Contacts of the strand formed by residues 432 - 437 (chain A) in PDB entry 6VSB


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 CYS 432 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368A  LEU*     6.3     0.7    -      -       -      -
    377A  PHE*     4.6     4.0    -      -       -      -
    378A  LYS      3.4     5.8    -      -       -      +
    379A  CYS*     2.0    43.3    -      -       -      +
    380A  TYR*     5.2     0.4    -      -       -      -
    387A  LEU*     4.8    17.3    -      -       -      -
    430A  THR*     3.6     1.5    -      -       -      -
    431A  GLY*     1.3    82.6    -      -       -      +
    433A  VAL*     1.3    62.5    +      -       -      +
    434A  ILE*     4.0    19.3    -      -       +      -
    512A  VAL*     3.7     0.9    -      -       -      -
    513A  LEU*     3.0    43.4    +      -       +      +
    515A  PHE*     5.3     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 433 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    376A  THR*     4.2     5.1    -      -       +      +
    377A  PHE*     4.0     1.0    -      -       -      -
    378A  LYS*     2.6    59.3    +      -       +      +
    380A  TYR*     3.8    21.1    -      -       +      -
    407A  VAL      5.5     0.9    -      -       -      +
    410A  ILE*     3.7    36.1    -      -       +      +
    425A  LEU*     5.4     3.8    -      -       +      -
    430A  THR*     4.1    15.5    -      -       +      -
    432A  CYS*     1.3    74.2    -      -       -      +
    434A  ILE*     1.3    61.1    +      -       -      +
    435A  ALA*     6.0     1.1    -      -       +      -
    510A  VAL*     4.7     7.0    -      -       +      -
    511A  VAL      4.1     2.2    -      -       -      -
    512A  VAL*     4.3    12.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 434 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  PHE*     4.2     8.5    -      -       +      -
    368A  LEU*     3.6    17.7    -      -       +      -
    374A  PHE*     3.4    35.0    -      -       +      -
    376A  THR      3.2    15.5    -      -       -      +
    377A  PHE*     3.6    33.9    -      -       +      -
    378A  LYS      5.0     0.2    -      -       -      +
    432A  CYS*     4.0    17.9    -      -       +      -
    433A  VAL*     1.3    79.8    -      -       -      +
    435A  ALA*     1.3    61.6    +      -       -      +
    436A  TRP*     4.3     2.0    -      -       -      -
    509A  ARG      4.2     0.2    -      -       -      +
    510A  VAL*     3.6     2.8    -      -       -      +
    511A  VAL*     2.9    37.7    +      -       -      +
    513A  LEU*     3.8    20.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 435 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    374A  PHE*     3.5     2.0    -      -       -      +
    375A  SER*     3.0     3.7    +      -       -      -
    376A  THR*     2.6    56.7    +      -       +      +
    407A  VAL*     5.1     8.1    -      -       +      -
    433A  VAL*     6.0     0.9    -      -       +      -
    434A  ILE*     1.3    75.6    -      -       -      +
    436A  TRP*     1.3    62.8    -      -       -      +
    508A  TYR*     4.9     9.0    -      -       +      -
    509A  ARG      3.4    12.6    -      -       -      +
    510A  VAL*     3.9    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 436 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  PHE*     3.4    31.2    +      +       -      -
    347A  PHE*     3.9     6.3    -      +       -      -
    373A  SER      3.7     9.0    -      -       -      +
    374A  PHE*     3.3    53.2    -      +       -      -
    375A  SER*     3.6     7.4    -      -       -      +
    434A  ILE      4.3     5.4    -      -       -      -
    435A  ALA*     1.3    77.7    -      -       -      +
    437A  ASN*     1.3    85.0    +      -       -      +
    438A  SER*     3.1    13.5    +      -       -      -
    508A  TYR*     3.3    10.1    -      -       -      -
    509A  ARG*     3.2    69.0    +      -       +      +
    511A  VAL*     3.6    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 437 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  SER*     3.7    13.8    +      -       -      +
    436A  TRP*     1.3    88.6    -      -       -      +
    438A  SER*     1.3    69.5    +      -       -      +
    439A  ASN*     2.7    26.9    +      -       -      +
    440A  ASN*     3.5    16.9    +      -       -      +
    503A  VAL*     5.3     0.4    -      -       -      +
    506A  GLN*     2.9    26.0    +      -       -      +
    508A  TYR*     3.1    38.6    +      -       +      -
----------------------------------------------------------
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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