3DNA Forum

Questions and answers => DNA/RNA-protein interactions (SNAP) => Topic started by: xiangjun on May 05, 2014, 01:22:59 am

Title: SNAP: software for characterizing DNA-protein interactions
Post by: xiangjun on May 05, 2014, 01:22:59 am: DNA/RNA-protein interactions underpin fundamental biological processes such as transcription, splicing, and translation. The increasing number of experimentally determined 3D structures of nucleic acid-protein complexes provides unprecedented opportunities to decipher the underlying principles governing the process of DNA/RNA-protein recognition. Existing bioinformatics tools are fragmented, with limited scope or usability. We have developed SNAP, a new 3DNA program for the characterization of 3D Structures of Nucleic Acid-Protein complexes. SNAP consolidates, refines, and significantly extends 3DNA's functionality for DNA-protein structural analysis.

Starting from a structure of a DNA-protein complex in PDB or PDBx/mmCIF format, SNAP automatically detects double-helical regions consisting of either canonical or non-canonical base-pairs using DSSR, and categorizes protein into secondary structural units (alpha-helices, beta-sheets, turns, and loops) using DSSP. The program aims to characterize DNA/RNA-protein interactions by checking all combinations between the two components: major groove, minor groove, and backbone for DNA/RNA, versus each alpha-helix, beta-sheet, turn, and loop for protein. SNAP recognizes and outputs base-amino-acid H-bonding and stacking interactions. To quantify the relative spatial relationship between interacting amino acids and bases, SNAP defines a local amino-acid reference frame in the side chain, and takes advantage of the standard base reference frame (see figures below). SNAP calculates all six rigid-body parameters to allow for the analysis of large sets of DNA/RNA-protein complexes consistently and rigorously.

Implemented in ANSI C as a standalone command-line program, SNAP follows the same minimalist design as DSSR (http://goo.gl/ap12xJ). It is tiny (executables are about 1MB) and self-contained, with zero runtime dependencies on third party libraries or configurations. The program is currently under active development, and your feedback will make a difference!

SNAP has been integrated into DSSR, and is available from the Columbia Technology Ventures (CTV) website (http://innovation.columbia.edu/technologies/CU20391).

Release history (in reverse chronological order) (http://forum.x3dna.org/dna-protein-interactions/snap-revision-history/)

List of users who has helped improve SNAP by reporting bugs, making comments/suggestions etc:
Auffinger (http://forum.x3dna.org/profile/?u=7); jdbrown444 (http://forum.x3dna.org/profile/?u=5949); ldfinger (http://forum.x3dna.org/profile/?u=4638); miaozhichao (http://forum.x3dna.org/profile/?u=6605); Phosphoserine (http://forum.x3dna.org/profile/?u=7020); jms89 (http://forum.x3dna.org/profile/?u=6290)

-- Xiang-Jun

Note: please start a new topic with a more specific title; do not post directly below this announcement.

Abbreviations used: AA: amino acid; BP: base-pair

(http://forum.x3dna.org/images/aa-frame.png)

(http://forum.x3dna.org/images/GC_Arg.png)

Here is a sample run on 1oct (http://www.rcsb.org/pdb/explore/explore.do?structureId=1oct) (see x3dna-snap -h for more info), the crystal structure of the Oct-1 POU domain bound to an octamer site solved by Pabo et al.:

Code: [Select]
Run: x3dna-snap --time-stamp=off --interface -i=1oct.pdb -o=1oct.out **************************************************************************** SNAP: a software tool for the characterization of 3D Structures of Nucleic Acid-Protein complexes v1.0.7-2020sep09, 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=1oct.pdb -o=1oct.out --interface --type=either File name: 1oct.pdb no. of peptide chains: 1 [C=131] no. of DNA/RNA chains: 2 [A=15,B=15] no. of amino acids: 131 no. of nucleotides: 30 no. of atoms: 1670 no. of waters: 0 no. of metals: 0 **************************************************************************** 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=14 strand-1 5'-GTATGCAAATAAGG-3' bp-type |||||||||||||| strand-2 3'-CATACGTTTATTCC-5' helix-form BBBBBBBBBBBBB 1 A.DG202 B.DC230 G-C WC 19-XIX cWW cW-W 2 A.DT203 B.DA229 T-A WC 20-XX cWW cW-W 3 A.DA204 B.DT228 A-T WC 20-XX cWW cW-W 4 A.DT205 B.DA227 T-A WC 20-XX cWW cW-W 5 A.DG206 B.DC226 G-C WC 19-XIX cWW cW-W 6 A.DC207 B.DG225 C-G WC 19-XIX cWW cW-W 7 A.DA208 B.DT224 A-T WC 20-XX cWW cW-W 8 A.DA209 B.DT223 A-T WC 20-XX cWW cW-W 9 A.DA210 B.DT222 A-T WC 20-XX cWW cW-W 10 A.DT211 B.DA221 T-A WC 20-XX cWW cW-W 11 A.DA212 B.DT220 A-T WC 20-XX cWW cW-W 12 A.DA213 B.DT219 A-T WC 20-XX cWW cW-W 13 A.DG214 B.DC218 G-C WC 19-XIX cWW cW-W 14 A.DG215 B.DC217 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 77 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 1oct G-thr A.DG202 C.THR26 12.73 -38.52 -6.47 10.19 4.03 -24.59 26.49 -13.54 2 1oct T-arg A.DT203 C.ARG20 19.41 -111.23 -15.89 8.93 6.68 -43.44 -11.44 -104.66 3 1oct T-ile A.DT203 C.ILE21 -17.63 -139.08 -13.56 5.93 -9.58 -15.64 62.29 -131.25 4 1oct T-thr A.DT203 C.THR26 -13.42 -56.68 -2.74 13.12 0.78 -17.93 32.10 -43.91 5 1oct T-gln A.DT203 C.GLN27 12.54 -132.49 -5.55 8.99 6.76 21.85 -81.09 -114.36 6 1oct T-gln A.DT203 C.GLN44 10.67 -115.42 -4.72 9.57 -0.05 65.02 27.06 -98.34 7 1oct T-ser A.DT203 C.SER48 11.31 -84.75 -8.12 6.44 4.54 29.42 7.18 -80.13 8 1oct A-lys A.DA204 C.LYS17 -18.07 175.87 14.34 -7.08 -8.42 7.85 -46.15 175.49 9 1oct A-gln A.DA204 C.GLN27 -11.98 163.47 5.68 -8.28 -6.55 20.04 -87.74 156.55 10 1oct A-gln A.DA204 C.GLN44 8.90 -147.71 -1.25 8.28 -3.00 62.13 -4.03 -142.09 11 1oct A-ser A.DA204 C.SER48 10.01 -126.61 -5.86 8.07 0.89 21.11 -7.37 -125.49 12 1oct A-glu A.DA204 C.GLU51 14.87 -145.96 -11.08 8.90 -4.38 87.37 -5.57 -132.18 13 1oct T-thr A.DT205 C.THR45 6.48 -148.19 -1.00 5.50 3.28 -35.77 2.63 -146.52 14 1oct T-ser A.DT205 C.SER48 -10.33 -151.96 -5.14 8.73 -2.03 28.42 -17.90 -150.69 15 1oct G-thr A.DG206 C.THR45 -7.46 178.53 -1.92 -7.19 0.56 34.46 -11.97 178.45 16 1oct G-arg A.DG206 C.ARG49 -11.02 175.51 3.67 -9.94 3.04 54.67 -28.85 174.77 17 1oct C-arg A.DC207 C.ARG49 -10.55 130.65 -1.73 -10.40 0.39 42.89 -25.07 125.22 18 1oct C-arg A.DC207 C.ARG105 10.64 61.56 -9.91 -3.22 2.16 3.33 59.24 17.22 19 1oct A-arg A.DA208 C.ARG105 10.98 -45.39 -10.37 -1.40 -3.30 18.22 38.36 -16.42 20 1oct A-arg A.DA208 C.ARG113 17.53 -87.05 -14.54 6.53 -7.31 61.91 23.81 -59.97 21 1oct A-arg A.DA209 C.ARG102 12.96 -64.64 -12.42 -3.69 0.50 19.39 38.44 -49.42 22 1oct A-arg A.DA209 C.ARG105 -10.54 -77.58 -9.01 0.77 -5.43 32.27 40.40 -59.98 23 1oct A-thr A.DA209 C.THR106 -12.45 76.08 -4.46 10.70 4.55 -24.22 -70.81 14.79 24 1oct A-ile A.DA209 C.ILE108 -14.17 -36.15 -5.74 12.87 -1.43 -1.65 -27.04 -24.16 25 1oct A-arg A.DA209 C.ARG113 -16.89 -120.22 -11.02 8.88 -9.21 63.56 10.27 -107.85 26 1oct A-trp A.DA209 C.TRP148 11.47 103.87 6.57 5.65 7.52 2.91 44.45 96.44 27 1oct A-asn A.DA209 C.ASN151 9.24 -165.14 -6.41 6.54 -1.24 44.17 60.06 -161.30 28 1oct A-lys A.DA209 C.LYS155 12.02 116.35 8.46 -4.66 7.15 1.16 62.24 103.95 29 1oct A-arg A.DA210 C.ARG102 13.00 -90.23 -12.62 -0.84 -3.03 31.67 30.70 -80.82 30 1oct A-lys A.DA210 C.LYS103 -13.17 -49.41 -7.21 9.69 5.25 -32.94 -36.47 -5.27 31 1oct A-lys A.DA210 C.LYS104 -14.22 106.94 5.65 12.26 -4.48 29.91 64.97 85.63 32 1oct A-arg A.DA210 C.ARG105 -12.13 -102.76 -8.14 2.20 -8.71 44.67 29.25 -91.36 33 1oct A-thr A.DA210 C.THR106 -13.69 -77.72 -3.34 13.06 2.39 -41.68 -63.09 -19.46 34 1oct A-val A.DA210 C.VAL144 12.95 98.31 5.37 9.78 6.57 9.45 78.15 64.48 35 1oct A-val A.DA210 C.VAL147 9.50 177.54 8.35 -4.40 1.13 -31.38 -26.50 177.38 36 1oct A-asn A.DA210 C.ASN151 7.95 169.39 3.58 -6.02 -3.76 -61.24 -46.91 166.41 37 1oct T-arg A.DT211 C.ARG102 -14.28 -123.19 -12.66 2.15 -6.23 35.07 24.54 -118.55 38 1oct T-lys A.DT211 C.LYS103 -14.60 -59.01 -4.92 13.51 2.53 -42.55 -18.37 -37.59 39 1oct T-val A.DT211 C.VAL147 -9.12 143.26 7.02 -5.17 -2.68 -31.13 -15.46 141.43 40 1oct C-ser B.DC217 C.SER128 -15.00 -66.88 -9.78 8.86 -7.13 36.24 36.65 -44.16 41 1oct C-lys B.DC217 C.LYS142 18.35 -89.91 -7.88 15.79 -5.07 36.13 69.78 -47.78 42 1oct C-arg B.DC217 C.ARG146 14.28 -55.97 -8.39 11.34 2.24 15.64 47.13 -26.68 43 1oct C-lys B.DC218 C.LYS125 15.78 -137.92 -15.08 2.61 -3.83 11.82 49.06 -133.24 44 1oct C-arg B.DC218 C.ARG146 13.18 -86.99 -2.76 12.86 -0.85 32.48 47.52 -68.28 45 1oct C-cys B.DC218 C.CYS150 11.54 -63.48 -5.57 8.38 5.65 2.43 35.14 -53.68 46 1oct C-arg B.DC218 C.ARG153 14.95 -110.67 -12.78 7.73 0.61 48.20 62.91 -84.80 47 1oct T-lys B.DT219 C.LYS125 -16.35 -155.82 -12.71 6.20 -8.22 28.65 34.22 -153.83 48 1oct T-cys B.DT219 C.CYS150 10.66 -81.40 -2.86 10.10 1.89 8.36 20.66 -78.81 49 1oct T-arg B.DT219 C.ARG153 13.68 -118.82 -9.41 9.25 -3.59 61.30 38.84 -101.70 50 1oct T-lys B.DT220 C.LYS157 15.34 -128.23 -11.99 9.55 0.74 26.77 7.97 -126.53 51 1oct T-ser B.DT223 C.SER56 13.43 -172.88 -11.81 5.85 2.61 78.96 -41.85 -169.98 52 1oct T-lys B.DT223 C.LYS58 -15.63 -104.26 -10.08 8.56 -8.32 47.88 32.02 -91.06 53 1oct T-asn B.DT223 C.ASN59 13.38 -79.77 -9.24 8.66 4.33 -40.87 3.90 -69.96 54 1oct T-lys B.DT223 C.LYS62 16.93 -82.77 -14.55 8.20 -2.75 16.71 20.50 -79.16 55 1oct T-arg B.DT223 C.ARG102 12.45 46.89 -11.36 4.59 2.22 27.19 -16.42 34.94 56 1oct T-phe B.DT224 C.PHE42 13.51 37.27 -1.91 12.27 5.32 -1.35 5.84 36.80 57 1oct T-thr B.DT224 C.THR46 10.40 140.67 5.66 1.06 8.65 -28.39 38.51 136.80 58 1oct T-arg B.DT224 C.ARG49 12.06 -116.46 -5.79 10.20 2.79 24.96 60.01 -102.74 59 1oct T-leu B.DT224 C.LEU55 11.64 144.35 9.48 -3.62 -5.72 -19.44 -72.43 134.61 60 1oct T-asn B.DT224 C.ASN59 -13.74 -111.77 -6.97 11.83 0.55 -36.46 15.99 -106.76 61 1oct T-lys B.DT224 C.LYS62 -17.62 -117.67 -12.18 11.04 -6.35 23.45 13.68 -115.67 62 1oct T-leu B.DT224 C.LEU63 16.98 -113.68 -11.93 10.63 5.74 -60.86 16.39 -100.17 63 1oct T-arg B.DT224 C.ARG102 -14.08 -32.87 -11.42 8.12 -1.33 20.82 -25.38 -1.63 64 1oct T-arg B.DT224 C.ARG105 10.20 47.44 -9.49 1.43 3.47 32.81 -33.87 5.35 65 1oct G-asp B.DG225 C.ASP41 -15.79 -162.72 -12.41 2.27 9.49 -41.38 -74.71 -156.40 66 1oct G-phe B.DG225 C.PHE42 12.92 10.20 2.40 12.63 1.36 -9.66 3.27 0.08 67 1oct G-ser B.DG225 C.SER43 10.76 -127.61 -8.48 6.55 -1.00 -33.95 77.50 -106.70 68 1oct G-thr B.DG225 C.THR45 8.31 -141.05 -5.19 5.96 2.57 27.42 16.56 -139.41 69 1oct G-thr B.DG225 C.THR46 9.41 109.20 7.44 -0.06 5.76 -23.33 51.56 97.72 70 1oct G-arg B.DG225 C.ARG49 10.84 -140.82 -1.39 10.75 -0.00 40.74 39.22 -135.24 71 1oct G-arg B.DG225 C.ARG102 -14.97 -49.97 -8.82 10.75 -5.55 3.36 -36.30 -34.77 72 1oct G-arg B.DG225 C.ARG105 -10.31 -55.06 -9.54 3.91 -0.13 12.03 -47.33 -26.24 73 1oct C-thr B.DC226 C.THR45 -7.82 -173.77 -2.54 7.16 -1.83 17.56 14.19 -173.64 74 1oct C-lys B.DC226 C.LYS104 -14.16 152.22 13.16 2.51 -4.59 66.99 37.28 144.36 75 1oct C-arg B.DC226 C.ARG105 -11.37 -65.61 -8.90 6.45 -2.94 -3.39 -34.34 -56.68 76 1oct A-thr B.DA227 C.THR45 -6.83 150.54 -0.53 -5.80 -3.56 -38.91 -1.49 148.71 77 1oct A-ser B.DA227 C.SER107 -13.93 120.59 3.63 1.86 -13.32 63.52 -38.15 103.24 **************************************************************************** List of 71 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 1oct AT-arg B.DA229 A.DT203 C.ARG20 -19.52 117.19 -15.97 -9.33 -6.22 -41.53 15.52 111.52 2 1oct AT-arg A.DA208 B.DT224 C.ARG49 -12.01 110.94 -6.48 -9.84 -2.30 21.51 -51.98 100.00 3 1oct AT-arg A.DA208 B.DT224 C.ARG102 14.29 -31.63 -11.90 -7.65 1.98 13.43 28.49 -2.95 4 1oct AT-arg A.DA208 B.DT224 C.ARG105 -10.59 -45.43 -9.93 -1.42 -3.39 25.50 36.06 -10.92 5 1oct AT-arg A.DA208 B.DT224 C.ARG113 17.31 -90.85 -14.39 6.97 -6.64 70.13 25.78 -55.99 6 1oct AT-arg A.DA209 B.DT223 C.ARG102 12.71 -54.74 -11.96 -4.19 -0.89 23.07 27.36 -42.12 7 1oct AT-arg A.DA209 B.DT223 C.ARG105 -10.29 -68.58 -8.18 0.74 -6.21 36.66 30.50 -50.81 8 1oct AT-arg A.DA209 B.DT223 C.ARG113 -16.87 -116.63 -10.50 9.30 -9.38 73.35 5.41 -98.06 9 1oct AT-arg A.DA210 B.DT222 C.ARG102 -13.20 -84.60 -12.59 -1.35 -3.71 32.25 24.46 -75.94 10 1oct AT-arg A.DA210 B.DT222 C.ARG105 -12.11 -97.17 -7.84 1.95 -9.02 45.82 23.66 -85.44 11 1oct AT-arg B.DA221 A.DT211 C.ARG102 14.18 115.79 -11.93 -1.95 7.41 37.89 -13.80 111.03 12 1oct AT-arg A.DA213 B.DT219 C.ARG153 -13.63 118.33 -9.60 -9.00 3.57 62.96 -35.71 101.15 13 1oct AT-asn A.DA208 B.DT224 C.ASN59 13.52 112.55 -7.23 -11.42 0.14 -38.45 -7.03 107.81 14 1oct AT-asn A.DA209 B.DT223 C.ASN59 -13.39 77.54 -9.96 -8.07 -3.88 -34.03 7.88 70.36 15 1oct AT-asn A.DA209 B.DT223 C.ASN151 9.34 -156.07 -6.69 6.48 -0.66 53.59 59.89 -148.51 16 1oct AT-asn A.DA210 B.DT222 C.ASN151 7.73 175.46 3.73 -5.97 -3.21 -66.31 -46.20 174.04 17 1oct AT-cys A.DA213 B.DT219 C.CYS150 -10.45 82.10 -3.17 -9.77 -1.89 9.43 -17.73 80.04 18 1oct AT-gln B.DA229 A.DT203 C.GLN27 -12.65 160.63 -11.13 -5.09 3.19 -44.88 -77.69 152.54 19 1oct AT-gln B.DA229 A.DT203 C.GLN44 -10.82 115.12 -4.79 -9.70 -0.08 67.58 -19.25 98.01 20 1oct AT-gln A.DA204 B.DT228 C.GLN27 -11.93 166.48 5.68 -8.49 -6.16 16.93 -84.96 161.38 21 1oct AT-gln A.DA204 B.DT228 C.GLN44 8.85 -145.35 -1.20 8.29 -2.86 64.97 -7.53 -138.55 22 1oct AT-glu A.DA204 B.DT228 C.GLU51 14.79 -90.29 -0.94 12.66 7.59 -40.17 80.28 -10.94 23 1oct AT-ile B.DA229 A.DT203 C.ILE21 17.69 140.07 -13.19 -6.51 9.84 -9.96 -57.42 133.98 24 1oct AT-ile A.DA209 B.DT223 C.ILE108 -14.05 -45.00 -5.64 12.74 -1.80 1.85 -39.75 -21.44 25 1oct AT-leu A.DA208 B.DT224 C.LEU55 -11.39 -149.57 9.27 3.36 5.69 -23.35 66.87 -142.43 26 1oct AT-leu A.DA208 B.DT224 C.LEU63 16.88 116.53 -12.54 -10.40 -4.43 -63.20 -7.65 103.50 27 1oct AT-lys A.DA204 B.DT228 C.LYS17 -18.00 178.12 14.14 -7.20 -8.51 4.21 -42.94 177.98 28 1oct AT-lys A.DA208 B.DT224 C.LYS62 17.46 113.44 -12.10 -10.36 7.14 21.84 -5.49 111.96 29 1oct AT-lys A.DA209 B.DT223 C.LYS58 15.58 97.17 -9.91 -8.49 8.52 54.71 -24.55 80.41 30 1oct AT-lys A.DA209 B.DT223 C.LYS62 16.98 76.57 -14.77 -7.60 3.52 23.46 -10.58 72.75 31 1oct AT-lys A.DA209 B.DT223 C.LYS155 12.22 111.66 8.02 -4.08 8.28 -9.80 54.07 101.45 32 1oct AT-lys A.DA210 B.DT222 C.LYS103 -13.29 -56.30 -7.88 9.58 4.78 -35.38 -43.65 -3.71 33 1oct AT-lys A.DA210 B.DT222 C.LYS104 -14.28 103.49 5.38 12.13 -5.25 22.30 62.89 84.32 34 1oct AT-lys B.DA221 A.DT211 C.LYS103 14.53 67.18 -5.13 -13.50 -1.59 -46.94 30.72 38.56 35 1oct AT-lys A.DA212 B.DT220 C.LYS157 -15.24 126.42 -12.14 -9.18 -0.66 26.14 -7.61 124.74 36 1oct AT-lys A.DA213 B.DT219 C.LYS125 16.19 156.20 -12.64 -6.01 8.15 31.37 -32.17 154.22 37 1oct AT-phe A.DA208 B.DT224 C.PHE42 -13.70 -40.01 -2.53 -12.67 -4.56 -10.22 -4.94 -38.43 38 1oct AT-ser B.DA229 A.DT203 C.SER48 -11.58 87.13 -8.41 -6.64 -4.39 30.60 0.15 82.61 39 1oct AT-ser A.DA204 B.DT228 C.SER48 9.93 -125.38 -5.92 7.94 0.78 23.33 -11.93 -123.79 40 1oct AT-ser B.DA227 A.DT205 C.SER48 10.37 152.19 -4.85 -8.92 2.09 26.76 18.96 150.98 41 1oct AT-ser B.DA227 A.DT205 C.SER107 -13.72 120.33 3.45 2.22 -13.09 64.99 -38.86 101.87 42 1oct AT-ser A.DA209 B.DT223 C.SER56 -13.35 90.10 -4.50 -12.57 0.15 -6.23 -78.04 48.75 43 1oct AT-thr B.DA229 A.DT203 C.THR26 13.45 58.18 -2.51 -13.19 -0.70 -17.63 -26.42 49.39 44 1oct AT-thr B.DA227 A.DT205 C.THR45 -6.65 149.36 -0.76 -5.65 -3.42 -37.34 -2.05 147.61 45 1oct AT-thr A.DA208 B.DT224 C.THR46 -10.47 -143.48 5.83 -1.89 -8.49 -35.34 -44.18 -138.31 46 1oct AT-thr A.DA209 B.DT223 C.THR106 -12.24 88.85 -4.96 10.54 3.77 -23.98 -84.29 16.44 47 1oct AT-thr A.DA210 B.DT222 C.THR106 -13.61 -84.35 -3.84 12.88 2.19 -42.84 -70.72 -18.40 48 1oct AT-trp A.DA209 B.DT223 C.TRP148 11.45 101.29 6.02 6.18 7.54 -7.55 35.76 96.20 49 1oct AT-val A.DA210 B.DT222 C.VAL144 12.90 94.14 4.85 10.35 5.99 2.43 74.57 62.19 50 1oct AT-val A.DA210 B.DT222 C.VAL147 9.44 -177.78 -8.53 3.83 1.33 37.06 24.02 -177.61 51 1oct AT-val B.DA221 A.DT211 C.VAL147 -9.19 -149.81 7.12 5.31 2.37 -42.28 11.70 -147.39 52 1oct GC-arg A.DG206 B.DC226 C.ARG49 11.14 174.67 3.34 -9.86 3.98 45.92 -30.78 173.98 53 1oct GC-arg A.DG206 B.DC226 C.ARG105 11.24 73.06 -8.49 -6.69 3.11 -0.59 41.26 61.67 54 1oct GC-arg B.DG225 A.DC207 C.ARG49 10.69 -135.66 -1.58 10.57 -0.18 41.82 32.16 -130.18 55 1oct GC-arg B.DG225 A.DC207 C.ARG102 -15.17 -52.80 -8.81 10.28 -6.84 -0.85 -42.84 -31.61 56 1oct GC-arg B.DG225 A.DC207 C.ARG105 -10.47 -57.77 -9.76 3.61 -1.15 7.66 -53.29 -21.80 57 1oct GC-arg A.DG214 B.DC218 C.ARG146 -13.22 81.82 -3.10 -12.84 0.55 33.12 -42.77 63.89 58 1oct GC-arg A.DG214 B.DC218 C.ARG153 -15.04 105.31 -13.12 -7.36 -0.34 48.96 -59.02 78.67 59 1oct GC-arg A.DG215 B.DC217 C.ARG146 -14.12 54.56 -8.22 -11.26 -2.24 17.71 -44.22 27.42 60 1oct GC-asp B.DG225 A.DC207 C.ASP41 -15.83 145.24 7.69 5.05 -12.89 14.51 -88.51 130.16 61 1oct GC-cys A.DG214 B.DC218 C.CYS150 -11.64 58.75 -6.02 -8.19 -5.66 2.88 -29.51 51.30 62 1oct GC-lys A.DG206 B.DC226 C.LYS104 14.00 -147.17 13.14 -1.87 4.47 60.50 -32.46 -139.97 63 1oct GC-lys A.DG214 B.DC218 C.LYS125 -15.77 133.59 -15.05 -2.40 4.03 15.10 -45.64 128.88 64 1oct GC-lys A.DG215 B.DC217 C.LYS142 -18.20 88.73 -7.54 -15.85 4.81 38.75 -67.02 47.26 65 1oct GC-phe B.DG225 A.DC207 C.PHE42 -12.94 16.35 2.22 12.74 0.40 -16.24 -1.72 0.81 66 1oct GC-ser B.DG225 A.DC207 C.SER43 10.70 -125.48 -8.19 6.60 -1.95 -34.20 69.17 -108.25 67 1oct GC-ser A.DG215 B.DC217 C.SER128 14.83 66.84 -9.41 -8.96 7.15 38.53 -33.77 44.47 68 1oct GC-thr A.DG202 B.DC230 C.THR26 12.81 -35.78 -6.69 10.25 3.78 -25.47 20.05 -15.35 69 1oct GC-thr A.DG206 B.DC226 C.THR45 -7.64 176.19 -2.23 -7.21 1.19 26.03 -13.35 176.06 70 1oct GC-thr B.DG225 A.DC207 C.THR45 8.13 -137.49 -5.46 5.69 1.99 29.38 9.20 -135.83 71 1oct GC-thr B.DG225 A.DC207 C.THR46 9.34 109.47 7.63 0.45 5.38 -31.44 53.14 95.45 **************************************************************************** List of 25 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 1oct OP1@A.DT203 NH2@C.ARG20 2.74 po4:sidechain:salt-bridge 2 1oct OP2@A.DT203 NH2@C.ARG20 3.02 po4:sidechain:salt-bridge 3 1oct OP2@A.DT203 N@C.GLN27 3.19 po4:backbone 4 1oct OP2@A.DA204 NE2@C.GLN27 2.79 po4:sidechain 5 1oct OP2@A.DA204 OG@C.SER48 2.60 po4:sidechain 6 1oct OP1@A.DA208 NH2@C.ARG113 2.69 po4:sidechain:salt-bridge 7 1oct OP1@A.DA210 N@C.THR106 2.96 po4:backbone 8 1oct OP1@A.DA210 OG1@C.THR106 2.37 po4:sidechain 9 1oct OP1@A.DT211 N@C.LYS103 3.10 po4:backbone 10 1oct OP1@B.DC217 NZ@C.LYS142 3.64 po4:sidechain:salt-bridge 11 1oct O5'@B.DC217 OG@C.SER128 3.41 po4:sidechain 12 1oct OP2@B.DC218 NE@C.ARG146 2.90 po4:sidechain:salt-bridge 13 1oct OP1@B.DT219 NZ@C.LYS125 3.21 po4:sidechain:salt-bridge 14 1oct OP2@B.DT219 NE@C.ARG153 3.04 po4:sidechain:salt-bridge 15 1oct OP2@B.DT219 NH2@C.ARG153 2.58 po4:sidechain:salt-bridge 16 1oct O3'@B.DC218 NZ@C.LYS125 3.44 po4:sidechain 17 1oct O3'@B.DC218 NH2@C.ARG153 3.14 po4:sidechain 18 1oct OP2@B.DT223 OG@C.SER56 2.61 po4:sidechain 19 1oct OP1@B.DT224 NZ@C.LYS62 2.42 po4:sidechain:salt-bridge 20 1oct OP2@B.DT224 ND2@C.ASN59 2.83 po4:sidechain 21 1oct OP1@B.DG225 N@C.SER43 3.26 po4:backbone 22 1oct OP2@B.DG225 N@C.SER43 3.12 po4:backbone 23 1oct OP2@B.DG225 OG@C.SER43 2.74 po4:sidechain 24 1oct OP2@B.DG225 OG1@C.THR46 2.45 po4:sidechain 25 1oct OP1@B.DC226 N@C.ARG105 3.82 po4:backbone **************************************************************************** List of 1 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 1oct O4'@A.DA208 NH2@C.ARG105 3.40 sugar:sidechain **************************************************************************** List of 12 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 1oct N7@A.DA204 NE2@C.GLN44 3.16 base:sidechain 2 1oct N6@A.DA204 OE1@C.GLN44 3.37 base:sidechain 3 1oct O4@A.DT205 OG1@C.THR45 2.93 base:sidechain 4 1oct N7@A.DG206 NH2@C.ARG49 3.44 base:sidechain 5 1oct N3@A.DA208 NH1@C.ARG105 3.23 base:sidechain 6 1oct N7@A.DA210 ND2@C.ASN151 3.47 base:sidechain 7 1oct N6@A.DA210 OD1@C.ASN151 3.54 base:sidechain 8 1oct N3@A.DA210 NH2@C.ARG102 3.85 base:sidechain 9 1oct O2@B.DT223 NH2@C.ARG102 3.69 base:sidechain 10 1oct O6@B.DG225 NH1@C.ARG49 2.84 base:sidechain 11 1oct O6@B.DG225 NH2@C.ARG49 3.21 base:sidechain 12 1oct N4@B.DC226 OG1@C.THR45 3.22 base:sidechain **************************************************************************** List of 7 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 1oct A-gln A.DA204 C.GLN44 0.05 9 2 1oct G-arg A.DG206 C.ARG49 1.68 26 3 1oct A-arg A.DA208 C.ARG105 0.33 44 4 1oct A-arg A.DA210 C.ARG102 2.12 37 5 1oct A-asn A.DA210 C.ASN151 0.70 27 6 1oct T-arg B.DT223 C.ARG102 1.17 49 7 1oct G-arg B.DG225 C.ARG49 0.44 32 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 1oct T-gln A.DT203 C.GLN44 3.79 1 2 1oct G-arg B.DG225 C.ARG105 3.31 37 **************************************************************************** List of 19 nucleotides interacting with amino acids 1 A.DG202 d=3.25 C5'@A.DG202 CG2@C.THR26 aas=1 T C.THR26 ... 2 A.DT203 d=2.74 OP1@A.DT203 NH2@C.ARG20 aas=6 RITQQS C.ARG20,C.ILE21,C.THR26,C.GLN27,C.GLN44,C.SER48 h..,...,...,h..,..s,... 3 A.DA204 d=2.60 OP2@A.DA204 OG@C.SER48 aas=5 KQQSE C.LYS17,C.GLN27,C.GLN44,C.SER48,C.GLU51 ...,h..,hp.,h..,... 4 A.DT205 d=2.93 O4@A.DT205 OG1@C.THR45 aas=2 TS C.THR45,C.SER48 h..,... 5 A.DG206 d=3.44 N7@A.DG206 NH2@C.ARG49 aas=2 TR C.THR45,C.ARG49 ...,hp. 6 A.DC207 d=3.53 N4@A.DC207 NH2@C.ARG49 aas=2 RR C.ARG49,C.ARG105 ...,... 7 A.DA208 d=2.69 OP1@A.DA208 NH2@C.ARG113 aas=2 RR C.ARG105,C.ARG113 hp.,h.. 8 A.DA209 d=3.35 O4'@A.DA209 NH1@C.ARG105 aas=8 RRTIRWNK C.ARG102,C.ARG105,C.THR106,C.ILE108,C.ARG113,C.TRP148,C.ASN151,C.LYS155 ...,...,...,...,...,...,...,... 9 A.DA210 d=2.37 OP1@A.DA210 OG1@C.THR106 aas=8 RKKRTVVN C.ARG102,C.LYS103,C.LYS104,C.ARG105,C.THR106,C.VAL144,C.VAL147,C.ASN151 hp.,...,...,...,h..,...,...,hp. 10 A.DT211 d=3.10 OP1@A.DT211 N@C.LYS103 aas=3 RKV C.ARG102,C.LYS103,C.VAL147 ...,h..,... 11 B.DC217 d=3.29 C5'@B.DC217 OG@C.SER128 aas=3 SKR C.SER128,C.LYS142,C.ARG146 h..,h..,... 12 B.DC218 d=2.90 OP2@B.DC218 NE@C.ARG146 aas=4 KRCR C.LYS125,C.ARG146,C.CYS150,C.ARG153 h..,h..,...,h.. 13 B.DT219 d=2.58 OP2@B.DT219 NH2@C.ARG153 aas=3 KCR C.LYS125,C.CYS150,C.ARG153 h..,...,h.. 14 B.DT220 d=3.96 OP2@B.DT220 CE@C.LYS157 aas=1 K C.LYS157 ... 15 B.DT223 d=2.61 OP2@B.DT223 OG@C.SER56 aas=5 SKNKR C.SER56,C.LYS58,C.ASN59,C.LYS62,C.ARG102 h..,...,...,...,hp. 16 B.DT224 d=2.42 OP1@B.DT224 NZ@C.LYS62 aas=9 FTRLNKLRR C.PHE42,C.THR46,C.ARG49,C.LEU55,C.ASN59,C.LYS62,C.LEU63,C.ARG102,C.ARG105 ...,...,...,...,h..,h..,...,...,... 17 B.DG225 d=2.45 OP2@B.DG225 OG1@C.THR46 aas=8 DFSTTRRR C.ASP41,C.PHE42,C.SER43,C.THR45,C.THR46,C.ARG49,C.ARG102,C.ARG105 ...,...,h..,...,h..,hp.,...,..s 18 B.DC226 d=3.22 N4@B.DC226 OG1@C.THR45 aas=3 TKR C.THR45,C.LYS104,C.ARG105 h..,...,h.. 19 B.DA227 d=3.71 OP1@B.DA227 OG@C.SER107 aas=2 TS C.THR45,C.SER107 ...,...