Contacts of the strand formed by residues 113 - 122 (chain M) in PDB entry 1VQN


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ARG 113 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111M  ASN      4.8     1.9    +      -       -      +
    112M  LEU*     1.3    79.5    -      -       -      +
    114M  VAL*     1.3    65.8    +      -       -      +
    115M  LEU      3.3     1.2    +      -       -      -
    133M  LEU*     3.3     3.8    -      -       -      -
    134M  ILE*     3.0    33.0    +      -       -      +
    136M  PRO*     3.7    24.6    -      -       +      +
    150M  ILE*     2.8    51.5    +      -       +      +
    151M  CYS*     3.4    11.9    +      -       -      +
    152M  ALA      2.9    25.5    +      -       -      -
    153M  ASP*     4.6     5.3    +      -       -      +
    155M  GLN*     3.6    16.5    -      -       -      +
    156M  ALA*     3.7    29.5    -      -       -      +
    157M  ASP      4.7     3.8    -      -       -      +
    158M  ARG*     4.2     4.7    -      -       -      -
   9318M   CL      3.6     9.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 114 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102M  GLU*     3.8    24.5    -      -       +      +
    106M  SER*     3.6    22.4    -      -       -      -
    112M  LEU      4.3     0.2    -      -       -      -
    113M  ARG*     1.3    69.0    -      -       -      +
    115M  LEU*     1.3    62.0    +      -       -      +
    116M  ASN      3.9     7.6    -      -       -      +
    131M  VAL*     3.7    20.9    -      -       +      -
    132M  ILE      3.8     3.6    -      -       -      -
    133M  LEU*     4.3     8.7    -      -       +      -
    150M  ILE*     3.9     0.9    -      -       -      +
    158M  ARG*     3.0    30.4    +      -       +      -
    159M  VAL*     3.6    15.7    -      -       +      -
    164M  THR*     3.9    15.0    -      -       -      +
   9318M   CL      3.1    20.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 115 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    4320    G      5.0     7.1    -      -       -      +
     52M  GLN      3.1    31.2    -      -       -      +
     53M  GLY*     4.1    12.8    -      -       -      +
    113M  ARG      3.3     0.8    +      -       -      -
    114M  VAL*     1.3    76.0    -      -       -      +
    116M  ASN*     1.3    78.1    +      -       +      +
    132M  ILE*     2.8    24.5    +      -       +      +
    134M  ILE*     3.8    27.4    -      -       +      -
    147M  LEU*     4.4    13.7    -      -       +      -
    149M  TRP*     3.5    32.4    -      -       +      -
    150M  ILE*     3.7    10.8    -      -       +      -
    158M  ARG*     4.1     7.7    +      -       -      +
    164M  THR*     5.1     2.5    +      -       -      -
    165M  GLY      5.3     3.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 116 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    4310    G      3.3    38.0    +      -       -      +
    4320    G      3.8    14.4    +      -       -      -
     52M  GLN*     3.2    39.3    +      -       +      +
    102M  GLU*     3.8     8.6    -      -       -      +
    114M  VAL*     3.7     3.2    -      -       -      +
    115M  LEU*     1.3    90.3    +      -       +      +
    117M  SER*     1.3    69.1    +      -       -      +
    131M  VAL*     3.7     2.6    -      -       -      +
    132M  ILE*     2.9    29.2    +      -       +      +
    164M  THR*     5.4     2.2    -      -       -      -
    165M  GLY      4.6     5.7    +      -       -      -
    166M  ALA      5.1     0.5    +      -       -      -
    169M  ARG*     4.5    11.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 117 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52M  GLN*     3.0    20.7    +      -       -      -
     98M  GLN*     2.6    38.7    +      -       -      +
    102M  GLU*     2.5    37.2    +      -       -      +
    116M  ASN*     1.3    81.0    +      -       -      +
    118M  TYR*     1.3    63.6    +      -       -      +
    129M  HIS*     5.2     3.4    -      -       -      -
    130M  GLU      3.3    14.8    -      -       -      -
    131M  VAL*     3.8     9.4    -      -       -      -
    132M  ILE      4.8     0.2    -      -       -      +
    169M  ARG*     4.9     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 118 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3810    G      5.2     0.2    -      -       -      +
     43M  PRO*     3.4    20.4    -      -       -      +
     44M  THR      3.7     1.2    +      -       -      -
     45M  ARG*     3.9    27.8    +      -       +      +
     48M  LYS*     3.6    29.4    -      -       +      -
     49M  ALA*     4.1    20.9    -      -       +      -
     52M  GLN*     3.5    19.3    -      -       -      +
     62M  VAL*     4.5     2.1    -      -       +      +
     98M  GLN*     4.0     5.4    -      -       -      +
    117M  SER*     1.3    78.8    +      -       -      +
    119M  SER*     1.3    69.5    +      -       -      +
    120M  VAL*     3.6    13.5    -      -       +      -
    129M  HIS*     3.3     8.2    -      -       -      -
    130M  GLU*     2.5    71.1    +      -       +      +
    132M  ILE*     4.5    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 119 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3810    G      4.6    20.9    +      -       -      +
     12M  TRP*     4.2     2.0    -      -       -      -
     45M  ARG*     2.9    35.0    +      -       -      +
     98M  GLN*     5.0     0.6    -      -       -      +
    118M  TYR*     1.3    75.5    -      -       -      +
    120M  VAL*     1.3    61.3    +      -       -      +
    121M  GLY*     3.3    14.4    +      -       -      -
    128M  TRP      3.8     2.0    +      -       -      -
    129M  HIS*     3.7    24.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 120 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  TRP*     3.7    17.2    -      -       +      -
     24M  GLN*     3.1    17.0    -      -       -      +
     31M  TRP*     3.3    26.2    -      -       +      -
     44M  THR*     4.4     6.7    -      -       -      -
     45M  ARG*     4.3     7.2    -      -       +      -
     64M  ARG*     4.5     2.9    -      -       +      -
    118M  TYR*     3.6    12.1    -      -       +      +
    119M  SER*     1.3    78.8    +      -       -      +
    121M  GLY*     1.3    57.4    +      -       -      +
    128M  TRP*     3.1    35.6    +      -       +      +
    129M  HIS      3.8     2.7    -      -       -      +
    130M  GLU*     3.3    39.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 121 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12M  TRP*     4.1     6.3    -      -       -      -
     15M  PRO*     6.3     1.8    -      -       -      -
     24M  GLN*     4.3     7.2    -      -       -      -
     28M  GLN*     4.7     0.9    -      -       -      -
    119M  SER*     3.3    11.2    +      -       -      -
    120M  VAL*     1.3    80.3    -      -       -      +
    122M  GLN*     1.3    65.8    +      -       -      +
    127M  LYS*     3.8     1.7    -      -       -      +
    128M  TRP*     3.1    29.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 122 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    4040    G      3.7    14.8    +      -       -      -
   21310    G      5.3     1.4    +      -       -      -
   21320    C      6.1     0.2    -      -       -      +
     28M  GLN*     3.4    19.8    +      -       -      +
     69M  LYS*     3.0    34.1    -      -       -      +
    121M  GLY*     1.3    77.6    -      -       -      +
    123M  ASP*     1.3    61.3    +      -       -      +
    126M  GLN      3.1    17.3    -      -       -      +
    127M  LYS*     3.3    31.1    +      -       +      +
    128M  TRP*     3.8     8.3    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il