Contacts of the strand formed by residues 112 - 118 (chain A) 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 A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  ILE*     4.1     7.2    -      -       -      +
     92A  ALA*     3.8    27.6    -      -       +      +
     94A  ILE*     4.8     4.5    -      -       -      -
    104A  LEU*     4.4    16.2    -      -       +      -
    107A  MET*     3.0    31.1    +      -       +      +
    108A  ILE*     3.7    37.5    -      -       +      +
    111A  GLY*     1.3    79.4    -      -       -      +
    113A  ASN*     1.3    67.1    +      -       -      +
    114A  ILE      3.7    21.5    -      -       -      +
    115A  ALA*     4.5    10.3    -      -       +      -
    134A  VAL*     5.3     3.6    -      -       +      -
    149A  ARG*     5.9     2.1    -      -       -      +
    151A  VAL*     4.1    30.2    -      -       +      +
    418A  VAL*     3.7    10.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 113 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  ARG*     2.5    33.6    +      -       -      +
     89A  SER*     3.1    13.3    +      -       -      -
     90A  ILE      3.0    16.5    +      -       -      +
    111A  GLY      3.2    13.1    +      -       -      -
    112A  MET*     1.3    76.1    +      -       -      +
    114A  ILE*     1.3    65.7    +      -       +      +
    149A  ARG*     6.2     3.6    -      -       -      +
    150A  PRO      4.9     1.4    +      -       -      -
    151A  VAL*     3.5    11.9    -      -       -      -
    152A  ALA      3.0    22.4    +      -       -      -
    507A  HIS*     3.6    40.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89A  SER*     4.9     1.6    -      -       -      -
     90A  ILE      3.1     3.5    +      -       -      +
     91A  ILE*     3.5    34.8    -      -       +      -
     92A  ALA      2.9    27.0    +      -       -      -
    112A  MET*     3.7     7.1    -      -       -      +
    113A  ASN*     1.3    89.1    -      -       +      +
    115A  ALA*     1.3    73.5    +      -       -      +
    151A  VAL*     4.6     0.2    -      -       -      -
    152A  ALA*     3.6    19.1    -      -       +      -
    154A  ALA*     4.0    18.2    -      -       +      -
    282A  ILE*     4.4     6.3    -      -       +      -
    284A  PHE*     4.7     2.0    -      -       +      -
    401A  CYS*     4.5     7.2    -      -       -      -
    507A  HIS*     4.1    20.2    -      -       +      +
    508A  LEU*     3.9    27.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ALA      3.5     3.8    -      -       -      -
     94A  ILE*     4.0    23.3    -      -       +      -
    112A  MET*     4.5     8.1    -      -       -      -
    114A  ILE*     1.3    75.6    -      -       -      +
    116A  ARG*     1.3    55.8    +      -       -      +
    117A  LEU*     4.0     4.4    +      -       +      -
    134A  VAL*     4.1    24.2    -      -       +      -
    151A  VAL*     4.2     1.9    -      -       +      +
    152A  ALA      2.9    14.6    +      -       -      +
    153A  ILE*     3.4     6.1    -      -       +      +
    154A  ALA*     2.7    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91A  ILE*     3.7    13.7    -      -       +      -
     92A  ALA      2.8    16.7    +      -       -      +
     93A  THR*     3.0    40.7    +      -       -      +
     94A  ILE*     3.0    26.0    +      -       -      +
    115A  ALA*     1.3    72.8    -      -       -      +
    117A  LEU*     1.3    62.0    +      -       -      +
    118A  ASN*     4.1    15.6    -      -       -      +
    154A  ALA*     3.4     4.5    -      -       -      +
    156A  ASP*     2.5    42.0    +      -       +      -
    284A  PHE*     3.9    16.4    -      -       +      -
    313A  LYS*     4.0     0.8    -      -       -      +
    403A  MET*     3.5    33.4    -      -       -      +
    405A  SER*     3.8    13.3    +      -       -      -
    581A  PGA      3.1    30.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ILE*     4.2    17.5    -      -       +      -
    115A  ALA*     5.0     3.6    -      -       +      -
    116A  ARG*     1.3    74.8    -      -       -      +
    118A  ASN*     1.3    59.7    +      -       -      +
    119A  PHE*     3.3    24.3    +      -       +      -
    127A  HIS*     3.9    20.6    -      -       +      +
    130A  SER*     4.1    23.3    -      -       -      -
    131A  ILE*     3.7    35.2    -      -       +      +
    134A  VAL*     5.4     2.0    -      -       +      -
    153A  ILE*     4.2    17.9    -      -       +      -
    154A  ALA      2.8    17.1    +      -       -      +
    155A  LEU*     4.6     1.6    -      -       -      -
    156A  ASP*     2.6    33.0    +      -       -      -
    280A  VAL*     4.9     6.1    -      -       +      -
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Residues in contact with ASN 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  THR*     4.2    11.3    -      -       +      +
     94A  ILE      5.3     3.7    +      -       -      +
    116A  ARG*     3.9    30.1    +      -       -      +
    117A  LEU*     1.3    70.0    -      -       -      +
    119A  PHE*     1.3    57.1    +      -       -      +
    120A  SER*     3.0    29.2    +      -       -      -
    121A  HIS*     3.1    38.9    +      -       +      +
    127A  HIS*     3.6     7.7    -      -       -      -
    156A  ASP*     4.0     5.8    -      -       -      -
    581A  PGA      4.5     4.9    +      -       -      -
    582A    K      3.1    12.9    -      -       -      -
----------------------------------------------------------
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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