Contacts of the strand formed by residues 508 - 516 (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 TYR 508 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    375A  SER*     4.5    12.1    -      -       -      -
    376A  THR*     5.7     2.9    -      -       -      -
    401A  VAL*     3.3     7.7    -      -       -      -
    402A  ILE*     2.9    32.0    +      -       +      +
    403A  ARG      4.7     4.7    -      -       -      +
    404A  GLY*     3.5    17.7    -      -       -      -
    407A  VAL*     5.7     6.5    -      -       +      -
    435A  ALA*     4.9     7.4    -      -       +      -
    436A  TRP*     3.3    26.5    -      -       -      +
    437A  ASN*     3.1    38.9    +      -       +      +
    438A  SER*     3.4     2.5    -      -       -      -
    503A  VAL*     3.4    41.5    -      -       -      +
    506A  GLN*     3.2    12.8    -      -       +      -
    507A  PRO*     1.3    76.4    -      -       -      +
    509A  ARG*     1.3    63.7    +      -       -      +
    510A  VAL*     3.8    11.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 509 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    342A  PHE      5.1     1.6    +      -       -      -
    343A  ASN      5.1     0.2    -      -       -      -
    344A  ALA      2.4    29.1    +      -       -      +
    345A  THR*     2.6    26.6    +      -       -      +
    346A  ARG*     3.9     4.0    -      -       -      +
    347A  PHE*     3.5    29.2    -      -       +      +
    400A  PHE      3.8     3.6    -      -       -      -
    401A  VAL*     3.8    17.5    -      -       +      -
    435A  ALA*     3.4     1.2    -      -       -      -
    436A  TRP*     3.2    66.9    +      -       +      +
    438A  SER*     2.7    20.9    +      -       -      +
    441A  LEU*     5.2     7.6    +      -       -      +
    442A  ASP*     3.0    34.7    +      -       -      -
    508A  TYR*     1.3    72.1    -      -       -      +
    510A  VAL*     1.3    60.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 510 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    347A  PHE*     3.9     1.0    -      -       -      -
    398A  ASP      3.5     1.0    -      -       -      +
    399A  SER*     3.4     6.2    -      -       -      -
    400A  PHE*     3.0    47.6    +      -       +      +
    402A  ILE*     3.9    34.3    -      -       +      -
    407A  VAL*     5.4     1.6    -      -       +      -
    410A  ILE*     4.5    12.8    -      -       +      -
    433A  VAL*     4.7     5.2    -      -       +      -
    434A  ILE      3.6     9.6    -      -       -      +
    435A  ALA*     3.9    15.7    -      -       +      -
    508A  TYR*     4.2     5.8    -      -       +      +
    509A  ARG*     1.3    76.2    -      -       -      +
    511A  VAL*     1.3    66.1    +      -       -      +
    512A  VAL*     4.0    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 511 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    341A  VAL*     3.7    32.5    -      -       +      +
    342A  PHE*     3.6    26.5    -      -       +      -
    347A  PHE*     3.8    13.2    -      -       +      -
    397A  ALA*     4.1     3.8    -      -       +      -
    398A  ASP      3.2     9.0    -      -       -      +
    399A  SER*     4.8     0.9    -      -       -      -
    434A  ILE*     2.9    31.5    +      -       -      +
    436A  TRP*     3.6    26.0    -      -       +      -
    509A  ARG      4.2     0.2    +      -       -      -
    510A  VAL*     1.3    79.2    -      -       -      +
    512A  VAL*     1.3    64.8    +      -       -      +
    513A  LEU*     3.9    17.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 512 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  ARG*     5.9     0.3    +      -       -      -
    396A  TYR      3.6     0.9    -      -       -      +
    397A  ALA*     3.2     5.1    -      -       -      -
    398A  ASP*     2.9    33.5    +      -       +      +
    400A  PHE*     4.5     4.7    -      -       +      -
    410A  ILE*     3.6    27.8    -      -       +      -
    423A  TYR*     3.6    29.8    -      -       +      +
    425A  LEU*     4.7     9.0    -      -       +      -
    430A  THR*     3.8    25.8    -      -       +      -
    432A  CYS      3.7     2.5    -      -       -      -
    433A  VAL*     4.3     9.6    -      -       +      -
    510A  VAL*     4.0    11.7    -      -       +      -
    511A  VAL*     1.3    77.0    -      -       -      +
    513A  LEU*     1.3    64.4    +      -       -      +
    514A  SER*     4.0     3.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 513 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338A  PHE*     4.9    10.1    -      -       +      -
    342A  PHE*     3.9    20.2    -      -       +      -
    358A  ILE*     5.1     0.4    -      -       +      -
    365A  TYR*     6.4     2.2    -      -       +      -
    368A  LEU*     5.9     0.4    -      -       +      -
    395A  VAL*     4.5    11.0    -      -       +      -
    396A  TYR      3.3     4.3    -      -       -      +
    397A  ALA*     3.7    24.9    -      -       +      -
    430A  THR*     3.2    11.5    -      -       -      +
    431A  GLY*     3.1    21.8    +      -       -      -
    432A  CYS*     3.0    31.4    +      -       +      +
    434A  ILE*     3.8    25.8    -      -       +      -
    511A  VAL*     3.9    13.7    -      -       +      +
    512A  VAL*     1.3    74.2    -      -       -      +
    514A  SER*     1.3    60.1    +      -       -      +
    515A  PHE*     4.5    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 514 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  ARG*     4.9    10.9    +      -       -      -
    395A  VAL*     3.3     3.5    -      -       -      -
    396A  TYR*     2.7    63.8    +      -       -      +
    430A  THR*     5.3     5.2    -      -       -      +
    431A  GLY      4.4     4.5    -      -       -      +
    512A  VAL*     5.2     4.0    -      -       -      -
    513A  LEU*     1.3    74.9    -      -       -      +
    515A  PHE*     1.3    63.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 515 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  TYR*     3.6    24.2    -      +       -      -
    382A  VAL*     6.0     1.3    -      -       +      -
    387A  LEU*     3.9    24.5    -      -       +      -
    392A  PHE*     3.5    43.7    -      +       +      -
    394A  ASN      3.3     3.4    -      -       -      -
    395A  VAL*     3.4    36.8    -      -       +      -
    396A  TYR*     5.4     1.3    -      -       -      -
    429A  PHE*     4.0    18.3    -      +       +      -
    431A  GLY*     3.5    34.1    -      -       -      -
    432A  CYS*     5.3     2.9    -      -       -      -
    513A  LEU*     4.5    13.2    -      -       +      -
    514A  SER*     1.3    76.7    +      -       -      +
    516A  GLU*     1.3    61.0    +      -       -      +
    517A  LEU*     3.6    14.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 516 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392A  PHE*     3.7     7.3    -      -       -      +
    393A  THR*     2.8    36.7    +      -       +      -
    394A  ASN*     2.7    41.8    +      -       +      +
    396A  TYR*     4.7     8.2    -      -       +      -
    514A  SER      4.3     0.2    +      -       -      -
    515A  PHE*     1.3    71.9    -      -       -      +
    517A  LEU*     1.3    59.7    +      -       -      +
    519A  HIS*     5.1     7.9    -      -       +      -
----------------------------------------------------------
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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