Contacts of the strand formed by residues 112 - 118 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90B  ILE*     4.1     7.6    -      -       -      +
     92B  ALA*     3.9    26.9    -      -       +      -
     94B  ILE*     4.6     5.6    -      -       -      -
    104B  LEU*     4.4    17.5    -      -       +      +
    107B  MET*     2.9    34.6    +      -       +      +
    108B  ILE*     3.7    38.6    +      -       +      +
    111B  GLY*     1.3    78.6    -      -       -      +
    113B  ASN*     1.3    65.6    +      -       -      +
    114B  ILE      3.5    21.1    -      -       -      +
    115B  ALA*     4.4    13.7    -      -       +      -
    134B  VAL*     5.3     3.1    -      -       +      -
    149B  ARG*     6.0     2.3    -      -       -      +
    150B  PRO      5.4     0.2    -      -       -      +
    151B  VAL*     4.1    28.5    -      -       +      +
    418B  VAL*     3.7     9.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86B  ARG*     2.4    34.1    +      -       -      +
     89B  SER*     3.2    15.5    +      -       -      -
     90B  ILE      2.9    17.2    +      -       -      +
    111B  GLY*     3.3    12.7    +      -       -      -
    112B  MET*     1.3    77.8    +      -       -      +
    114B  ILE*     1.3    64.5    +      -       +      +
    149B  ARG*     6.1     4.8    -      -       -      +
    150B  PRO      4.9     1.2    +      -       -      -
    151B  VAL*     3.6    11.3    -      -       -      -
    152B  ALA      3.0    22.5    +      -       -      -
    507B  HIS*     3.8    33.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     89B  SER*     4.9     1.6    -      -       -      -
     90B  ILE      3.1     2.6    +      -       -      +
     91B  ILE*     3.8    36.3    -      -       +      -
     92B  ALA      2.9    26.5    +      -       -      -
    112B  MET*     3.5     8.7    -      -       -      +
    113B  ASN*     1.3    92.2    -      -       +      +
    115B  ALA*     1.3    70.7    +      -       -      +
    151B  VAL*     4.6     0.2    -      -       -      -
    152B  ALA*     3.7    19.7    -      -       +      +
    154B  ALA*     4.0    18.4    -      -       +      -
    282B  ILE*     4.4     6.1    -      -       +      -
    284B  PHE*     4.6     1.8    -      -       +      -
    401B  CYS*     4.5     3.4    -      -       -      -
    507B  HIS*     4.2    20.4    -      -       +      +
    508B  LEU*     4.0    25.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  ALA      3.5     4.0    -      -       -      -
     94B  ILE*     4.0    24.7    -      -       +      -
    112B  MET*     4.4     8.7    -      -       -      -
    114B  ILE*     1.3    73.0    -      -       -      +
    116B  ARG*     1.3    57.5    +      -       -      +
    117B  LEU*     3.9     3.9    +      -       +      -
    134B  VAL*     4.1    22.2    -      -       +      -
    151B  VAL*     4.1     1.9    -      -       +      +
    152B  ALA      3.0    14.8    +      -       -      +
    153B  ILE*     3.5     5.7    -      -       +      +
    154B  ALA*     2.7    33.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 116 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  ILE*     3.8    13.9    -      -       +      -
     92B  ALA      2.7    17.9    +      -       -      +
     93B  THR*     3.0    40.5    +      -       +      +
     94B  ILE*     3.0    25.3    +      -       -      +
    114B  ILE      3.9     0.2    +      -       -      -
    115B  ALA*     1.3    74.4    -      -       -      +
    117B  LEU*     1.3    62.1    +      -       -      +
    118B  ASN*     4.0    17.2    -      -       -      +
    154B  ALA*     3.5     4.5    -      -       -      +
    156B  ASP*     2.5    40.8    +      -       +      +
    284B  PHE*     4.0    15.8    -      -       +      -
    313B  LYS*     4.0     0.4    -      -       -      +
    403B  MET*     3.5    37.9    -      -       -      +
    405B  SER*     3.9     8.7    +      -       -      -
    581B  PGA      2.7    29.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 117 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94B  ILE*     4.3    17.0    -      -       +      -
    115B  ALA*     4.8     3.8    -      -       +      +
    116B  ARG*     1.3    77.4    -      -       -      +
    118B  ASN*     1.3    59.1    +      -       -      +
    119B  PHE*     3.4    23.1    +      -       +      -
    127B  HIS*     3.9    21.3    -      -       +      +
    130B  SER*     4.1    22.9    -      -       -      -
    131B  ILE*     3.8    34.8    -      -       +      +
    134B  VAL*     5.4     1.6    -      -       +      -
    153B  ILE*     4.2    19.5    -      -       +      -
    154B  ALA      2.8    18.0    +      -       -      +
    155B  LEU*     4.6     1.3    -      -       -      -
    156B  ASP*     2.6    35.0    +      -       -      +
    280B  VAL*     4.9     5.4    -      -       +      -
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Residues in contact with ASN 118 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93B  THR*     4.1    19.1    -      -       +      +
     94B  ILE      5.3     3.7    +      -       -      +
    116B  ARG*     3.8    25.1    +      -       -      +
    117B  LEU*     1.3    69.8    -      -       -      +
    119B  PHE*     1.3    57.0    +      -       -      +
    120B  SER*     2.9    29.5    +      -       -      -
    121B  HIS*     3.1    40.6    +      -       +      +
    127B  HIS*     3.6     6.5    -      -       -      -
    156B  ASP*     3.9     5.8    -      -       -      -
    163B  ARG*     6.0     0.2    -      -       -      +
    581B  PGA      4.4     5.3    +      -       -      -
    586B    K      3.2     9.5    -      -       -      -
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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