Contacts of the strand formed by residues 698 - 703 (chain A) in PDB entry 2VWK


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 VAL 698 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  THR*     3.8    29.2    -      -       +      -
    291A  TYR*     3.8     7.5    -      -       +      +
    292A  ALA*     3.6    16.6    +      -       -      +
    293A  GLU*     3.5     8.8    -      -       -      +
    663A  TYR*     3.9    17.7    -      -       +      -
    664A  GLU      3.3    18.8    -      -       -      +
    665A  GLN*     3.8    17.9    -      -       +      +
    696A  GLY      5.4     0.7    -      -       -      +
    697A  THR*     1.3    73.4    -      -       -      +
    699A  ILE*     1.3    75.0    +      -       -      +
    700A  SER*     5.4     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 699 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  GLU*     3.2    12.3    -      -       +      +
    662A  ILE      3.6     0.2    -      -       -      +
    663A  TYR*     3.5     5.0    -      -       -      -
    664A  GLU*     2.9    39.8    +      -       +      +
    666A  ILE*     3.8    21.3    -      -       +      -
    670A  LEU*     4.0    21.3    -      -       +      -
    679A  HIS*     4.7     4.9    -      -       +      -
    682A  VAL*     4.5    11.0    -      -       +      -
    686A  LEU*     5.0     2.0    -      -       +      -
    693A  ILE*     3.8    39.7    -      -       +      -
    697A  THR      3.7     0.4    +      -       -      -
    698A  VAL*     1.3    78.7    -      -       -      +
    700A  SER*     1.3    66.2    +      -       -      +
    701A  TYR*     3.5    33.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 700 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291A  TYR*     4.0    12.6    -      -       -      +
    293A  GLU*     3.3    24.4    +      -       -      +
    661A  VAL*     3.8    13.5    -      -       -      -
    662A  ILE      3.7     3.6    -      -       -      -
    663A  TYR*     3.2    28.9    -      -       -      -
    682A  VAL*     5.2     1.7    -      -       -      +
    699A  ILE*     1.3    75.5    +      -       -      +
    701A  TYR*     1.3    62.7    +      -       -      +
    716A  PRO*     3.4     5.4    -      -       -      +
    717A  PHE*     3.2    25.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 701 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614A  ASP*     3.9     6.8    +      -       -      +
    661A  VAL*     3.7     5.5    -      -       -      +
    662A  ILE*     2.8    74.4    +      -       +      +
    664A  GLU*     2.7    31.8    +      -       +      -
    678A  PRO*     3.7    30.8    -      -       +      +
    679A  HIS*     4.1     2.8    +      +       -      -
    682A  VAL*     3.7    20.2    -      -       +      -
    699A  ILE*     3.5    30.1    -      -       +      -
    700A  SER*     1.3    74.0    -      -       -      +
    702A  ILE*     1.3    59.3    +      -       -      +
    703A  VAL*     3.9    13.2    -      -       +      -
    714A  ALA*     3.9    16.4    -      -       +      -
    715A  ILE      3.3    14.8    -      -       -      +
    717A  PHE*     4.1     3.1    -      -       -      +
    731A  TYR*     5.0     1.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 702 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    657A  PRO*     4.0    22.4    -      -       +      +
    660A  LEU*     4.0    12.1    -      -       +      +
    701A  TYR*     1.3    74.5    -      -       -      +
    703A  VAL*     1.3    72.0    +      -       -      +
    704A  LEU*     3.8     4.4    +      -       +      +
    714A  ALA*     3.3     3.4    -      -       -      -
    715A  ILE*     3.0    50.0    +      -       +      +
    717A  PHE*     4.5    14.1    -      -       +      +
    720A  PHE*     3.7    46.4    -      -       +      -
    727A  TYR*     4.2    13.0    -      -       +      -
    732A  TYR*     3.4    14.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 703 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    662A  ILE*     4.0     4.7    -      -       +      -
    678A  PRO*     4.3     4.5    -      -       +      -
    701A  TYR*     3.9    23.6    -      -       +      -
    702A  ILE*     1.3    73.9    -      -       -      +
    704A  LEU*     1.3    63.0    +      -       -      +
    711A  GLY*     3.8    26.5    -      -       -      +
    713A  ARG      3.5    10.3    -      -       -      +
    714A  ALA*     4.1     5.8    -      -       +      -
    727A  TYR*     3.4    11.8    -      -       -      +
    728A  ASP*     3.0    23.4    +      -       +      -
    731A  TYR*     3.7    45.8    -      -       +      -
    732A  TYR*     3.0    14.6    +      -       +      +
----------------------------------------------------------
 Back to top of page


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