Contacts of the strand formed by residues 322 - 326 (chain A) in PDB entry 4OE4


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 ASN 322 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320A  GLY*     3.5     9.1    +      -       -      -
    321A  LYS*     1.3    75.5    -      -       -      +
    323A  PHE*     1.3    58.0    -      -       -      +
    350A  LYS      4.8     0.2    +      -       -      -
    351A  CYS      2.7    27.4    +      -       -      -
    352A  SER*     3.1     9.3    -      -       -      +
    353A  ALA      2.9    25.2    +      -       -      +
    354A  ALA*     3.7     1.5    -      -       -      -
    355A  SER*     3.0    28.2    +      -       -      -
    356A  ARG*     3.2     7.7    +      -       -      +
    488A  ALA*     4.5     0.2    -      -       -      -
    489A  LEU*     3.2    15.1    +      -       -      +
    490A  THR*     3.0    47.5    +      -       -      +
    521A  CYS*     4.0     4.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 323 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322A  ASN*     1.3    77.3    -      -       -      +
    324A  HIS*     1.3    67.1    +      -       -      +
    325A  LEU*     4.2    12.1    -      -       +      -
    356A  ARG*     3.3    41.3    -      -       +      +
    358A  TYR*     3.9    10.8    -      -       +      -
    481A  ILE*     4.0    21.1    -      -       +      -
    488A  ALA*     4.5     1.3    -      -       +      -
    490A  THR      3.5     4.7    +      -       -      -
    491A  GLY*     3.2    18.5    -      -       -      -
    492A  ALA      2.9    46.5    +      -       -      -
    508A  LEU*     3.9    31.0    -      -       +      -
    511A  SER*     3.7    27.8    -      -       -      -
    512A  ALA*     4.3     3.6    -      -       +      -
    515A  PHE*     4.3     6.1    -      +       -      -
    521A  CYS*     4.2     0.3    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 324 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  PHE*     1.3    79.9    -      -       -      +
    325A  LEU*     1.3    59.6    +      -       -      +
    326A  VAL      4.1     0.2    -      -       -      -
    338A  SER      3.6    23.6    -      -       -      -
    339A  THR*     2.9    26.3    +      -       +      +
    342A  GLY*     4.7     1.3    -      -       -      -
    354A  ALA*     3.8    12.6    -      -       +      +
    356A  ARG      2.9     8.8    +      -       -      +
    357A  LEU*     3.3    20.5    -      -       +      +
    358A  TYR*     2.8    28.1    +      -       -      -
    464A  LEU*     6.5     0.2    -      -       +      -
    492A  ALA*     3.6     9.2    -      -       +      -
    494A  PHE*     3.4    26.6    -      +       +      -
    520A  LYS*     3.7     5.1    -      -       +      +
    521A  CYS*     3.1    41.6    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 325 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323A  PHE*     4.1    10.1    -      -       +      -
    324A  HIS*     1.3    73.4    -      -       -      +
    326A  VAL*     1.3    67.4    +      -       -      +
    358A  TYR*     3.7    20.9    -      -       +      -
    469A  TYR*     4.3     2.7    -      -       +      -
    474A  PHE*     3.7    31.0    -      -       +      -
    477A  ILE*     3.7    25.8    -      -       +      -
    478A  CYS*     3.8    17.9    -      -       -      -
    481A  ILE*     4.5     7.4    -      -       +      -
    492A  ALA      2.8    15.0    +      -       -      +
    493A  ILE*     3.2    14.5    -      -       +      +
    494A  PHE*     2.9    26.6    +      -       -      -
    504A  ALA*     4.5     0.2    -      -       +      -
    508A  LEU*     4.2    17.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 326 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325A  LEU*     1.3    77.4    -      -       -      +
    327A  HIS*     1.3    65.8    +      -       -      +
    330A  ALA*     3.9    13.9    -      -       +      -
    332A  ILE*     4.5    13.2    -      -       +      -
    335A  ALA*     4.5    11.2    -      -       +      -
    339A  THR*     5.4     0.4    -      -       -      +
    357A  LEU*     3.9    14.6    -      -       +      -
    358A  TYR      2.9    15.5    +      -       -      +
    359A  LEU*     3.7    23.3    -      -       +      -
    360A  PRO*     3.1    22.9    -      -       +      +
    363A  LYS*     5.6     0.2    -      -       +      -
    367A  PHE*     4.0    11.0    -      -       +      -
    469A  TYR*     2.6    27.9    +      -       -      -
    494A  PHE*     3.7     9.6    -      -       +      -
----------------------------------------------------------
 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