Contacts of the strand formed by residues 313 - 318 (chain B) in PDB entry 3COG


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 313 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161B  ASN*     3.5    14.6    -      -       -      +
    164B  GLN*     3.9    29.9    +      -       -      +
    190B  PHE*     4.3    17.3    -      -       +      +
    213B  TYR*     3.7     8.7    -      -       +      +
    290B  ILE      4.7     0.2    -      -       -      +
    291B  TYR*     3.2    21.3    -      -       -      -
    292B  PRO*     4.6     0.5    -      -       -      +
    311B  THR*     3.1    17.6    +      -       -      +
    312B  GLY*     1.3    73.8    -      -       -      +
    314B  VAL*     1.3    59.7    +      -       -      +
    315B  THR      4.3     0.4    -      -       -      -
    341B  LEU*     2.8    52.7    -      -       +      -
    375B  ARG*     3.6    16.4    -      -       -      +
    376B  LEU      3.6    14.1    -      -       -      +
    377B  SER*     3.7    15.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 314 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273B  GLY*     3.6    22.7    -      -       -      +
    276B  VAL*     4.4     4.3    -      -       +      -
    277B  ALA*     4.1    10.1    -      -       +      -
    280B  LEU*     4.0    26.5    -      -       +      -
    289B  VAL*     4.0    17.9    -      -       +      -
    290B  ILE      4.2     4.3    -      -       -      +
    291B  TYR*     3.7    12.1    -      -       +      -
    312B  GLY      3.3    11.9    +      -       -      +
    313B  MET*     1.3    78.8    -      -       -      +
    315B  THR*     1.3    62.7    +      -       -      +
    375B  ARG*     5.2     0.4    -      -       -      +
    376B  LEU*     2.8    50.0    +      -       +      +
    378B  VAL*     4.1     9.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 315 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162B  PRO      2.5    30.9    +      -       -      +
    164B  GLN*     4.0     5.1    +      -       -      +
    289B  VAL*     3.6     3.1    -      -       -      +
    290B  ILE*     2.7    58.6    +      -       +      +
    313B  MET      4.3     0.2    -      -       -      -
    314B  VAL*     1.3    75.5    +      -       -      +
    316B  PHE*     1.3    62.6    +      -       -      +
    317B  TYR*     5.1     0.4    -      -       +      -
    373B  LEU*     3.6    31.2    -      -       +      -
    374B  ILE      3.4    11.0    -      -       -      +
    375B  ARG*     4.0    15.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 316 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280B  LEU*     3.6    25.8    -      -       +      -
    286B  VAL*     3.7    25.6    -      -       +      -
    288B  LYS      3.2    13.0    -      -       -      +
    289B  VAL*     4.0    14.1    -      -       +      -
    314B  VAL      5.2     0.2    -      -       -      -
    315B  THR*     1.3    76.5    -      -       -      +
    317B  TYR*     1.3    72.7    +      -       -      +
    318B  ILE*     4.0    12.3    -      -       +      -
    328B  PHE*     3.9    22.7    -      +       -      -
    372B  THR      3.6     0.5    -      -       -      +
    373B  LEU*     3.5     3.2    -      -       -      +
    374B  ILE*     2.8    79.5    +      -       +      +
    376B  LEU*     4.0    20.6    -      -       +      -
    394B  LEU*     4.3     5.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 317 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    163B  THR*     4.6     7.1    -      -       -      +
    286B  VAL*     3.5     4.2    -      -       -      +
    287B  GLU*     2.7    46.6    +      -       +      -
    288B  LYS*     2.7    44.6    +      -       +      +
    290B  ILE*     3.9    27.5    -      -       +      +
    315B  THR*     5.1     0.4    -      -       +      -
    316B  PHE*     1.3    77.2    -      -       -      +
    318B  ILE*     1.3    54.5    +      -       -      +
    370B  SER*     3.5    31.4    -      -       -      -
    372B  THR*     3.2    16.6    -      -       -      +
    373B  LEU*     3.3    37.3    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 318 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    285B  TRP      3.7    11.0    -      -       -      +
    286B  VAL*     4.5     0.2    -      -       -      +
    287B  GLU*     4.1     4.4    -      -       -      +
    316B  PHE*     3.8     7.8    -      -       +      -
    317B  TYR*     1.3    74.1    -      -       -      +
    319B  LYS*     1.3    73.9    +      -       -      +
    320B  GLY      3.6     0.2    +      -       -      -
    321B  THR      4.4     0.9    -      -       -      +
    324B  HIS*     3.7    23.3    -      -       +      +
    325B  ALA*     3.8    23.1    -      -       +      +
    328B  PHE*     3.7    21.1    -      -       +      -
    372B  THR*     3.0    45.1    +      -       +      +
    374B  ILE*     4.0     8.3    -      -       +      -
    394B  LEU*     3.8    20.0    -      -       +      -
    397B  ALA*     4.1    11.0    -      -       +      -
    398B  HIS*     4.2     3.6    -      -       +      +
----------------------------------------------------------
 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