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Author Topic: SNAP: software for characterizing DNA-protein interactions  (Read 3446 times)

Offline xiangjun

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DNA/RNA-protein interactions underpin fundamental biological processes such as transcription, splicing, and translation. The increasing number of experimentally determined three-dimensional 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 three-dimensional Structures of Nucleic Acid-Protein complexes. The program is currently in beta testing release, focusing on DNA-protein interactions. 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 less than 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!

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.


Release history (in reverse chronological order):
Abbreviations used: AA: amino acid; BP: base-pair

  • beta-r14-2018jan05 -- added the --nmr option; classified H-bonds into six categories: phosphate/sugar/base moieties for nucleotides vs backbone/sidechain for amino acids.
  • beta-r13-2017dec31 -- simplified output of H-bonds into mutually exclusive sections (phosphate group, sugar, or base with amino acid); added option --auxfile for producing additional auxiliary files (the default is now only the main output file); miscellaneous bug fixed and code refinements.
  • beta-r12-2017dec26 -- added a summary section of nucleotides with interacting amino acids; revised code to avoid warning messages with GCC v7.
  • beta-r11-2017dec11 -- revised output wording/formatting; added a list of additional files for pairwise H-bonding, base-amino acid pairing/stacking interactions; plus numerous code refinements.
  • beta-r10-2017apr10 -- documented the --type=string where string can be "base" (the default), "backbone", "either", or "both". The "base" argument reports protein interactions with only DNA/RNA base atoms, "backbone" with only DNA/RNA backbone atoms, "either" with base or backbone atoms, and "both" with base plus backbone atoms.
  • beta-r09-2016sept28 -- fixed a bug with the --cleanup option (thanks to jms89).
  • beta-r08-2016jun02 -- added the --tshape (or --t-shape) option to fix issues reported in the Supplemental Table S1 of the Wilson et al. paper "Topology of RNA–protein nucleobase–amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts". Specifically, the authors said:

    "Furthermore, although the recently released beta-r06-2015oct23 version of 3DNA-SNAP (Lu and Olson 2008) is able to distinguish between such errors, and accurately detects stacking interactions between nucleobases and amino acids, it unfortunately is currently unable to identify T-shaped interactions (see, for example, Supplemental Table S1)."

  • beta-r07-2016may21 -- fixed the "Segmentation fault" bug (due to undefined reference frames for certain amino acids with missing side-chain atoms); miscellaneous internal code refinements.
  • beta-r06-2015oct23 -- detected aromatic stacking interactions between bases and amino acids; numerous refinements along with DSSR.
  • beta-r05-2015may03 -- added option --get-hbond to output a list of H-bonds between protein and nucleic acid; numerous internal code refinements.
  • beta-r04-2014sep30 -- removed the (undocumented) --rna option so that RNA-protein complexes are handled the same way as DNA-protein complexes; relaxed default settings so SNAP now runs on pure nucleic acid or protein structures in addition to their complexes; added DSSP output for the protein component in file snap-dssp.txt.
  • beta-r03-2014sep16 -- listed base-AA pseudo-pairs and output an associated PDB ensemble file (snap-pseudoPairs.pdb); significant code speed-up.
  • beta-r02-2014may31 -- detailed listing of H-bonding interactions between a component of nucleotide (base/phosphate/sugar) and an amino acid.
  • beta-r01-2014may05 -- initial release to kick the ball rolling. SNAP identifies base-AA or BP-AA interactions based on a distance cutoff (default to 4.5 angstrom), calculates six parameters to uniquely quantify the spatial relationships, and sets the coordinates in the standard base or BP reference frame for easy visualization and for deriving knowledge-based potentials.




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.:

Code: [Select]
Run: x3dna-snap --interface -i=1oct.pdb -o=1oct.out
****************************************************************************
    SNAP: a program for the characterization of three-dimensional
             Structures of Nucleic Acid-Protein complexes
              beta-r14-2018jan05, by xiangjun@x3dna.org

  This program 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.

****************************************************************************
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
Date and time: Thu Jan  4 23:08:09 2018
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 30 nucleotide/amino-acid interactions
       id   nt-aa   nt           aa              Tdst    Rdst     Tx      Ty      Tz      Rx      Ry      Rz
   1  1oct  T-gln  A.DT203      C.GLN44         10.67 -115.42   -4.72    9.57   -0.05   65.02   27.06  -98.34
   2  1oct  A-gln  A.DA204      C.GLN44          8.90 -147.71   -1.25    8.28   -3.00   62.13   -4.03 -142.09
   3  1oct  A-ser  A.DA204      C.SER48         10.01 -126.61   -5.86    8.07    0.89   21.11   -7.37 -125.49
   4  1oct  T-thr  A.DT205      C.THR45          6.48 -148.19   -1.00    5.50    3.28  -35.77    2.63 -146.52
   5  1oct  T-ser  A.DT205      C.SER48        -10.33 -151.96   -5.14    8.73   -2.03   28.42  -17.90 -150.69
   6  1oct  G-thr  A.DG206      C.THR45         -7.46  178.53   -1.92   -7.19    0.56   34.46  -11.97  178.45
   7  1oct  G-arg  A.DG206      C.ARG49        -11.02  175.51    3.67   -9.94    3.04   54.67  -28.85  174.77
   8  1oct  C-arg  A.DC207      C.ARG49        -10.55  130.65   -1.73  -10.40    0.39   42.89  -25.07  125.22
   9  1oct  C-arg  A.DC207      C.ARG105        10.64   61.56   -9.91   -3.22    2.16    3.33   59.24   17.22
  10  1oct  A-arg  A.DA208      C.ARG105        10.98  -45.39  -10.37   -1.40   -3.30   18.22   38.36  -16.42
  11  1oct  A-arg  A.DA209      C.ARG102        12.96  -64.64  -12.42   -3.69    0.50   19.39   38.44  -49.42
  12  1oct  A-arg  A.DA209      C.ARG105       -10.54  -77.58   -9.01    0.77   -5.43   32.27   40.40  -59.98
  13  1oct  A-asn  A.DA209      C.ASN151         9.24 -165.14   -6.41    6.54   -1.24   44.17   60.06 -161.30
  14  1oct  A-arg  A.DA210      C.ARG102        13.00  -90.23  -12.62   -0.84   -3.03   31.67   30.70  -80.82
  15  1oct  A-val  A.DA210      C.VAL147         9.50  177.54    8.35   -4.40    1.13  -31.38  -26.50  177.38
  16  1oct  A-asn  A.DA210      C.ASN151         7.95  169.39    3.58   -6.02   -3.76  -61.24  -46.91  166.41
  17  1oct  T-val  A.DT211      C.VAL147        -9.12  143.26    7.02   -5.17   -2.68  -31.13  -15.46  141.43
  18  1oct  T-cys  B.DT219      C.CYS150        10.66  -81.40   -2.86   10.10    1.89    8.36   20.66  -78.81
  19  1oct  T-arg  B.DT223      C.ARG102        12.45   46.89  -11.36    4.59    2.22   27.19  -16.42   34.94
  20  1oct  T-arg  B.DT224      C.ARG49         12.06 -116.46   -5.79   10.20    2.79   24.96   60.01 -102.74
  21  1oct  T-leu  B.DT224      C.LEU55         11.64  144.35    9.48   -3.62   -5.72  -19.44  -72.43  134.61
  22  1oct  T-arg  B.DT224      C.ARG102       -14.08  -32.87  -11.42    8.12   -1.33   20.82  -25.38   -1.63
  23  1oct  T-arg  B.DT224      C.ARG105        10.20   47.44   -9.49    1.43    3.47   32.81  -33.87    5.35
  24  1oct  G-ser  B.DG225      C.SER43         10.76 -127.61   -8.48    6.55   -1.00  -33.95   77.50 -106.70
  25  1oct  G-thr  B.DG225      C.THR45          8.31 -141.05   -5.19    5.96    2.57   27.42   16.56 -139.41
  26  1oct  G-arg  B.DG225      C.ARG49         10.84 -140.82   -1.39   10.75   -0.00   40.74   39.22 -135.24
  27  1oct  G-arg  B.DG225      C.ARG105       -10.31  -55.06   -9.54    3.91   -0.13   12.03  -47.33  -26.24
  28  1oct  C-thr  B.DC226      C.THR45         -7.82 -173.77   -2.54    7.16   -1.83   17.56   14.19 -173.64
  29  1oct  C-arg  B.DC226      C.ARG105       -11.37  -65.61   -8.90    6.45   -2.94   -3.39  -34.34  -56.68
  30  1oct  A-thr  B.DA227      C.THR45         -6.83  150.54   -0.53   -5.80   -3.56  -38.91   -1.49  148.71

****************************************************************************
List of 24 base-pair/amino-acid interactions
       id   bp-aa     nt1          nt2          aa              Tdst    Rdst    Tx      Ty      Tz      Rx      Ry      Rz
   1  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
   2  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
   3  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
   4  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
   5  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
   6  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
   7  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
   8  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
   9  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
  10  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
  11  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
  12  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
  13  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
  14  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
  15  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
  16  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
  17  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
  18  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
  19  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
  20  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
  21  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
  22  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
  23  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
  24  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

****************************************************************************
List of 26 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  O3'@A.DA209      N@C.THR106         3.48 po4:backbone
  10  1oct  OP1@A.DT211      N@C.LYS103         3.10 po4:backbone
  11  1oct  OP1@B.DC217      NZ@C.LYS142        3.64 po4:sidechain:salt-bridge
  12  1oct  O5'@B.DC217      OG@C.SER128        3.41 po4:sidechain
  13  1oct  OP2@B.DC218      NE@C.ARG146        2.90 po4:sidechain:salt-bridge
  14  1oct  OP1@B.DT219      NZ@C.LYS125        3.21 po4:sidechain:salt-bridge
  15  1oct  OP2@B.DT219      NE@C.ARG153        3.04 po4:sidechain:salt-bridge
  16  1oct  OP2@B.DT219      NH2@C.ARG153       2.58 po4:sidechain:salt-bridge
  17  1oct  O3'@B.DC218      NZ@C.LYS125        3.44 po4:sidechain
  18  1oct  O3'@B.DC218      NH2@C.ARG153       3.14 po4:sidechain
  19  1oct  OP2@B.DT223      OG@C.SER56         2.61 po4:sidechain
  20  1oct  OP1@B.DT224      NZ@C.LYS62         2.42 po4:sidechain:salt-bridge
  21  1oct  OP2@B.DT224      ND2@C.ASN59        2.83 po4:sidechain
  22  1oct  OP1@B.DG225      N@C.SER43          3.26 po4:backbone
  23  1oct  OP2@B.DG225      N@C.SER43          3.12 po4:backbone
  24  1oct  OP2@B.DG225      OG@C.SER43         2.74 po4:sidechain
  25  1oct  OP2@B.DG225      OG1@C.THR46        2.45 po4:sidechain
  26  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 13 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
  13  1oct  N6@B.DA227       OG1@C.THR45        3.76 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 1 base/amino-acid stacks
       id   nt-aa   nt           aa      vertical-distance   plane-angle
   1  1oct  G-arg  B.DG225      C.ARG105        3.31             37

****************************************************************************
List of 17 nucleotides interacting with amino acids
   1 A.DT203  d=2.74 OP1@A.DT203   NH2@C.ARG20   aas=3 QRQ C.GLN44,C.ARG20,C.GLN27 ...,h..,h..
   2 A.DA204  d=2.60 OP2@A.DA204   OG@C.SER48    aas=3 QSQ C.GLN44,C.SER48,C.GLN27 hp.,h..,h..
   3 A.DT205  d=2.93 O4@A.DT205    OG1@C.THR45   aas=2 TS C.THR45,C.SER48 h..,...
   4 A.DG206  d=3.44 N7@A.DG206    NH2@C.ARG49   aas=2 TR C.THR45,C.ARG49 ...,hp.
   5 A.DC207  d=3.53 N4@A.DC207    NH2@C.ARG49   aas=2 RR C.ARG49,C.ARG105 ...,...
   6 A.DA208  d=2.69 OP1@A.DA208   NH2@C.ARG113  aas=2 RR C.ARG105,C.ARG113 hp.,h..
   7 A.DA209  d=3.35 O4'@A.DA209   NH1@C.ARG105  aas=4 RRNT C.ARG102,C.ARG105,C.ASN151,C.THR106 ...,...,...,h..
   8 A.DA210  d=2.37 OP1@A.DA210   OG1@C.THR106  aas=4 RVNT C.ARG102,C.VAL147,C.ASN151,C.THR106 hp.,...,hp.,h..
   9 A.DT211  d=3.10 OP1@A.DT211   N@C.LYS103    aas=2 VK C.VAL147,C.LYS103 ...,h..
  10 B.DC217  d=3.29 C5'@B.DC217   OG@C.SER128   aas=2 KS C.LYS142,C.SER128 h..,h..
  11 B.DC218  d=2.90 OP2@B.DC218   NE@C.ARG146   aas=3 RKR C.ARG146,C.LYS125,C.ARG153 h..,h..,h..
  12 B.DT219  d=2.58 OP2@B.DT219   NH2@C.ARG153  aas=3 CKR C.CYS150,C.LYS125,C.ARG153 ...,h..,h..
  13 B.DT223  d=2.61 OP2@B.DT223   OG@C.SER56    aas=2 RS C.ARG102,C.SER56 hp.,h..
  14 B.DT224  d=2.42 OP1@B.DT224   NZ@C.LYS62    aas=6 RLRRKN C.ARG49,C.LEU55,C.ARG102,C.ARG105,C.LYS62,C.ASN59 ...,...,...,...,h..,h..
  15 B.DG225  d=2.45 OP2@B.DG225   OG1@C.THR46   aas=5 STRRT C.SER43,C.THR45,C.ARG49,C.ARG105,C.THR46 h..,...,hp.,..s,h..
  16 B.DC226  d=3.22 N4@B.DC226    OG1@C.THR45   aas=2 TR C.THR45,C.ARG105 h..,h..
  17 B.DA227  d=3.76 N6@B.DA227    OG1@C.THR45   aas=1 T C.THR45 h..

****************************************************************************
Time used: 00:00:00:00
« Last Edit: January 04, 2018, 11:08:58 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.