Contacts of the strand formed by residues 362 - 368 (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 MET 362 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  GLY*     4.1     7.0    -      -       -      +
      7A  PRO*     3.5    40.2    -      -       +      +
      8A  VAL*     5.8     2.0    -      -       +      -
     87A  VAL*     4.3     1.6    -      -       +      -
     88A  GLY*     3.8    21.8    -      -       -      +
     89A  THR      3.1    26.5    -      -       -      +
     90A  VAL*     3.7    16.6    -      -       +      -
    305A  ASP*     5.9     0.2    -      -       -      +
    332A  ARG*     3.6     4.9    -      -       -      +
    333A  ASN*     3.1    33.0    +      -       -      +
    361A  GLY*     1.3    71.2    -      -       -      -
    363A  TYR*     1.3    64.1    +      -       -      +
    377A  SER*     5.2     1.3    -      -       -      +
    378A  ALA*     3.7    21.8    -      -       -      +
    379A  GLU*     3.6    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 363 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    303A  ILE*     3.7     6.4    -      -       +      +
    316A  TRP*     3.7    29.2    -      +       +      -
    330A  TRP*     4.8     2.5    -      +       +      -
    331A  LEU      3.3     8.1    -      -       -      +
    332A  ARG*     3.5    42.0    +      -       +      -
    337A  LEU*     4.3    11.2    -      -       +      -
    343A  VAL*     5.5     1.8    -      -       +      +
    350A  LEU*     3.9    16.2    -      -       +      -
    352A  PHE*     3.7    25.0    -      +       -      -
    359A  ASP*     3.0    41.4    +      -       -      +
    361A  GLY*     3.4    18.4    -      -       -      -
    362A  MET*     1.3    73.4    -      -       -      +
    364A  GLN*     1.3    67.8    +      -       -      +
    377A  SER*     3.4     0.9    -      -       -      -
    378A  ALA      3.1    31.6    +      -       -      +
    380A  LEU*     3.8    11.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 364 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  PHE*     4.8     2.2    -      -       -      -
     89A  THR      4.9     0.2    -      -       -      +
     90A  VAL*     3.6    15.3    -      -       +      +
     91A  VAL*     3.2    57.7    +      -       -      +
    303A  ILE*     4.4     0.9    -      -       -      -
    330A  TRP*     3.3    12.0    -      -       -      -
    331A  LEU*     2.7    54.0    +      -       +      +
    334A  GLY      4.7     4.0    +      -       -      -
    363A  TYR*     1.3    74.2    -      -       -      +
    365A  CYS*     1.3    62.8    +      -       -      +
    366A  VAL*     4.9     1.1    -      -       +      -
    375A  TYR*     4.8     9.8    -      -       +      +
    376A  ALA      3.2     8.1    -      -       -      +
    377A  SER*     3.1    35.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 365 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  TRP*     3.5    15.8    -      -       -      -
    303A  ILE*     4.6     1.8    -      -       -      +
    318A  CYS*     2.0    53.6    -      -       +      -
    328A  VAL*     4.2     4.0    -      -       +      -
    329A  ARG      3.6    10.3    -      -       -      +
    330A  TRP*     4.1    14.1    -      -       +      -
    364A  GLN*     1.3    72.7    -      -       -      +
    366A  VAL*     1.3    65.1    +      -       -      +
    375A  TYR*     3.7     1.2    -      -       -      -
    376A  ALA*     3.0    45.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 366 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    299A  TRP*     4.5     0.2    -      -       -      -
    327A  THR      3.0     4.7    -      -       -      +
    328A  VAL*     4.1     1.7    -      -       -      +
    329A  ARG*     2.6    65.1    +      -       +      +
    331A  LEU*     3.7    36.1    -      -       +      -
    364A  GLN*     4.7     1.1    -      -       +      +
    365A  CYS*     1.3    81.5    -      -       -      +
    367A  ALA*     1.3    57.7    +      -       -      +
    368A  GLU*     4.0     0.6    +      -       +      -
    373A  THR*     3.5    30.1    -      -       +      -
    374A  ILE      3.6     3.1    -      -       -      +
    375A  TYR*     3.7    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 367 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  PRO*     4.2     2.5    -      -       +      +
    299A  TRP*     3.6    23.6    -      -       +      -
    320A  ALA*     3.6    25.6    -      -       +      -
    326A  PRO*     4.3     7.2    -      -       +      -
    327A  THR      3.2     6.7    -      -       -      +
    328A  VAL*     4.2     8.1    -      -       +      +
    366A  VAL*     1.3    72.0    -      -       -      +
    368A  GLU*     1.3    63.2    +      -       -      +
    372A  GLY      3.9     0.5    -      -       -      +
    373A  THR*     3.3     1.4    -      -       -      +
    374A  ILE*     3.0    39.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 368 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    297A  PRO*     4.3     0.4    -      -       -      -
    326A  PRO*     3.4     9.5    -      -       -      +
    327A  THR*     2.8    49.5    +      -       -      +
    329A  ARG*     3.2    36.0    +      -       -      +
    367A  ALA*     1.3    76.3    -      -       -      +
    369A  ASN*     1.3    63.9    +      -       -      +
    372A  GLY      3.2     6.1    -      -       -      +
    373A  THR*     3.4    31.3    +      -       +      +
----------------------------------------------------------
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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