Contacts of the strand formed by residues 82 - 85 (chain A) in PDB entry 2BGY


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 PHE 82 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  VAL*     3.1    43.1    -      -       +      -
     76A  ILE*     3.4    29.5    -      -       +      +
     81A  PHE*     1.3    75.6    -      -       -      +
     83A  ARG*     1.3    59.4    +      -       -      +
     84A  LEU*     3.5     8.6    -      -       +      +
     93A  TYR*     3.2     7.5    -      -       -      +
     94A  SER      2.8    46.8    +      -       -      +
     95A  ARG      3.9     3.1    -      -       -      -
     96A  ASN      3.5    13.0    -      -       -      +
     97A  GLY*     3.8    12.3    -      -       -      -
     99A  PHE*     4.2     4.5    -      +       +      -
    115A  LEU*     3.7    23.8    -      -       +      -
    314A  ILE*     3.5    35.7    -      -       +      -
    315A  VAL      4.3     4.7    -      -       -      -
    316A  LEU*     4.5     2.5    -      -       +      -
    355A  LEU*     5.7     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81A  PHE      3.8     1.5    +      -       -      +
     82A  PHE*     1.3    72.9    -      -       -      +
     84A  LEU*     1.3    63.3    +      -       -      +
     85A  VAL*     4.2     8.7    -      -       -      +
     91A  VAL*     3.7    40.4    -      -       +      +
     92A  PHE      3.5     3.4    -      -       -      -
     93A  TYR*     3.8    15.1    +      -       +      -
    115A  LEU*     4.1     1.3    -      -       -      +
    116A  THR*     2.7    67.7    +      -       -      +
    132A  ASN*     5.3     2.4    -      -       -      +
    133A  PRO*     3.8    28.8    +      -       -      +
    315A  VAL*     4.2    16.3    +      -       +      +
    317A  ALA*     5.2     1.1    -      -       +      -
    344A  LEU*     3.8    36.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 84 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  PHE*     3.5    23.1    -      -       +      +
     83A  ARG*     1.3    72.8    -      -       -      +
     85A  VAL*     1.3    61.6    +      -       -      +
     91A  VAL*     3.3     7.3    -      -       -      +
     92A  PHE*     2.8    42.0    +      -       +      +
     93A  TYR      4.0     2.9    -      -       -      -
     94A  SER*     3.7    24.9    -      -       -      +
     96A  ASN      6.0     0.2    -      -       -      +
     99A  PHE*     4.2    13.0    -      -       +      -
    109A  ASN*     4.7     9.4    -      -       +      +
    113A  MET*     4.1    25.8    -      -       +      +
    114A  GLN      3.2     5.8    -      -       -      +
    115A  LEU*     3.5    42.6    -      -       +      +
    116A  THR*     4.3     0.7    -      -       -      -
    332A  VAL*     5.6     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83A  ARG*     4.2     7.2    -      -       -      +
     84A  LEU*     1.3    78.8    -      -       -      +
     86A  ASP*     1.3    70.2    +      -       -      +
     89A  GLY*     4.0    17.3    -      -       -      +
     90A  SER      3.1    11.7    -      -       -      +
     91A  VAL*     4.0    11.9    -      -       +      -
     92A  PHE*     4.9     0.4    -      -       -      -
    113A  MET*     3.5     5.7    -      -       -      -
    114A  GLN*     2.8    42.0    +      -       +      +
    116A  THR*     3.8    23.3    -      -       +      -
    135A  PRO*     3.9    21.8    -      -       +      -
----------------------------------------------------------
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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