Contacts of the strand formed by residues 435 - 441 (chain A) in PDB entry 4WXS


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 THR 435 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247A  GLU*     6.1     0.3    -      -       -      +
    431A  ILE*     3.3     4.8    -      -       -      +
    432A  ILE      2.9    37.4    +      -       -      -
    433A  CYS      4.2     3.3    +      -       -      -
    434A  GLY*     1.3    77.5    -      -       -      +
    436A  LEU*     1.3    71.0    +      -       -      +
    437A  TYR*     3.3    31.9    +      -       +      +
    452A  ALA*     3.9    10.8    -      -       +      -
    453A  TYR      3.4    16.8    -      -       -      +
    454A  ASP*     3.6    22.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 436 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    391A  ILE*     3.8    35.9    -      -       +      -
    401A  ILE*     3.8    24.7    -      -       +      -
    403A  LEU*     4.3    17.9    -      -       +      -
    419A  THR*     4.1    17.0    -      -       +      -
    429A  ALA*     4.0    12.6    -      -       +      -
    430A  PHE      3.6    12.1    -      -       -      +
    431A  ILE*     4.2     8.2    -      -       +      +
    434A  GLY      4.1     1.4    +      -       -      -
    435A  THR*     1.3    71.8    -      -       -      +
    437A  TYR*     1.3    62.7    +      -       -      +
    438A  THR*     4.2    15.0    -      -       +      -
    451A  PHE*     3.7     5.0    -      -       +      +
    452A  ALA*     3.1     6.6    -      -       -      -
    453A  TYR*     2.9    47.4    +      -       +      +
    455A  THR*     5.2     1.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 437 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    246A  GLY      4.5     0.7    +      -       -      -
    247A  GLU*     3.3    16.9    -      -       +      +
    248A  LEU*     2.9    41.3    +      -       +      -
    429A  ALA*     3.2     5.7    -      -       -      +
    430A  PHE*     2.8    56.0    +      +       +      -
    432A  ILE*     3.7    32.9    +      -       +      -
    435A  THR*     3.3    37.4    -      -       +      +
    436A  LEU*     1.3    73.9    -      -       -      +
    438A  THR*     1.3    63.0    +      -       -      +
    449A  VAL*     3.8    15.0    -      -       +      -
    451A  PHE      3.3     3.8    -      -       -      -
    452A  ALA*     3.8    13.7    -      -       +      -
    463A  LEU*     3.7    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 438 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    401A  ILE*     3.7    30.7    -      -       +      -
    421A  ILE*     4.4     1.1    -      -       +      -
    426A  VAL*     3.6    20.9    -      -       +      +
    428A  ASN      3.6     4.5    -      -       -      -
    429A  ALA*     4.3     3.6    -      -       +      -
    436A  LEU*     4.2     7.4    -      -       +      -
    437A  TYR*     1.3    78.2    -      -       -      +
    439A  VAL*     1.3    63.5    +      -       -      +
    449A  VAL*     3.3     7.8    -      -       -      +
    450A  ASN*     2.8    44.9    +      -       -      +
    451A  PHE*     3.0    37.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 439 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    426A  VAL*     3.3     3.2    -      -       -      +
    427A  ALA*     2.6    36.8    +      -       +      -
    428A  ASN      2.9    19.3    +      -       -      +
    430A  PHE*     3.6    32.1    -      -       +      -
    438A  THR*     1.3    75.2    -      -       -      +
    440A  SER*     1.3    58.1    +      -       -      +
    447A  ALA*     3.8    11.7    -      -       +      -
    448A  THR      3.4     5.8    -      -       -      +
    449A  VAL*     4.2     7.9    -      -       +      -
    450A  ASN*     4.0     0.9    -      -       -      -
    467A  PHE*     3.4    41.5    -      -       +      -
    477A  ILE*     4.5    13.5    -      -       +      -
----------------------------------------------------------
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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  SER      4.2    17.0    -      -       -      -
    426A  VAL*     4.4     1.3    -      -       -      -
    427A  ALA*     4.0     4.5    -      -       -      +
    439A  VAL*     1.3    77.7    -      -       -      +
    441A  SER*     1.3    61.6    +      -       -      +
    442A  TYR*     4.0     8.6    +      -       -      -
    447A  ALA*     3.4     2.1    -      -       -      -
    448A  THR*     2.9    35.6    +      -       -      +
    450A  ASN*     3.3    34.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 441 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    372A  SER*     4.5     6.3    +      -       -      -
    427A  ALA*     4.2    11.4    -      -       -      +
    440A  SER*     1.3    73.7    -      -       -      +
    442A  TYR*     1.3    65.2    +      -       -      +
    443A  THR      3.4    20.2    +      -       -      -
    446A  ASP      3.5     6.3    -      -       -      -
    447A  ALA*     4.2     4.9    -      -       -      +
    602A  GOL      3.6    28.3    +      -       -      -
----------------------------------------------------------
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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