Contacts of the strand formed by residues 322 - 326 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    320B  GLY      3.6     9.6    +      -       -      -
    321B  LYS*     1.3    74.7    -      -       -      +
    323B  PHE*     1.3    59.3    +      -       -      +
    350B  LYS      4.8     0.4    +      -       -      -
    351B  CYS      2.8    25.8    +      -       -      -
    352B  SER*     3.0     8.6    -      -       -      +
    353B  ALA      2.8    26.6    +      -       -      +
    354B  ALA*     4.3     1.1    -      -       -      -
    355B  SER*     2.9    28.2    +      -       -      -
    356B  ARG*     3.2     8.0    +      -       -      +
    458B  GLU*     5.4     0.2    +      -       -      -
    488B  ALA*     4.4     0.2    -      -       -      -
    489B  LEU*     3.2    15.9    +      -       -      +
    490B  THR*     2.9    49.2    +      -       -      +
    521B  CYS*     4.0     2.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 323 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    322B  ASN*     1.3    76.6    -      -       -      +
    324B  HIS*     1.3    69.7    +      -       -      +
    325B  LEU*     4.2    10.8    -      -       +      -
    354B  ALA*     5.2     0.2    -      -       -      -
    356B  ARG*     3.3    42.2    -      -       +      +
    358B  TYR*     4.0     9.6    -      -       +      -
    481B  ILE*     4.1    19.7    -      -       +      -
    488B  ALA*     4.5     1.6    -      -       +      -
    490B  THR      3.4     6.3    +      -       -      -
    491B  GLY*     3.3    24.1    -      -       -      -
    492B  ALA      3.0    39.4    +      -       -      -
    508B  LEU*     3.8    31.4    -      -       +      -
    511B  SER*     3.9    26.9    -      -       -      -
    512B  ALA*     4.4     2.7    -      -       +      -
    515B  PHE*     4.1     9.9    -      +       -      -
    521B  CYS*     4.2     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 324 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323B  PHE*     1.3    83.8    -      -       -      +
    325B  LEU*     1.3    60.8    +      -       -      +
    326B  VAL      4.0     0.2    -      -       -      -
    338B  SER      3.6    23.8    -      -       -      -
    339B  THR*     3.1    26.4    +      -       +      +
    342B  GLY*     4.8     0.7    -      -       -      -
    354B  ALA*     3.9    13.7    -      -       +      +
    356B  ARG      2.9     9.5    +      -       -      +
    357B  LEU*     3.3    21.4    -      -       +      +
    358B  TYR*     2.8    27.4    +      -       -      -
    464B  LEU*     6.4     0.2    -      -       +      -
    492B  ALA*     3.7    13.2    -      -       +      +
    494B  PHE*     3.4    18.9    -      +       +      -
    520B  LYS*     3.6    11.8    -      -       +      +
    521B  CYS*     3.0    39.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 325 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    323B  PHE*     4.1    11.4    -      -       +      -
    324B  HIS*     1.3    70.8    -      -       -      +
    326B  VAL*     1.3    63.0    +      -       -      +
    358B  TYR*     3.7    22.7    -      -       +      -
    469B  TYR*     4.3     7.0    -      -       +      +
    474B  PHE*     3.6    32.1    -      -       +      -
    477B  ILE*     3.8    20.9    -      -       +      -
    478B  CYS*     3.9    18.4    -      -       -      -
    481B  ILE*     4.5     8.5    -      -       +      -
    492B  ALA      2.7    15.8    +      -       -      +
    493B  ILE*     3.2    13.8    -      -       +      +
    494B  PHE*     2.8    26.9    +      -       -      -
    504B  ALA*     4.4     0.2    -      -       +      -
    508B  LEU*     4.2    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 326 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    325B  LEU*     1.3    78.1    -      -       -      +
    327B  HIS*     1.3    65.0    +      -       -      +
    330B  ALA*     3.9    13.7    -      -       +      -
    332B  ILE*     4.3    15.5    -      -       +      -
    335B  ALA*     4.2     5.8    -      -       +      -
    339B  THR*     5.3     0.4    -      -       -      +
    357B  LEU*     4.0    15.3    -      -       +      -
    358B  TYR      2.9    15.5    +      -       -      +
    359B  LEU*     3.9    20.9    -      -       +      -
    360B  PRO*     3.1    21.6    -      -       +      +
    363B  LYS*     5.7     0.2    -      -       +      -
    367B  PHE*     4.1    11.4    -      -       +      -
    469B  TYR*     2.7    26.1    +      -       -      -
    494B  PHE*     3.8    18.6    -      -       +      -
----------------------------------------------------------
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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