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. 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.Release history (in reverse chronological order)
List of users who has helped improve SNAP by reporting bugs, making comments/suggestions etc:
Auffinger;
jdbrown444;
ldfinger;
miaozhichao;
Phosphoserine;
jms89-- 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
Here is a sample run on
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.:
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 ...,...
Topic: SNAP: software for characterizing DNA-protein interactions (Read 29845 times)