Contacts of the strand formed by residues 220 - 225 (chain B) in PDB entry 4OMC


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 ARG 220 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146B  GLY*     5.2    15.3    +      -       -      +
    147B  ILE      3.0    12.5    +      -       -      +
    148B  VAL*     3.6    18.9    -      -       +      +
    149B  VAL*     3.1    28.1    +      -       -      +
    166B  ASN*     3.3    10.8    -      -       -      +
    167B  TYR      5.6     0.7    -      -       -      +
    168B  ASP*     2.9    45.3    +      -       +      +
    218B  ASN      5.2     2.7    -      -       -      +
    219B  ALA*     1.3    76.4    -      -       -      +
    221B  ILE*     1.3    60.5    +      -       -      +
    246B  HIS*     3.1    21.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  VAL*     3.5    22.7    -      -       +      +
    151B  ILE*     3.6    31.6    -      -       +      -
    156B  ILE*     4.1    16.2    -      -       +      -
    163B  LEU*     4.4    15.7    -      -       +      +
    166B  ASN*     2.9    29.4    +      -       +      +
    167B  TYR*     3.3    10.0    -      -       +      +
    168B  ASP*     2.8    27.0    +      -       -      -
    199B  ALA*     4.1    18.2    -      -       +      +
    202B  VAL*     4.3     8.3    -      -       +      -
    203B  ALA*     3.9    13.9    -      -       +      -
    220B  ARG*     1.3    75.0    -      -       -      +
    222B  GLY*     1.3    62.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149B  VAL      2.8    10.5    +      -       -      -
    150B  SER*     3.5     0.6    -      -       -      -
    151B  ILE*     3.0    29.9    +      -       -      +
    156B  ILE*     4.1     6.1    -      -       -      +
    167B  TYR*     4.5     2.0    -      -       -      -
    168B  ASP      3.8     0.7    -      -       -      -
    171B  ALA*     3.5    21.6    -      -       -      +
    172B  SER*     3.2    13.2    -      -       -      -
    221B  ILE*     1.3    77.1    -      -       -      +
    223B  GLY*     1.3    58.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  SER*     4.2     0.2    -      -       -      -
    151B  ILE*     3.4    11.4    -      -       -      -
    155B  GLY      5.5     0.9    -      -       -      -
    156B  ILE*     3.7    22.5    -      -       -      +
    171B  ALA      3.4     1.4    +      -       -      -
    172B  SER*     2.8    31.1    +      -       -      -
    173B  PHE      3.1     2.9    +      -       -      -
    182B  PRO*     3.3    10.1    -      -       -      +
    222B  GLY*     1.3    74.8    -      -       -      -
    224B  VAL*     1.3    64.7    +      -       -      -
    225B  ARG      4.0     0.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 224 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150B  SER*     3.8    13.2    -      -       -      +
    151B  ILE      2.9     7.1    +      -       -      +
    152B  LEU*     3.8    19.1    -      -       +      -
    153B  ASP      3.0    27.2    +      -       -      +
    155B  GLY*     4.3     2.3    +      -       -      -
    173B  PHE*     3.2    10.5    -      -       +      +
    175B  VAL*     3.9    16.8    -      -       +      -
    223B  GLY*     1.3    74.8    -      -       -      +
    225B  ARG*     1.3    61.5    +      -       -      +
    226B  MET*     3.2    10.6    +      -       +      +
    239B  SER*     3.5    26.5    -      -       -      +
    242B  LEU*     3.5    36.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 225 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153B  ASP      3.7     3.4    -      -       -      -
    154B  ASP      3.8    18.2    +      -       -      +
    155B  GLY*     3.8    11.2    -      -       -      +
    173B  PHE      2.9     8.6    +      -       -      +
    174B  ASP*     2.8    49.3    +      -       -      +
    175B  VAL      2.9    23.6    +      -       -      -
    176B  ASN*     3.2    18.9    +      -       -      +
    177B  ASP*     2.9    26.8    +      -       -      -
    182B  PRO*     3.9     9.5    -      -       +      +
    183B  GLN      3.5    25.5    +      -       -      -
    185B  ARG*     3.6    23.5    -      -       -      +
    223B  GLY      4.0     1.4    +      -       -      -
    224B  VAL*     1.3    70.3    -      -       -      +
    226B  MET*     1.3    57.4    +      -       -      +
    228B  ASP*     2.9    39.2    +      -       +      +
----------------------------------------------------------
 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