Contacts of the strand formed by residues 472 - 474 (chain A) in PDB entry 3GEB


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 472 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331A  ILE      4.0     5.0    -      -       -      +
    332A  HIS*     3.8    15.6    -      -       -      -
    333A  VAL*     4.6     1.3    -      -       +      +
    391A  TYR*     3.4    27.8    -      -       +      +
    445A  LEU*     3.4    30.3    -      -       +      +
    447A  THR*     4.8     8.3    -      -       +      -
    451A  LEU*     4.2    19.6    -      -       +      +
    454A  ALA*     5.0     4.5    -      -       +      -
    455A  LEU*     3.5    26.7    -      -       +      -
    458A  VAL*     4.3    14.1    -      -       +      -
    467A  PHE*     4.3     7.6    -      -       +      -
    468A  PRO      4.2     4.3    -      -       -      +
    469A  ILE*     3.3    15.6    +      -       -      +
    470A  GLU      3.5     0.4    -      -       -      -
    471A  ASN*     1.3    80.2    -      -       -      +
    473A  TYR*     1.3    72.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 473 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    331A  ILE*     3.6    24.7    -      -       +      -
    332A  HIS*     3.6    21.3    +      +       -      -
    444A  VAL*     4.0     4.0    -      -       +      -
    445A  LEU      2.7    15.2    +      -       -      +
    446A  VAL*     3.3    11.1    -      -       +      +
    447A  THR*     2.8    30.9    +      -       -      +
    470A  GLU      3.9     4.1    +      -       -      -
    471A  ASN*     3.6    24.0    -      -       -      -
    472A  ILE*     1.3    78.2    -      -       -      +
    474A  SER*     1.3    60.4    +      -       -      +
    475A  ALA      3.4     1.3    +      -       -      -
    483A  CYS*     4.4    11.4    -      -       +      -
    486A  ARG*     3.7    26.7    +      -       +      +
    487A  ILE*     3.8    37.4    -      -       +      +
    490A  ARG*     3.0    33.9    +      -       -      +
    491A  PHE*     5.0     0.4    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 474 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    329A  ASP*     5.5     1.7    -      -       -      +
    330A  GLN      3.9     8.5    +      -       -      +
    331A  ILE*     3.0    39.2    +      -       -      +
    447A  THR*     3.2     8.1    -      -       -      -
    449A  THR      2.8    11.5    +      -       -      -
    450A  GLN*     3.5     3.3    -      -       -      -
    451A  LEU*     3.5    22.6    +      -       -      +
    472A  ILE      4.3     0.2    -      -       -      -
    473A  TYR*     1.3    70.0    -      -       -      +
    475A  ALA*     1.3    58.0    +      -       -      +
    476A  THR*     2.4    34.6    +      -       -      -
    477A  LYS      4.3     1.9    +      -       -      -
    483A  CYS*     4.4     2.0    -      -       -      -
----------------------------------------------------------
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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