Contacts of the strand formed by residues 112 - 118 (chain C) in PDB entry 2VGB


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 MET 112 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90C  ILE*     4.3     6.3    -      -       -      -
     92C  ALA*     3.9    16.6    -      -       +      +
     94C  ILE*     4.7     4.9    -      -       -      -
    104C  LEU*     4.5    16.4    -      -       +      -
    107C  MET*     2.9    41.1    +      -       +      +
    108C  ILE*     3.7    38.5    +      -       +      +
    111C  GLY*     1.3    78.2    -      -       -      +
    113C  ASN*     1.3    67.3    +      -       -      +
    114C  ILE      3.6    20.6    -      -       -      +
    115C  ALA*     4.4    12.3    -      -       +      -
    134C  VAL*     5.4     3.1    -      -       +      -
    149C  ARG*     5.9     2.3    -      -       -      +
    150C  PRO      5.4     0.2    -      -       -      +
    151C  VAL*     4.2    29.1    -      -       +      +
    418C  VAL*     3.6    11.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 113 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86C  ARG*     2.4    34.8    +      -       -      +
     89C  SER*     3.2    11.4    -      -       -      -
     90C  ILE      3.0    17.1    +      -       -      +
    111C  GLY*     3.2    11.0    +      -       -      +
    112C  MET*     1.3    77.2    +      -       -      +
    114C  ILE*     1.3    64.9    +      -       +      +
    149C  ARG*     6.2     4.0    -      -       -      +
    150C  PRO      4.9     0.8    +      -       -      -
    151C  VAL*     3.5    11.3    -      -       -      -
    152C  ALA      2.9    23.1    +      -       -      -
    507C  HIS*     3.5    42.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 114 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89C  SER*     5.1     1.1    -      -       -      -
     90C  ILE      3.1     4.0    +      -       -      +
     91C  ILE*     3.4    34.0    -      -       +      -
     92C  ALA      2.9    26.9    +      -       -      -
    112C  MET*     3.6     7.7    -      -       -      +
    113C  ASN*     1.3    88.1    -      -       +      +
    115C  ALA*     1.3    71.0    +      -       -      +
    151C  VAL*     4.6     0.2    -      -       -      -
    152C  ALA*     3.7    19.1    -      -       +      -
    154C  ALA*     3.9    20.4    -      -       +      -
    282C  ILE*     4.2     6.7    -      -       +      -
    284C  PHE*     4.7     1.1    -      -       +      -
    401C  CYS*     4.6     2.5    -      -       -      -
    507C  HIS*     4.0    23.3    -      -       +      +
    508C  LEU*     3.8    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 115 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92C  ALA      3.5     4.0    -      -       -      -
     94C  ILE*     4.0    24.2    -      -       +      -
    112C  MET*     4.4     8.7    -      -       -      -
    114C  ILE*     1.3    74.5    -      -       -      +
    116C  ARG*     1.3    56.4    +      -       -      +
    117C  LEU*     3.9     3.1    +      -       +      -
    134C  VAL*     4.1    23.1    -      -       +      -
    151C  VAL*     4.1     2.1    -      -       +      +
    152C  ALA      3.0    15.5    +      -       -      +
    153C  ILE*     3.5     6.1    -      -       +      +
    154C  ALA*     2.7    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 116 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91C  ILE*     3.8    14.4    -      -       +      -
     92C  ALA      2.7    17.0    +      -       -      +
     93C  THR*     3.1    38.4    +      -       -      +
     94C  ILE*     3.0    24.8    +      -       -      +
    114C  ILE      3.9     0.2    +      -       -      -
    115C  ALA*     1.3    72.5    -      -       -      +
    117C  LEU*     1.3    63.9    +      -       -      +
    118C  ASN*     3.7    15.0    +      -       -      +
    154C  ALA*     3.4     4.7    -      -       -      +
    156C  ASP*     2.4    48.3    +      -       +      +
    284C  PHE*     4.1    11.5    -      -       +      -
    313C  LYS*     4.0     0.6    -      -       -      +
    403C  MET*     3.6    35.6    -      -       -      +
    405C  SER*     3.8     8.7    +      -       -      -
    581C  PGA      3.1    27.9    +      -       -      -
    590C    K      4.0     2.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 117 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94C  ILE*     4.3    15.9    -      -       +      -
    115C  ALA*     4.9     4.3    -      -       +      +
    116C  ARG*     1.3    76.3    -      -       -      +
    118C  ASN*     1.3    59.2    +      -       -      +
    119C  PHE*     3.4    23.0    +      -       +      -
    127C  HIS*     4.0    20.2    -      -       +      +
    130C  SER*     4.0    25.1    -      -       -      +
    131C  ILE*     3.8    33.7    -      -       +      +
    134C  VAL*     5.4     1.8    -      -       +      -
    153C  ILE*     4.1    18.6    -      -       +      -
    154C  ALA      2.7    18.1    +      -       -      +
    155C  LEU*     3.9     2.0    -      -       -      -
    156C  ASP*     2.6    33.6    +      -       -      +
    280C  VAL*     4.9     5.4    -      -       +      -
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Residues in contact with ASN 118 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93C  THR*     4.2    10.7    -      -       +      +
     94C  ILE      5.2     4.1    +      -       -      +
    116C  ARG*     3.7    30.4    +      -       -      +
    117C  LEU*     1.3    71.5    -      -       -      +
    119C  PHE*     1.3    56.2    +      -       -      +
    120C  SER*     3.0    17.6    +      -       -      -
    121C  HIS*     2.9    44.2    +      -       +      +
    127C  HIS*     3.5     6.8    -      -       -      -
    156C  ASP*     4.0     4.7    -      -       -      -
    581C  PGA      4.5     4.0    +      -       -      -
    590C    K      2.9    25.3    -      -       -      -
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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