Contacts of the strand formed by residues 349 - 352 (chain A) in PDB entry 2OM5


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 349 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316A  TRP      3.5    11.0    -      -       -      +
    317A  GLY*     3.9     4.3    -      -       -      -
    330A  TRP*     3.7     8.7    +      -       -      +
    344A  GLU*     3.5    10.7    -      -       -      +
    345A  VAL*     3.6     2.4    -      -       -      -
    346A  LEU*     2.4    64.3    +      -       +      +
    347A  ALA      3.5     0.4    -      -       -      -
    348A  GLY*     1.3    80.0    -      -       -      +
    350A  LEU*     1.3    60.5    +      -       -      +
    351A  ARG*     3.9     2.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314A  LEU      3.3     4.5    -      -       -      +
    315A  ARG*     3.9     0.6    -      -       -      -
    316A  TRP*     2.9    51.8    +      -       +      +
    330A  TRP*     3.6    46.4    -      -       +      -
    337A  LEU*     4.1     9.4    -      -       +      -
    343A  VAL*     3.8    15.0    -      -       +      -
    344A  GLU      3.7     0.4    -      -       -      -
    345A  VAL*     3.8    26.7    -      -       +      -
    349A  ASP*     1.3    71.8    -      -       -      +
    351A  ARG*     1.3    59.7    +      -       -      +
    352A  PHE*     3.6    32.4    +      -       +      -
    363A  TYR*     3.9    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313A  ASN*     5.1     7.8    -      -       -      +
    314A  LEU      3.4     7.6    -      -       -      +
    315A  ARG*     5.0     8.3    -      -       +      +
    343A  VAL*     3.8     1.5    -      -       -      -
    344A  GLU*     2.9    83.2    +      -       +      +
    349A  ASP*     3.9     3.1    -      -       +      -
    350A  LEU*     1.3    71.6    -      -       -      +
    352A  PHE*     1.3    68.5    +      -       -      +
    353A  SER*     3.5     7.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    313A  ASN*     2.6    34.1    +      -       -      +
    314A  LEU*     3.1    34.9    +      -       +      +
    316A  TRP*     3.8    16.2    -      +       -      -
    342A  ARG*     4.3     2.9    -      -       +      -
    343A  VAL*     3.7    30.7    -      -       +      -
    350A  LEU*     3.6    34.5    -      -       +      -
    351A  ARG*     1.3    71.3    -      -       -      +
    353A  SER*     1.3    54.6    +      -       -      +
    354A  LYS      3.0     5.1    +      -       -      +
    355A  LEU*     3.6    28.7    -      -       +      +
    359A  ASP*     4.4     8.5    -      -       -      -
    363A  TYR*     3.7    31.2    -      +       -      -
    380A  LEU*     3.8    15.5    -      -       +      -
----------------------------------------------------------
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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