Contacts of the strand formed by residues 428 - 431 (chain W) in PDB entry 5O9G


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 HIS 428 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    415W  ILE*     4.3     9.0    -      -       +      -
    418W  LEU*     5.2     9.9    -      -       +      +
    419W  ILE*     3.8    24.5    -      -       +      +
    424W  GLN*     3.0    34.1    +      -       +      +
    426W  GLY*     3.1    20.9    +      -       -      -
    427W  PRO*     1.3    76.3    +      -       -      +
    429W  ILE*     1.3    60.8    +      -       -      +
    430W  ILE*     3.3    23.4    +      -       +      +
    486W  ASN      2.6    24.5    +      -       -      +
    487W  VAL*     3.5    12.6    -      -       +      -
    488W  LEU      3.9     1.2    +      -       -      -
    507W  TRP*     3.8     2.0    -      -       -      -
    508W  GLN*     4.8    12.3    -      -       +      -
    509W  PHE*     3.4    40.2    +      +       +      +
----------------------------------------------------------
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Residues in contact with ILE 429 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    428W  HIS*     1.3    72.0    -      -       -      +
    430W  ILE*     1.3    62.8    +      -       -      +
    431W  VAL*     4.1    24.7    -      -       +      -
    488W  LEU*     4.4    14.8    -      -       +      -
    490W  THR*     5.0     5.6    -      -       -      +
    495W  ILE*     5.9     2.0    -      -       +      -
    502W  LEU*     5.2    12.1    -      -       +      -
    507W  TRP*     3.4    52.3    -      -       +      +
    509W  PHE      3.2    21.1    +      -       -      +
    510W  MET*     3.3    35.9    -      -       +      +
    511W  ALA      3.4     1.7    +      -       -      -
    529W  LEU*     6.1     0.9    -      -       +      -
    532W  PHE*     5.5    13.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 430 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    411W  THR*     5.4     0.4    -      -       +      -
    415W  ILE*     3.7    29.4    -      -       +      -
    428W  HIS*     3.3    26.2    -      -       +      +
    429W  ILE*     1.3    77.7    -      -       -      +
    431W  VAL*     1.3    62.4    +      -       -      +
    432W  VAL*     3.5    20.9    +      -       +      +
    440W  TRP*     4.3    17.3    -      -       +      -
    487W  VAL*     3.8    20.4    -      -       +      -
    488W  LEU      2.9    24.4    +      -       -      +
    489W  LEU*     3.3    13.4    -      -       +      -
    490W  THR      3.8     0.6    +      -       -      -
    509W  PHE*     4.9     1.6    -      -       +      -
    511W  ALA*     3.4    32.5    -      -       +      +
    512W  VAL*     5.5     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 431 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    429W  ILE*     4.1    22.8    -      -       +      -
    430W  ILE*     1.3    71.0    -      -       -      +
    432W  VAL*     1.3    64.2    +      -       -      +
    433W  PRO*     4.5     1.1    -      -       -      +
    490W  THR*     3.4    19.1    -      -       -      +
    492W  TYR*     4.4    12.3    -      -       +      -
    495W  ILE*     3.6    28.5    -      -       +      -
    510W  MET*     5.0     9.9    -      -       +      -
    511W  ALA      3.0    17.5    +      -       -      +
    512W  VAL*     3.6    32.4    -      -       +      +
    513W  ASP      3.9     4.0    +      -       -      -
    529W  LEU*     5.1    11.4    -      -       +      -
----------------------------------------------------------
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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