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


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 D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146D  GLY*     5.5    13.3    +      -       -      +
    147D  ILE      2.9    12.5    +      -       -      +
    148D  VAL*     3.5    16.3    -      -       +      +
    149D  VAL*     2.9    29.1    +      -       -      +
    166D  ASN*     3.4    13.2    -      -       -      +
    167D  TYR      5.7     0.4    -      -       -      +
    168D  ASP*     3.0    41.3    +      -       +      +
    203D  ALA*     5.1     0.2    -      -       -      -
    218D  ASN      5.2     2.7    -      -       -      +
    219D  ALA*     1.3    75.3    -      -       -      +
    221D  ILE*     1.3    59.5    +      -       -      +
    246D  HIS*     3.2    24.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 221 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149D  VAL*     3.4    15.5    -      -       +      +
    151D  ILE*     3.8    24.0    -      -       +      -
    156D  ILE*     4.3     7.0    -      -       +      -
    163D  LEU*     4.4    17.5    -      -       +      +
    166D  ASN*     3.0    30.4    +      -       +      +
    167D  TYR*     3.3    10.0    -      -       +      +
    168D  ASP*     2.9    26.1    +      -       -      -
    199D  ALA*     4.1    20.6    -      -       +      +
    202D  VAL*     4.1    30.1    -      -       +      -
    203D  ALA*     3.8    12.3    -      -       +      -
    219D  ALA      3.8     0.6    +      -       -      -
    220D  ARG*     1.3    74.1    -      -       -      +
    222D  GLY*     1.3    62.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 222 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149D  VAL      2.8    10.3    +      -       -      +
    150D  SER*     3.5     0.6    -      -       -      -
    151D  ILE*     2.9    29.4    +      -       -      +
    156D  ILE*     4.0     6.3    -      -       -      +
    167D  TYR*     4.6     1.3    -      -       -      -
    168D  ASP      3.8     1.1    -      -       -      -
    171D  ALA*     3.6    22.7    -      -       -      +
    172D  SER*     3.3    13.0    -      -       -      -
    221D  ILE*     1.3    77.8    -      -       -      +
    223D  GLY*     1.3    58.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 223 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151D  ILE*     3.4    11.0    -      -       -      -
    155D  GLY      5.5     0.9    -      -       -      -
    156D  ILE*     3.7    22.1    -      -       -      +
    171D  ALA      3.4     2.0    +      -       -      -
    172D  SER*     3.0    31.4    +      -       -      -
    173D  PHE      3.1     3.1    +      -       -      -
    182D  PRO*     3.3     9.9    -      -       -      +
    222D  GLY*     1.3    74.9    -      -       -      -
    224D  VAL*     1.3    65.1    +      -       -      -
    225D  ARG      4.0     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 224 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150D  SER*     3.6     7.9    -      -       -      +
    151D  ILE      2.9     8.5    +      -       -      +
    152D  LEU*     3.4    29.8    -      -       +      -
    153D  ASP      3.1    27.2    +      -       -      +
    155D  GLY*     4.3     2.6    +      -       -      -
    173D  PHE*     3.2    12.3    -      -       +      +
    175D  VAL*     3.8    17.9    -      -       +      -
    223D  GLY*     1.3    74.1    -      -       -      +
    225D  ARG*     1.3    60.3    +      -       -      +
    226D  MET*     3.1     6.6    +      -       +      +
    239D  SER*     3.6    27.6    -      -       -      +
    242D  LEU*     3.5    31.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 225 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153D  ASP      3.7     3.6    -      -       -      -
    154D  ASP      4.0    15.1    +      -       -      +
    155D  GLY*     3.8    10.8    -      -       -      +
    173D  PHE      2.8     9.0    +      -       -      +
    174D  ASP*     3.0    43.9    +      -       -      +
    175D  VAL*     2.9    23.9    +      -       -      +
    176D  ASN*     3.3    17.0    +      -       -      +
    177D  ASP*     3.0    26.8    +      -       -      -
    182D  PRO*     4.1    11.3    -      -       +      +
    183D  GLN      3.5    25.0    +      -       -      -
    185D  ARG*     3.7    25.3    -      -       -      +
    223D  GLY      4.0     1.4    -      -       -      -
    224D  VAL*     1.3    70.0    -      -       -      +
    226D  MET*     1.3    58.1    +      -       -      +
    228D  ASP*     3.0    39.5    +      -       +      +
----------------------------------------------------------
 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