Contacts of the strand formed by residues 630 - 636 (chain A) in PDB entry 2C11


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 630 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    525A  HIS*     5.9     1.1    -      -       -      +
    576A  ALA*     4.9     6.5    -      -       +      -
    577A  PHE      3.6     9.9    -      -       -      +
    578A  LEU*     3.2    35.0    -      -       +      -
    579A  VAL*     3.4     9.7    -      -       -      +
    626A  SER      4.1    13.5    -      -       -      -
    627A  TRP      3.0     6.1    +      -       -      +
    628A  GLU      3.1     0.6    +      -       -      -
    629A  ARG*     1.3   116.7    +      -       -      +
    631A  GLN*     1.3    60.3    +      -       -      +
    632A  LEU*     4.1    13.2    -      -       -      +
    633A  ALA*     4.6     3.8    -      -       +      -
    660A  PHE*     3.8    27.8    -      +       +      -
    661A  SER*     4.0    11.5    +      -       -      -
    664A  ILE*     3.2    32.7    -      -       +      +
    677A  TRP      5.5     0.9    -      -       -      +
    679A  THR*     2.8    30.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 631 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    577A  PHE*     2.8    10.3    +      -       +      +
    578A  LEU      2.6    22.6    +      -       -      -
    579A  VAL*     3.4    20.2    -      -       +      -
    580A  GLY*     3.5     3.8    -      -       -      +
    581A  SER*     2.8    31.4    +      -       -      +
    583A  THR*     3.6    20.9    +      -       +      +
    607A  MET*     3.7    26.7    -      -       +      +
    611A  ALA*     6.0     1.8    -      -       +      -
    630A  TYR*     1.3    74.1    -      -       -      +
    632A  LEU*     1.3    64.2    +      -       +      +
    677A  TRP      4.2     0.2    -      -       -      -
    678A  VAL*     3.5     1.9    -      -       -      -
    679A  THR*     2.7    38.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 632 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575A  ALA      4.1     2.9    -      -       -      +
    577A  PHE*     2.5    43.5    +      -       +      +
    583A  THR*     6.3     0.9    -      -       +      -
    587A  LEU*     4.3    24.7    -      -       +      -
    605A  ILE*     4.3    28.0    -      -       +      +
    607A  MET*     4.2    13.9    -      -       -      -
    630A  TYR*     4.2     3.6    -      -       -      +
    631A  GLN*     1.3    85.5    -      -       +      +
    633A  ALA*     1.3    73.5    +      -       -      +
    634A  VAL*     4.5     7.2    -      -       +      -
    676A  ALA*     3.9     7.9    -      -       +      -
    677A  TRP      3.1    29.6    -      -       -      +
    678A  VAL*     3.7    15.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 633 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575A  ALA      3.5     8.3    -      -       -      -
    576A  ALA*     3.7    17.7    -      -       +      +
    630A  TYR*     4.6    10.3    -      -       +      -
    632A  LEU*     1.3    79.1    -      -       -      +
    634A  VAL*     1.3    67.7    +      -       -      +
    635A  THR*     5.3     0.4    -      -       +      -
    660A  PHE*     4.6     3.6    -      -       +      -
    664A  ILE*     4.4    16.2    -      -       +      -
    676A  ALA*     3.3     0.2    -      -       -      -
    677A  TRP*     2.7    46.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 634 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    539A  VAL*     4.3    17.9    -      -       +      -
    572A  GLU*     3.8    22.5    -      -       -      +
    575A  ALA*     3.7    29.1    +      -       +      +
    576A  ALA*     4.5     0.6    -      -       -      +
    587A  LEU*     6.3     1.8    -      -       +      -
    589A  LEU*     4.4    16.8    -      -       +      -
    605A  ILE*     5.9     0.2    -      -       +      -
    632A  LEU*     4.5    10.5    -      -       +      -
    633A  ALA*     1.3    82.9    -      -       -      +
    635A  THR*     1.3    72.3    +      -       -      +
    664A  ILE*     6.0     0.2    -      -       -      +
    669A  ILE*     4.0     4.5    -      -       +      +
    674A  LEU*     4.1    22.9    -      -       +      -
    675A  VAL      3.5    12.3    -      -       -      +
    676A  ALA*     4.2    11.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 635 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572A  GLU*     3.7    15.5    -      -       +      +
    633A  ALA*     5.2     0.9    -      -       +      -
    634A  VAL*     1.3    84.1    -      -       -      +
    636A  GLN*     1.3    63.9    +      -       -      +
    641A  GLU*     4.4     6.0    +      -       -      -
    660A  PHE*     5.7     0.2    -      -       +      -
    663A  PHE*     3.4    31.5    -      -       +      +
    664A  ILE*     4.6     9.2    -      -       +      -
    669A  ILE*     4.6     1.3    -      -       -      -
    674A  LEU*     3.1    14.2    -      -       -      +
    675A  VAL*     2.8    39.2    +      -       -      +
    677A  TRP*     3.0    30.0    +      -       +      +
   1738A   CA      4.4     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 636 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572A  GLU*     3.4     6.0    +      -       -      +
    635A  THR*     1.3    77.5    +      -       -      +
    637A  ARG*     1.3    53.0    +      -       -      +
    638A  LYS*     2.6    43.6    +      -       +      +
    641A  GLU*     4.0     6.1    -      -       -      +
    667A  GLU*     2.7    43.8    +      -       -      +
    668A  THR*     3.1    27.6    +      -       -      +
    669A  ILE*     5.0     1.1    -      -       +      -
    672A  LYS*     3.9    30.5    -      -       +      +
    673A  ASP      3.4     6.7    -      -       -      +
    674A  LEU*     4.1     3.1    -      -       +      -
    675A  VAL*     4.0     1.1    -      -       -      +
----------------------------------------------------------
 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