Contacts of the strand formed by residues 584 - 588 (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 584 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555B  SER*     2.5    38.4    +      -       -      +
    557B  LYS*     3.6    13.9    -      -       +      +
    558B  LYS*     4.7     2.0    -      -       -      -
    559B  PHE*     3.5    56.5    -      -       +      +
    575B  ALA*     3.6     5.6    -      -       +      -
    576B  VAL      3.3    32.8    -      -       -      +
    577B  ARG*     3.8     6.1    -      -       +      +
    582B  LEU      4.0     2.1    +      -       -      +
    583B  GLU*     1.3   104.1    +      -       -      +
    585B  LEU*     1.3    60.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 585 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533B  LEU*     4.1    23.3    -      -       +      -
    535B  LYS*     3.9    22.7    -      -       +      +
    543B  PHE*     5.2     7.9    -      -       +      -
    552B  LEU*     5.0    17.0    -      -       +      -
    553B  THR*     3.4    24.5    -      -       -      +
    554B  GLU*     3.7    15.5    -      -       +      +
    555B  SER*     3.6     4.0    -      -       -      -
    575B  ALA*     3.3     2.3    -      -       -      -
    576B  VAL      3.3    30.6    +      -       -      +
    578B  ASP*     4.5    13.9    -      -       +      +
    583B  GLU*     3.9    24.2    -      -       +      +
    584B  ILE*     1.3    76.3    -      -       -      +
    586B  ASP*     1.3    66.5    +      -       -      +
    587B  ILE*     4.5     3.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 586 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551B  VAL      3.7     0.5    -      -       -      +
    552B  LEU*     3.4     8.1    -      -       -      +
    553B  THR*     2.9    42.8    +      -       +      +
    555B  SER*     3.2    19.5    -      -       -      -
    557B  LYS*     3.8    17.9    +      -       -      +
    574B  ASP*     2.7    19.7    -      -       -      +
    575B  ALA*     4.2     2.5    -      -       -      +
    585B  LEU*     1.3    74.5    -      -       -      +
    587B  ILE*     1.3    90.3    +      -       -      +
    588B  THR*     3.4    24.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 587 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541B  PHE*     3.9    38.4    -      -       +      -
    543B  PHE*     6.2     2.9    -      -       +      -
    546B  LEU*     4.6     1.6    -      -       +      -
    549B  THR      4.5     7.2    -      -       -      +
    550B  GLY*     4.6     1.6    -      -       -      -
    551B  VAL      3.9     3.1    -      -       -      -
    552B  LEU*     3.5    20.9    -      -       +      -
    573B  THR*     3.9    22.5    -      -       -      +
    574B  ASP*     2.3    37.8    +      -       -      +
    576B  VAL*     3.8    29.6    -      -       +      -
    585B  LEU      4.5     4.7    -      -       -      +
    586B  ASP*     1.3    78.9    +      -       -      +
    588B  THR*     1.3    66.9    +      -       -      +
    589B  PRO*     4.1     2.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 588 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    550B  GLY*     3.6     2.3    -      -       -      -
    551B  VAL*     2.8    51.7    +      -       -      +
    553B  THR*     4.8    10.0    -      -       +      +
    586B  ASP*     3.4    25.9    -      -       -      +
    587B  ILE*     1.3    78.3    -      -       -      +
    589B  PRO*     1.3    70.7    -      -       +      +
----------------------------------------------------------
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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