Contacts of the strand formed by residues 476 - 479 (chain A) in PDB entry 4PKO


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 TYR 476 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417A  VAL*     3.7     6.1    -      -       -      +
    421A  ARG*     3.3    20.1    +      -       -      +
    468A  THR*     3.6    23.6    +      -       -      -
    469A  VAL*     4.1     8.8    -      -       -      +
    472A  GLY*     4.1    20.6    -      -       -      -
    473A  ASP      3.4    17.0    +      -       -      +
    474A  GLY      3.3     1.2    -      -       -      -
    475A  ASN*     1.3    75.9    -      -       -      +
    477A  GLY*     1.3    58.2    +      -       -      +
    485A  TYR*     3.3    42.4    -      +       +      +
    486A  GLY*     3.4    22.4    -      -       -      -
    487A  ASN*     4.5     3.4    -      -       -      +
    488A  MET*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 477 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    417A  VAL*     4.6     4.7    -      -       -      -
    469A  VAL*     4.4    12.1    -      -       -      -
    475A  ASN      3.3     1.6    +      -       -      -
    476A  TYR*     1.3    76.6    -      -       -      +
    478A  TYR*     1.3    61.7    +      -       -      -
    479A  ASN      3.9     0.2    +      -       -      -
    485A  TYR*     3.3    10.9    -      -       -      +
    486A  GLY      2.7    36.2    +      -       -      +
    488A  MET*     3.6    18.6    -      -       -      +
    491A  MET*     5.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    415A  GLY*     4.9     6.3    -      -       -      -
    417A  VAL*     6.0     0.2    -      -       -      +
    451A  LEU*     5.4     8.8    -      -       +      +
    454A  ILE*     6.1     0.7    -      -       +      -
    455A  VAL*     4.2    14.8    -      -       +      -
    458A  CYS*     5.1     4.7    -      -       -      -
    460A  GLU*     3.2    30.9    +      -       +      -
    465A  VAL*     3.6    34.1    -      -       +      -
    469A  VAL*     4.0     8.3    -      -       +      +
    477A  GLY*     1.3    73.2    -      -       -      -
    479A  ASN*     1.3    71.9    +      -       -      +
    480A  ALA*     3.6    18.3    +      -       +      +
    483A  GLU*     3.3    36.5    +      -       -      +
    484A  GLU*     4.1     2.9    -      -       -      -
    485A  TYR*     3.1    36.6    -      +       +      -
    488A  MET*     3.8    17.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 479 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    477A  GLY      3.9     1.2    +      -       -      -
    478A  TYR*     1.3    73.9    -      -       -      +
    480A  ALA*     1.3    58.6    +      -       -      +
    481A  ALA*     3.0    12.9    +      -       -      +
    482A  THR*     2.6    46.2    +      -       -      +
    483A  GLU*     2.9    28.8    +      -       -      -
    484A  GLU      3.1    20.4    +      -       -      +
    488A  MET*     4.8     0.9    -      -       -      -
    491A  MET*     3.7    26.5    +      -       -      +
    493A  ILE*     3.0    33.3    -      -       +      +
----------------------------------------------------------
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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