Contacts of the strand formed by residues 477 - 479 (chain A) in PDB entry 3IW4


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 477 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399A  PHE*     3.3    34.1    -      -       +      +
    425A  LEU*     4.8     1.6    -      -       +      -
    443A  TYR*     3.5    40.6    -      -       +      -
    446A  GLU*     3.0    34.1    +      -       +      +
    447A  ILE*     3.7    29.2    -      -       +      +
    469A  VAL*     4.6     8.7    -      -       +      -
    470A  MET      3.3     6.5    -      -       -      +
    471A  LEU*     3.8    11.4    -      -       +      -
    476A  HIS*     1.3    74.6    -      -       -      +
    478A  LYS*     1.3    63.7    +      -       -      +
    479A  ILE*     3.5    30.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 478 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    398A  PRO*     2.4    37.2    +      -       -      +
    399A  PHE      3.3     1.6    -      -       -      -
    400A  LEU      3.7    11.7    +      -       -      +
    401A  THR*     4.3     9.6    -      -       +      +
    402A  GLN*     4.4     6.9    -      -       -      +
    418A  GLU*     2.6    36.9    +      -       -      +
    420A  VAL*     3.9    30.1    -      -       +      -
    469A  VAL*     3.7     1.7    -      -       -      +
    470A  MET*     2.8    36.4    +      -       +      +
    472A  ASP*     4.0    29.2    -      -       +      +
    477A  ILE*     1.3    75.8    -      -       -      +
    479A  ILE*     1.3    63.8    +      -       -      +
    480A  ALA      3.9     0.5    +      -       -      -
    608A  ARG*     4.9     6.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 479 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399A  PHE*     2.7    21.1    +      -       +      +
    400A  LEU*     4.1    16.8    -      -       +      +
    401A  THR*     3.2    22.8    +      -       -      -
    447A  ILE*     3.6    38.8    -      -       +      +
    450A  GLY*     4.4     5.2    -      -       -      -
    451A  LEU*     5.3     2.9    -      -       +      +
    461A  TYR*     3.4    39.7    -      -       +      +
    464A  LEU*     5.2     1.3    -      -       +      -
    468A  ASN      3.6     7.4    -      -       -      +
    469A  VAL*     4.5    12.1    -      -       +      +
    477A  ILE*     3.5    17.5    -      -       +      -
    478A  LYS*     1.3    72.0    -      -       -      +
    480A  ALA*     1.3    59.8    +      -       -      +
    482A  PHE*     3.5    13.6    -      -       +      -
----------------------------------------------------------
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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