Contacts of the strand formed by residues 285 - 290 (chain B) 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 ILE 285 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36B  VAL*     4.4     9.2    -      -       +      -
     37B  TYR      4.0    20.6    -      -       -      +
     38B  TYR*     3.1    35.8    +      -       +      -
    220B  PHE*     4.0    19.4    -      -       +      -
    221B  SER*     5.0     1.9    -      -       -      -
    222B  ALA*     4.1    15.5    +      -       +      +
    277B  LEU*     4.1    21.1    -      -       +      -
    278B  LYS      3.2     8.7    -      -       -      +
    279B  TYR*     3.6    23.1    -      -       +      +
    284B  THR*     1.3    82.9    +      -       -      +
    286B  THR*     1.3    59.7    +      -       -      +
    287B  ASP      3.3    24.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 286 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  PHE*     3.1    19.2    -      -       -      -
    278B  LYS*     3.0    17.7    +      -       +      +
    280B  ASN*     3.2    33.3    +      -       -      +
    284B  THR*     4.1     4.7    +      -       -      +
    285B  ILE*     1.3    72.8    -      -       -      +
    287B  ASP*     1.3    75.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 287 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220B  PHE*     3.4    15.3    -      -       -      +
    277B  LEU*     4.1     0.2    -      -       -      -
    278B  LYS*     3.2    41.2    +      -       +      +
    285B  ILE*     3.3    11.1    -      -       -      +
    286B  THR*     1.3    92.8    -      -       -      +
    288B  ALA*     1.3    66.7    +      -       -      +
    306B  PHE*     3.4    30.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 288 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  THR*     5.3     0.2    +      -       -      -
     36B  VAL*     4.2     4.5    -      -       +      -
     58B  PHE*     4.0    23.3    -      -       +      -
    220B  PHE*     3.9    20.4    -      -       +      -
    275B  PHE*     4.4     4.9    -      -       +      -
    276B  LEU      3.3    11.2    -      -       -      +
    277B  LEU*     4.2    17.3    -      -       +      -
    287B  ASP*     1.3    79.7    -      -       -      +
    289B  VAL*     1.3    67.3    +      -       -      +
    290B  ASP      4.3     0.2    -      -       -      -
    306B  PHE*     3.6     4.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 289 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  PHE*     4.7     0.4    -      -       -      -
    275B  PHE*     3.2    13.4    -      -       -      +
    276B  LEU*     3.1    38.8    +      -       +      -
    288B  ALA*     1.3    73.3    -      -       -      +
    290B  ASP*     1.3    61.9    +      -       -      +
    291B  CYS*     3.4     1.4    +      -       -      -
    297B  SER*     3.8    26.9    -      -       -      +
    300B  LYS*     3.8    32.3    -      -       +      +
    301B  CYS*     3.7    19.3    -      -       -      -
    306B  PHE*     3.5    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 290 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  PRO*     3.7     4.9    -      -       -      +
     58B  PHE*     2.9    51.8    +      -       +      +
    273B  ARG*     3.2    20.4    +      -       -      +
    275B  PHE*     3.3    22.7    -      -       +      -
    289B  VAL*     1.3    71.8    -      -       -      +
    291B  CYS*     1.3    61.9    +      -       -      +
    292B  ALA      2.8    15.5    +      -       -      -
    293B  LEU*     3.2    23.5    +      -       +      +
    297B  SER*     3.1    22.3    +      -       -      +
----------------------------------------------------------
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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