Contacts of the strand formed by residues 288 - 292 (chain C) 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 288 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248C  HIS      3.1    18.4    +      -       -      +
    249C  ILE*     3.4    14.2    -      -       +      +
    250C  TYR*     2.8    30.0    +      -       -      +
    282C  ARG*     3.9    16.4    -      -       -      +
    286C  GLY      3.9     3.1    -      -       -      +
    287C  SER*     1.3    71.7    -      -       -      +
    289C  PHE*     1.3    59.8    +      -       -      +
    290C  VAL*     4.3     9.0    -      -       +      -
    315C  LEU*     3.5    26.5    -      -       +      -
    378C  ILE*     4.0    21.3    -      -       +      -
    382C  LEU*     4.6     8.1    -      -       +      -
    388C  LEU      5.6     0.2    -      -       -      +
    389C  THR      4.5     0.7    -      -       -      +
    390C  TRP*     3.6    31.6    -      -       +      +
    393C  MET*     4.1    17.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 289 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240C  LEU*     3.7    42.2    -      -       +      -
    250C  TYR*     3.7    34.3    -      +       +      -
    273C  ALA      4.3     1.3    -      -       -      -
    274C  PHE*     3.6    44.4    -      +       +      -
    277C  GLY*     4.2     9.6    -      -       -      -
    278C  VAL*     4.2     5.6    -      -       +      -
    287C  SER*     3.7    29.4    +      -       -      -
    288C  ILE*     1.3    73.3    -      -       -      +
    290C  VAL*     1.3    60.2    +      -       -      +
    291C  TRP*     4.8     4.5    -      +       +      -
    313C  TYR      3.6    19.8    +      -       -      +
    314C  THR*     3.2    15.7    -      -       +      -
    315C  LEU*     2.8    30.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 290 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249C  ILE*     4.0    17.7    -      -       +      -
    250C  TYR      2.9    13.8    +      -       -      +
    251C  SER*     3.7     2.1    +      -       -      -
    252C  ALA*     2.9    29.3    +      -       -      +
    288C  ILE*     4.3     4.5    -      -       +      -
    289C  PHE*     1.3    74.1    -      -       -      +
    291C  TRP*     1.3    65.3    +      -       -      +
    315C  LEU*     3.7     6.1    -      -       +      +
    317C  ILE*     3.9    22.0    -      -       +      -
    371C  ALA*     3.4    30.7    -      -       +      +
    374C  ALA*     4.1     4.9    -      -       +      -
    375C  ALA*     4.1     8.5    -      -       +      -
    378C  ILE*     3.7    27.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 291 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    240C  LEU*     3.9    12.3    -      -       +      -
    250C  TYR*     6.5     0.2    -      -       +      -
    252C  ALA*     3.6    28.9    -      -       +      -
    254C  TRP*     2.8    54.0    +      +       -      -
    255C  GLY*     4.6     0.4    -      -       -      -
    274C  PHE*     3.5    24.7    -      +       -      -
    289C  PHE*     4.0     5.6    +      +       +      -
    290C  VAL*     1.3    77.9    -      -       -      +
    292C  ALA*     1.3    81.5    +      -       -      +
    308C  TYR*     3.4    40.2    -      +       +      +
    309C  THR*     3.7    20.2    -      -       +      -
    314C  THR*     3.8    27.6    -      -       +      +
    315C  LEU      3.0    10.9    +      -       -      +
    316C  SER*     3.5     2.0    -      -       -      -
    317C  ILE*     2.8    32.6    +      -       -      +
    371C  ALA*     3.9     4.7    -      -       -      -
      5J  00S      4.1     2.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 292 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252C  ALA      3.2    14.9    +      -       -      +
    253C  SER*     4.0     7.4    -      -       -      -
    291C  TRP*     1.3    72.9    -      -       -      +
    293C  SER*     1.3    60.2    +      -       -      +
    294C  GLY      3.3     0.2    -      -       -      -
    309C  THR*     3.4     5.0    -      -       -      +
    317C  ILE      3.9     4.3    -      -       -      -
    367C  THR*     3.3    31.2    -      -       -      +
    371C  ALA*     3.8     9.8    -      -       +      +
      5J  00S      2.9    44.6    +      -       +      -
----------------------------------------------------------
 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