Contacts of the strand formed by residues 91 - 93 (chain B) in PDB entry 2GRA


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 ILE 91 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  ASP      3.6    10.1    +      -       -      +
     65B  VAL*     3.4    12.2    -      -       +      +
     66B  LEU      2.6    32.7    +      -       -      +
     90B  HIS*     1.3    76.6    -      -       -      +
     92B  VAL*     1.3    62.6    +      -       -      +
     93B  VAL*     4.1     5.6    +      -       +      -
    116B  ARG*     3.0    58.3    -      -       +      +
    118B  ILE*     4.3    15.5    -      -       +      -
    145B  ASP*     3.1    37.2    -      -       -      +
    148B  LEU*     5.7     3.8    -      -       +      -
    149B  MET*     6.0     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  LEU*     3.5    39.9    -      -       +      +
     68B  LEU*     3.9    31.9    -      -       +      -
     82B  ILE*     5.3     1.1    -      -       +      -
     86B  ILE*     5.2     5.6    -      -       +      -
     90B  HIS*     5.2     3.4    -      -       +      +
     91B  ILE*     1.3    78.5    -      -       -      +
     93B  VAL*     1.3    68.5    +      -       -      +
     94B  SER*     3.6     4.7    +      -       -      +
    104B  ILE*     6.3     2.0    -      -       +      -
    108B  LEU*     4.9    18.6    -      -       +      -
    116B  ARG      3.3     7.6    +      -       -      +
    117B  VAL*     3.8     8.7    -      -       +      +
    118B  ILE*     2.9    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65B  VAL*     4.5     5.8    -      -       +      -
     66B  LEU      2.9     7.7    +      -       -      +
     67B  PHE*     3.3    35.8    -      -       +      -
     68B  LEU      3.4    18.5    +      -       -      -
     91B  ILE*     4.7     5.2    -      -       +      +
     92B  VAL*     1.3    76.1    -      -       -      +
     94B  SER*     1.3    56.1    +      -       -      +
     95B  CYS*     2.9    44.3    +      -       -      +
    118B  ILE*     2.9    20.0    -      -       +      +
    120B  CYS*     4.1     8.3    -      -       +      -
    149B  MET*     4.1    27.8    -      -       +      -
    153B  LEU*     5.5     4.0    -      -       +      -
----------------------------------------------------------
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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