O3'@I.DA3 NZ@G.LYS243 3.34 po4:sidechain 41 5ef6 OP2@I.DC5 NE2@G.GLN265 2.72 po4:sidechain 42 5ef6 OP1@I.DT6 NE@G.ARG268 2.94 po4:sidechain:salt-bridge 43 5ef6 OP2@I.DT6 NH2@G.ARG268 2.64 po4:sidechain:salt-bridge 44 5ef6 OP1@K.DT8 NZ@J.LYS270 2.80 po4:sidechain:salt-bridge 45 5ef6 OP1@K.DT9 N@J.TYR223 2.83 po4:backbone 46 5ef6 OP2@K.DT9 NE1@J.TRP263 3.61 po4:sidechain 47 5ef6 O3'@K.DT8 NH1@J.ARG220 3.78 po4:sidechain 48 5ef6 OP1@K.DA10 N@J.ILE221 3.54 po4:backbone 49 5ef6 OP2@K.DA10 OH@J.TYR223 2.55 po4:sidechain 50 5ef6 OP2@K.DA10 NE2@J.GLN259 2.98 po4:sidechain 51 5ef6 O3'@K.DT9 N@J.ILE221 3.55 po4:backbone 52 5ef6 OP1@K.DC17 N@A.LYS243 2.83 po4:backbone 53 5ef6 OP1@L.DC4 NZ@J.LYS243 2.68 po4:sidechain:salt-bridge 54 5ef6 OP1@L.DC4 NH2@J.ARG246 2.66 po4:sidechain:salt-bridge 55 5ef6 OP2@L.DC5 NE2@J.GLN265 2.93 po4:sidechain 56 5ef6 OP1@L.DT6 NE@J.ARG268 2.94 po4:sidechain:salt-bridge 57 5ef6 OP2@L.DT6 NH2@J.ARG268 2.66 po4:sidechain:salt-bridge **************************************************************************** List of 9 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ef6 O4'@C.DT9 NH1@A.ARG220 3.29 sugar:sidechain 2 5ef6 O4'@C.5CM11 NH1@A.ARG217 2.84 sugar:sidechain 3 5ef6 O4'@F.DA13 NH2@A.ARG220 2.74 sugar:sidechain 4 5ef6 O4'@D.DT9 NH1@B.ARG220 3.30 sugar:sidechain 5 5ef6 O4'@E.DA13 NH2@B.ARG220 2.72 sugar:sidechain 6 5ef6 O4'@H.DT9 NH1@G.ARG220 3.45 sugar:sidechain 7 5ef6 O4'@I.DA13 NH2@G.ARG220 2.85 sugar:sidechain 8 5ef6 O4'@K.DT9 NH1@J.ARG220 3.33 sugar:sidechain 9 5ef6 O4'@L.DA13 NH2@J.ARG220 2.76 sugar:sidechain **************************************************************************** List of 17 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5ef6 O2@C.DT8 NE@A.ARG220 3.38 base:sidechain 2 5ef6 N7@C.DA10 ND2@A.ASN266 3.13 base:sidechain 3 5ef6 N6@C.DA10 OD1@A.ASN266 3.55 base:sidechain 4 5ef6 N3@C.DA10 NH1@A.ARG217 2.57 base:sidechain 5 5ef6 N3@F.DA10 NH2@A.ARG217 3.10 base:sidechain 6 5ef6 N3@F.DA12 NE@A.ARG220 2.69 base:sidechain 7 5ef6 O2@D.DT8 NE@B.ARG220 3.39 base:sidechain 8 5ef6 N7@D.DA10 ND2@B.ASN266 3.44 base:sidechain 9 5ef6 N6@D.DA10 OD1@B.ASN266 3.46 base:sidechain 10 5ef6 N3@E.DA12 NE@B.ARG220 2.59 base:sidechain 11 5ef6 N7@H.DA10 ND2@G.ASN266 3.20 base:sidechain 12 5ef6 N6@H.DA10 OD1@G.ASN266 3.20 base:sidechain 13 5ef6 N3@I.DA12 NE@G.ARG220 2.78 base:sidechain 14 5ef6 O2@K.DT8 NE@J.ARG220 3.48 base:sidechain 15 5ef6 N7@K.DA10 ND2@J.ASN266 3.15 base:sidechain 16 5ef6 N6@K.DA10 OD1@J.ASN266 3.19 base:sidechain 17 5ef6 N3@L.DA12 NE@J.ARG220 2.54 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5ef6 A-asn C.DA10 A.ASN266 0.77 40 2 5ef6 A-asn D.DA10 B.ASN266 0.28 37 3 5ef6 A-asn H.DA10 G.ASN266 1.13 29 4 5ef6 A-asn K.DA10 J.ASN266 0.38 26 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5ef6 T-asn C.DT9 A.ASN266 3.68 30 2 5ef6 T-asn D.DT9 B.ASN266 3.03 26 3 5ef6 T-asn H.DT9 G.ASN266 4.29 24 4 5ef6 T-asn K.DT9 J.ASN266 3.71 17