Contacts of the helix formed by residues 364 - 369 (chain O) in PDB entry 2I2X


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 ASP 364 (chain O).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233O  LEU*     3.7     3.5    -      -       -      +
    240O  HIS*     2.4    32.5    +      -       -      -
    298O  VAL*     3.3    29.6    -      -       +      -
    360O  ASP      4.3     0.6    +      -       -      -
    361O  ARG      4.0     0.9    -      -       -      +
    362O  TYR      3.3     2.0    -      -       -      -
    363O  ARG*     1.3    81.7    -      -       -      +
    365O  PRO*     1.3    78.3    -      -       -      +
    366O  GLN*     2.7    38.3    +      -       -      +
    367O  ALA*     3.1     3.3    +      -       -      +
    368O  TYR*     2.9    21.5    +      -       -      +
    412O  LEU*     4.2     4.5    -      -       -      -
     15P  ARG*     3.1    16.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 365 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240O  HIS*     4.1    16.2    -      -       +      +
    241O  THR*     4.0    15.9    -      -       +      -
    244O  VAL*     3.3    14.0    -      -       +      +
    364O  ASP*     1.3    98.4    -      -       -      +
    366O  GLN*     1.3    61.6    +      -       -      +
    368O  TYR*     3.5     9.7    -      -       +      +
    369O  MET      3.1    20.3    +      -       -      -
    404O  ILE*     3.5    32.6    -      -       +      +
    412O  LEU*     4.2     4.2    -      -       +      -
    414O  LEU*     3.9    20.6    -      -       +      -
    418O  GLU*     4.7     0.9    -      -       -      +
     15P  ARG*     3.8    12.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 366 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227O  MET*     3.2    36.1    +      -       -      +
    231O  GLY      5.1     2.0    +      -       -      -
    240O  HIS*     3.4    41.9    +      -       -      +
    243O  ALA*     3.5    18.8    -      -       -      +
    244O  VAL*     3.7    22.7    -      -       +      +
    247O  ARG*     5.2     2.5    +      -       +      +
    298O  VAL*     4.2     9.1    -      -       +      +
    299O  MET*     4.1    13.4    -      -       +      +
    364O  ASP*     2.7    23.9    +      -       -      +
    365O  PRO*     1.3    79.8    -      -       -      +
    367O  ALA*     1.3    57.8    +      -       -      +
    369O  MET      4.2     0.2    +      -       -      -
    370O  LEU*     3.3    27.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 367 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    298O  VAL*     3.6    23.5    -      -       +      +
    299O  MET*     3.9    20.4    -      -       +      +
    302O  LEU*     3.5     9.9    -      -       +      +
    360O  ASP*     3.3    26.7    -      -       +      +
    361O  ARG      4.2     0.7    -      -       -      -
    364O  ASP*     3.1     9.6    +      -       -      +
    366O  GLN*     1.3    78.6    -      -       -      +
    368O  TYR*     1.3    68.4    +      -       -      +
    370O  LEU*     2.9    13.1    +      -       -      +
    371O  ALA      3.2     8.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 368 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361O  ARG*     3.2    69.2    +      -       +      +
    362O  TYR*     4.0    15.0    -      +       -      -
    364O  ASP      2.9    14.4    +      -       -      +
    365O  PRO*     3.2    11.2    +      -       +      +
    367O  ALA*     1.3    78.1    -      -       -      +
    369O  MET*     1.3    63.1    +      -       -      +
    370O  LEU      3.3     0.3    +      -       -      -
    371O  ALA*     3.4     8.1    +      -       -      +
    374O  ASN*     2.8    29.2    +      -       -      -
    403O  ILE*     3.5    37.6    +      -       +      -
    404O  ILE*     4.0     9.4    -      -       +      -
    406O  GLU*     4.4     2.8    -      -       -      +
    407O  GLY*     3.3    27.4    +      -       -      -
    412O  LEU*     4.2    14.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 369 (chain O). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244O  VAL*     3.1    51.4    -      -       +      +
    247O  ARG*     4.0     9.0    -      -       +      -
    248O  ALA*     3.5    24.2    -      -       +      +
    275O  ILE*     4.0    15.5    -      -       -      -
    365O  PRO      3.1     4.5    +      -       -      +
    366O  GLN      4.7     0.7    -      -       -      +
    368O  TYR*     1.3    82.8    -      -       -      +
    370O  LEU*     1.3    72.0    +      -       +      +
    371O  ALA      3.3     0.4    -      -       -      -
    374O  ASN*     3.3     7.8    -      -       -      +
    375O  ALA*     3.2    24.1    +      -       -      -
    378O  VAL*     4.0    20.4    -      -       +      -
    400O  CYS*     3.8    12.6    -      -       +      -
    403O  ILE*     4.6     6.3    -      -       +      -
    404O  ILE*     4.3     7.2    -      -       +      -
----------------------------------------------------------
 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