Contacts of the strand formed by residues 512 - 516 (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 VAL 512 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  SER      5.6     0.7    -      -       -      +
    481B  ALA*     4.1    13.5    -      -       +      +
    485B  SER*     4.0    14.1    -      -       -      -
    493B  VAL*     3.3    15.9    -      -       +      +
    495B  ALA*     3.7    22.4    -      -       +      -
    506B  VAL*     2.7    38.9    -      -       +      +
    507B  HIS*     4.6     8.8    +      -       -      -
    509B  CYS*     3.3    31.2    +      -       +      +
    511B  GLY*     1.3    80.5    -      -       -      +
    513B  PHE*     1.3    69.1    -      -       -      +
    514B  PRO*     3.8     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 513 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85B  ALA*     3.5    25.4    -      -       +      -
     86B  ARG      3.5    26.9    -      -       -      -
     87B  SER*     4.1    12.8    -      -       -      -
    492B  ALA*     3.4    29.2    -      -       +      -
    493B  VAL      2.8    12.4    +      -       -      +
    494B  ILE*     3.4    11.4    -      -       +      +
    495B  ALA      2.9    22.1    +      -       -      -
    507B  HIS*     6.6     0.2    -      +       -      -
    511B  GLY*     3.3    26.5    -      -       -      -
    512B  VAL*     1.3    74.7    -      -       -      +
    514B  PRO*     1.3    68.6    -      -       +      +
    515B  LEU*     3.7     4.0    +      -       +      +
    543B  ARG*     5.8     2.0    -      -       -      +
    545B  PHE*     4.2    27.8    -      +       +      -
----------------------------------------------------------
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Residues in contact with PRO 514 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  PRO*     4.0    20.1    -      -       +      +
    495B  ALA*     3.4    11.9    -      -       +      +
    497B  THR*     5.7     0.9    -      -       +      -
    503B  ALA*     3.2    42.4    -      -       +      +
    506B  VAL*     4.3    11.9    -      -       +      -
    507B  HIS*     3.7    31.9    -      -       +      +
    512B  VAL      3.8     6.5    -      -       -      +
    513B  PHE*     1.3    83.3    -      -       +      +
    515B  LEU*     1.3    71.6    +      -       -      +
    543B  ARG*     4.8     2.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 515 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  PRO      6.1     0.2    -      -       -      +
    148B  TYR      6.1     0.2    -      -       -      -
    150B  PRO*     5.6     0.2    -      -       -      -
    494B  ILE*     3.7    30.3    -      -       +      -
    495B  ALA      2.7    12.4    +      -       -      +
    496B  VAL*     3.6     4.8    -      -       +      +
    497B  THR*     3.1    27.6    +      -       -      +
    513B  PHE*     4.2     6.7    -      -       +      +
    514B  PRO*     1.3    95.1    -      -       -      +
    516B  LEU*     1.3    62.7    +      -       -      +
    517B  TYR      3.7     0.2    +      -       -      -
    535B  PHE*     3.9    15.7    -      -       +      -
    536B  GLY*     4.1     9.6    -      -       -      -
    539B  SER*     3.1    35.9    -      -       -      +
    540B  GLY      4.9     0.4    -      -       -      +
    543B  ARG*     3.4    39.3    -      -       -      +
    545B  PHE*     5.6     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 516 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145B  PRO*     5.2     3.8    -      -       -      +
    148B  TYR*     4.8    23.2    -      -       +      +
    150B  PRO*     5.3     5.0    -      -       +      +
    497B  THR*     3.2    17.9    -      -       +      +
    498B  ARG*     3.5    24.2    -      -       -      +
    499B  SER      4.0     2.2    -      -       -      +
    500B  ALA*     3.7    33.7    -      -       +      +
    503B  ALA*     4.6     9.5    -      -       +      +
    514B  PRO      4.2     0.4    -      -       -      -
    515B  LEU*     1.3    71.6    -      -       -      +
    517B  TYR*     1.3    66.1    +      -       -      +
    518B  ARG*     4.1    37.9    +      -       +      +
    535B  PHE*     3.6    16.4    -      -       -      -
----------------------------------------------------------
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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