Contacts of the strand formed by residues 438 - 443 (chain A) in PDB entry 3WSZ


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 MET 438 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390A  LEU*     4.3    11.4    -      -       +      -
    427A  THR*     4.1     7.9    -      -       +      -
    428A  LEU      3.4     3.8    -      -       -      -
    429A  ILE*     3.7    17.0    -      -       +      -
    437A  ASN*     1.3    82.2    -      -       -      +
    439A  ARG*     1.3    69.8    +      -       -      +
    482A  SER*     3.4    30.5    -      -       -      +
    485A  LEU*     3.6    36.8    -      -       +      -
    486A  ASN*     5.1     9.6    -      -       -      +
    513A  ASN*     3.1    22.3    +      -       -      +
    514A  LEU*     3.3    35.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 439 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    427A  THR*     3.4     5.7    -      -       -      +
    428A  LEU*     2.7    46.0    +      -       +      +
    437A  ASN      4.9     4.7    -      -       -      +
    438A  MET*     1.3    82.6    -      -       -      +
    440A  SER*     1.3    64.1    +      -       -      +
    441A  VAL*     5.4     1.1    -      -       +      -
    452A  PHE*     3.2    39.2    -      -       +      -
    472A  GLY*     2.5    36.4    +      -       -      -
    476A  HIS*     3.7    15.0    -      -       +      -
    512A  LYS*     3.3    27.5    +      -       -      +
    514A  LEU*     4.2     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 440 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    425A  ILE*     5.0     4.6    -      -       -      +
    426A  ALA      3.5     6.9    -      -       -      -
    427A  THR*     4.2     5.5    +      -       -      -
    439A  ARG*     1.3    75.5    +      -       -      +
    441A  VAL*     1.3    68.6    +      -       -      +
    452A  PHE*     4.2     3.8    -      -       -      -
    453A  LEU*     3.3    29.6    +      -       -      +
    474A  SER*     4.4     3.8    +      -       -      -
    475A  LEU      3.8    13.1    -      -       -      +
    476A  HIS*     3.3     8.1    +      -       -      +
    477A  LEU*     2.8    42.7    +      -       -      +
    479A  GLN*     5.9     0.3    +      -       -      -
    514A  LEU*     4.4     1.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 441 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    386A  LEU*     3.7    19.3    -      -       +      -
    425A  ILE*     3.5     3.8    -      -       -      +
    426A  ALA      3.0    37.6    +      -       -      +
    428A  LEU*     3.6    28.9    -      -       +      -
    439A  ARG*     5.4     0.9    -      -       +      -
    440A  SER*     1.3    79.4    -      -       -      +
    442A  ILE*     1.3    57.3    +      -       -      +
    450A  TRP*     3.6    26.6    -      -       +      -
    451A  GLU      3.1    19.7    -      -       -      +
    452A  PHE*     3.9    20.4    -      -       +      -
    453A  LEU*     3.4     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 442 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    423A  VAL*     4.4     2.9    -      -       +      -
    424A  TYR      3.3    13.7    -      -       -      +
    425A  ILE*     3.7    20.2    -      -       +      -
    441A  VAL*     1.3    75.0    -      -       -      +
    443A  THR*     1.3    64.4    +      -       -      +
    444A  PHE*     3.4    38.3    -      -       +      -
    450A  TRP*     3.7     2.9    -      -       -      -
    451A  GLU*     3.0    41.1    +      -       +      +
    453A  LEU*     3.3    27.1    -      -       +      +
    454A  GLN*     4.9     5.8    -      -       -      +
    526A  ALA      3.6    17.0    -      -       -      +
    527A  GLY*     3.9    15.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 443 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422A  GLY      3.0     9.9    -      -       -      +
    423A  VAL*     3.2     2.3    -      -       -      +
    424A  TYR*     3.2    30.0    +      -       +      +
    442A  ILE*     1.3    74.3    -      -       -      +
    444A  PHE*     1.3    61.9    +      -       -      +
    445A  ASP*     2.2    52.2    +      -       -      +
    447A  GLY      3.5     5.3    +      -       -      +
    449A  THR*     2.6    19.6    +      -       -      -
    450A  TRP*     3.5    37.0    -      -       +      -
----------------------------------------------------------
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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