Contacts of the strand formed by residues 351 - 355 (chain F) in PDB entry 4OMC


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 ILE 351 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122F  TRP*     4.5     2.9    -      -       +      -
    123F  TYR*     3.5    37.2    -      -       +      +
    201F  GLU*     3.6    33.7    -      -       +      +
    341F  TYR      4.0     8.5    -      -       -      +
    342F  SER*     3.9    24.0    -      -       -      +
    350F  GLN*     1.3    85.5    -      -       -      +
    352F  VAL*     1.3    67.2    -      -       -      +
    353F  THR*     4.9     0.2    -      -       -      -
    361F  THR      3.7     1.0    -      -       -      +
    362F  GLU*     3.3     8.6    -      -       -      -
    363F  SER      3.5     0.2    +      -       -      -
    364F  HIS*     3.0    46.5    +      -       +      +
    369F  ALA*     3.6    18.8    -      -       +      -
    373F  LEU*     4.5     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 352 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117F  LYS*     3.8    29.2    -      -       +      -
    120F  GLN*     4.0    28.5    -      -       +      +
    121F  GLN*     3.1    25.9    +      -       +      +
    123F  TYR*     2.9    24.1    +      -       -      +
    201F  GLU*     5.2     2.4    -      -       -      +
    211F  CYS*     4.5     1.8    -      -       -      -
    212F  GLY      4.9     0.4    -      -       -      +
    350F  GLN      3.8     4.9    +      -       -      +
    351F  ILE*     1.3    73.5    -      -       -      +
    353F  THR*     1.3    68.3    +      -       -      +
    360F  CYS*     4.4     6.1    -      -       -      -
    361F  THR      3.2     8.5    -      -       -      +
    362F  GLU*     3.6    28.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 353 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    197F  ARG*     2.7    43.5    +      -       +      +
    200F  GLY*     3.2    17.3    -      -       -      -
    201F  GLU*     3.2    11.4    +      -       -      -
    211F  CYS*     3.4    14.4    -      -       -      -
    212F  GLY      6.0     0.4    -      -       -      +
    351F  ILE      5.0     0.2    -      -       -      -
    352F  VAL*     1.3    77.6    -      -       -      +
    354F  THR*     1.3    65.4    +      -       -      +
    361F  THR*     2.9    46.7    +      -       +      +
    364F  HIS*     3.8    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 354 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160F  HIS*     3.4    22.9    -      -       +      +
    162F  ASP*     3.4    38.6    -      -       +      +
    163F  LEU*     4.1     9.6    -      -       +      +
    196F  THR*     3.0    26.3    +      -       -      +
    197F  ARG*     3.1    28.2    +      -       -      +
    200F  GLY*     3.1    12.3    -      -       -      -
    204F  ALA*     4.4     9.6    -      -       +      -
    211F  CYS*     4.5     4.3    -      -       -      -
    353F  THR*     1.3    79.2    +      -       -      +
    355F  ASP*     1.3    58.9    +      -       -      +
    359F  LYS      3.8     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 355 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160F  HIS*     3.2    11.8    -      -       -      -
    193F  ARG*     3.6    14.7    +      -       -      +
    196F  THR*     4.0     5.2    -      -       -      -
    197F  ARG*     2.9    42.5    +      -       -      +
    353F  THR      3.7     0.2    +      -       -      -
    354F  THR*     1.3    75.0    -      -       -      +
    356F  LEU*     1.3    80.7    +      -       -      +
    359F  LYS*     2.8    44.1    +      -       +      +
    360F  CYS      5.2     0.2    -      -       -      +
    361F  THR*     3.8    17.7    -      -       -      -
----------------------------------------------------------
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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