Contacts of the strand formed by residues 504 - 510 (chain F) in PDB entry 2VKX


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 SER 504 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    502F  SER      4.9     2.0    -      -       -      -
    503F  PRO*     1.3    75.6    -      -       -      +
    505F  ILE*     1.3    60.4    +      -       -      +
    506F  ASP*     3.1    14.7    +      -       -      +
    519F  PHE*     3.0     3.8    -      -       -      -
    520F  ASP*     2.7    49.8    +      -       -      +
    588F  SER*     5.0     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 505 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    654E  GLY*     4.1    14.6    -      -       -      +
    503F  PRO      4.2     0.2    +      -       -      -
    504F  SER*     1.3    74.3    +      -       -      +
    506F  ASP*     1.3    59.8    +      -       -      +
    507F  GLN      3.4    25.4    -      -       -      +
    508F  VAL*     3.6    11.4    -      -       +      -
    517F  VAL*     3.4    15.7    -      -       +      -
    518F  GLN      3.5     3.6    -      -       -      -
    519F  PHE*     3.6     2.0    -      -       -      -
    574F  VAL*     3.5    28.5    -      -       +      +
    575F  ARG*     4.1     4.5    -      -       -      -
    576F  LEU*     3.5    28.0    -      -       +      -
    588F  SER*     4.0    19.2    -      -       -      +
    589F  ALA      4.2     4.0    -      -       -      +
    591F  SER*     3.8    19.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 506 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    653E  SER*     3.1    40.7    +      -       -      +
    654E  GLY*     4.4     5.8    -      -       -      -
    504F  SER*     3.1    17.3    +      -       -      +
    505F  ILE*     1.3    75.2    -      -       -      +
    507F  GLN*     1.3    65.6    +      -       +      +
    518F  GLN*     2.6    19.2    +      -       +      +
    519F  PHE      3.7     6.1    -      -       -      +
    520F  ASP*     2.3    36.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 507 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    623E  LYS*     6.3     0.7    -      -       -      +
    626E  ASP*     3.4    26.7    +      -       -      +
    630E  PRO*     3.5    10.8    -      -       +      +
    631E  ILE*     2.6    49.8    +      -       -      +
    653E  SER*     3.7     6.7    +      -       -      +
    505F  ILE*     3.4     2.6    -      -       -      +
    506F  ASP*     1.3    91.0    -      -       +      +
    508F  VAL*     1.3    75.2    +      -       -      +
    509F  GLU*     4.2     1.3    -      -       +      +
    516F  GLN      4.4     1.1    -      -       -      +
    518F  GLN*     2.8    60.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 508 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    623E  LYS*     4.3    19.8    -      -       +      +
    624E  GLN      4.8     2.3    -      -       -      +
    626E  ASP*     5.3     1.4    -      -       -      +
    505F  ILE*     3.6    18.6    -      -       +      -
    507F  GLN*     1.3    90.3    +      -       -      +
    509F  GLU*     1.3    62.3    +      -       -      +
    510F  PRO*     3.2    11.3    -      -       -      +
    515F  ALA*     4.4    11.2    -      -       +      -
    516F  GLN      3.5     4.7    -      -       -      +
    517F  VAL*     4.0    16.4    -      -       +      -
    574F  VAL*     4.2     8.1    -      -       +      -
    591F  SER*     3.8    15.0    -      -       -      +
    593F  PHE*     3.5    42.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 509 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    625E  ASP*     2.9    28.0    -      -       -      +
    626E  ASP*     2.7    51.5    +      -       -      +
    628E  GLY*     4.2     6.4    +      -       -      -
    507F  GLN*     5.3     1.7    -      -       +      +
    508F  VAL*     1.3    72.2    -      -       -      +
    510F  PRO*     1.3    64.4    -      -       -      +
    511F  TYR*     3.5    38.4    -      -       +      +
    515F  ALA*     3.4     2.9    -      -       -      -
    516F  GLN*     2.9    43.8    +      -       +      +
    596F  GLN*     4.1     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 510 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    623E  LYS      4.4     2.5    -      -       -      +
    624E  GLN*     3.9    14.6    -      -       -      +
    625E  ASP      3.8    12.8    -      -       -      +
    508F  VAL*     3.2    13.5    -      -       +      +
    509F  GLU*     1.3    93.5    -      -       -      +
    511F  TYR*     1.3    57.3    +      -       -      +
    515F  ALA*     4.1     7.4    -      -       +      -
    593F  PHE*     3.7    25.4    -      -       +      -
    594F  LYS      3.4    26.9    -      -       -      +
    595F  THR*     3.9     5.4    -      -       +      -
    596F  GLN*     2.6    31.2    +      -       +      -
----------------------------------------------------------
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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