Contacts of the strand formed by residues 573 - 577 (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 THR 573 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541B  PHE*     5.7     0.7    -      -       -      -
    546B  LEU*     3.9    26.3    -      -       +      +
    565B  PHE*     4.1    21.3    -      -       +      -
    566B  GLY      3.3    14.1    -      -       -      +
    567B  ARG*     3.8     6.7    -      -       +      +
    571B  ASP*     3.9    11.9    -      -       -      +
    572B  THR*     1.3    75.7    +      -       -      +
    574B  ASP*     1.3    62.0    +      -       -      +
    576B  VAL*     4.1     3.7    -      -       -      +
    587B  ILE*     3.9    30.5    -      -       -      +
    976C  VAL*     6.5     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 574 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    557B  LYS*     4.4    13.7    +      -       -      +
    566B  GLY      3.0     5.4    +      -       -      -
    567B  ARG*     3.7     2.4    -      -       -      +
    568B  ASP*     3.1    41.3    +      -       +      +
    572B  THR*     2.9    23.8    +      -       -      +
    573B  THR*     1.3    75.9    -      -       -      +
    575B  ALA*     1.3    57.1    +      -       +      +
    586B  ASP*     2.7    13.2    -      -       -      +
    587B  ILE*     2.3    47.5    +      -       -      +
    855C  PHE*     5.7     1.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 575 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    557B  LYS*     3.7    30.7    -      -       +      +
    559B  PHE*     3.7     6.5    -      -       +      -
    565B  PHE*     3.2     2.9    -      -       -      +
    566B  GLY*     2.6    36.9    +      -       -      +
    574B  ASP*     1.3    80.4    -      -       -      +
    576B  VAL*     1.3    63.3    +      -       -      +
    584B  ILE*     3.6    20.4    -      -       +      -
    585B  LEU      3.3    11.2    -      -       -      +
    586B  ASP*     4.3     0.2    -      -       -      -
    587B  ILE*     4.9     0.2    -      -       -      -
     43C  PHE*     5.6     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 576 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543B  PHE*     3.2    38.5    -      -       +      +
    546B  LEU*     4.1    22.4    -      -       +      -
    564B  GLN*     3.7    12.3    -      -       +      +
    565B  PHE*     3.5    20.9    -      -       +      +
    573B  THR*     4.1     4.0    -      -       -      +
    575B  ALA*     1.3    81.0    -      -       -      +
    577B  ARG*     1.3    63.3    +      -       -      +
    578B  ASP      3.8     1.6    +      -       -      -
    584B  ILE*     3.3    12.6    -      -       -      +
    585B  LEU*     3.3    19.4    +      -       -      +
    587B  ILE*     3.8    24.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 577 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543B  PHE*     3.2    13.1    -      -       -      -
    559B  PHE*     3.2    24.4    -      -       +      +
    560B  LEU      2.7    26.7    +      -       -      -
    561B  PRO*     4.4    13.9    +      -       -      +
    563B  GLN      2.6    27.2    +      -       -      -
    564B  GLN*     2.8    38.4    +      -       -      +
    576B  VAL*     1.3    73.7    -      -       -      +
    578B  ASP*     1.3    69.2    +      -       -      +
    579B  PRO*     3.4     1.7    -      -       -      +
    582B  LEU*     3.5    57.7    +      -       +      +
    583B  GLU      3.3     6.7    -      -       -      +
    584B  ILE*     3.8     7.5    -      -       +      +
----------------------------------------------------------
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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