Contacts of the strand formed by residues 134 - 137 (chain B) in PDB entry 3EOV


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 PHE 134 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  PHE*     3.7    32.1    -      +       -      -
     59B  PHE*     3.8    21.1    -      +       +      -
     71B  TYR*     3.9    13.9    -      +       -      -
     76B  PHE*     4.1    26.2    -      +       -      -
     86B  GLN*     3.5     6.2    -      -       -      +
     87B  GLY      3.0    35.2    +      -       -      +
     88B  GLY*     3.4    22.4    -      -       -      -
    120B  LEU*     3.4    20.6    -      -       +      -
    121B  SER      3.3    13.7    -      -       -      +
    122B  MET*     4.6     1.6    -      -       -      -
    123B  ALA*     4.2     1.6    -      -       -      +
    132B  SER      3.8    11.9    -      -       -      +
    133B  GLN*     1.3    74.5    -      -       -      +
    135B  PHE*     1.3    71.6    +      -       -      +
    136B  ILE*     4.3     7.2    -      -       +      -
    151B  PHE*     4.2    11.4    -      -       +      -
    181B  ILE*     4.6     5.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  MET*     4.0    23.1    -      -       +      -
     85B  ILE      3.2    15.3    -      -       -      +
     86B  GLN*     4.1     1.1    -      -       -      -
    115B  HIS*     3.6    10.5    -      +       -      -
    119B  ALA      3.5     2.3    -      -       -      +
    120B  LEU*     3.5     3.4    -      -       -      -
    121B  SER*     3.0    70.0    +      -       -      -
    122B  MET      3.6    17.7    -      -       -      -
    123B  ALA      4.3     0.2    -      -       -      -
    134B  PHE*     1.3    80.9    -      -       -      +
    136B  ILE*     1.3    63.8    +      -       -      +
    137B  THR*     3.3    30.7    -      -       +      -
    144B  LEU*     3.8    21.5    -      -       +      -
    148B  HIS*     4.1     5.8    -      -       +      -
      4D  MVA      3.5    31.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31B  PHE*     5.3     1.1    -      -       +      -
     43B  ILE*     4.5     8.7    -      -       +      -
     45B  ILE*     4.3    10.1    -      -       +      -
     76B  PHE*     5.0     2.2    -      -       +      -
     84B  MET*     3.3     1.8    -      -       -      +
     85B  ILE*     3.0    44.9    +      -       +      +
    118B  GLY*     4.4     3.4    -      -       -      -
    119B  ALA      3.3     8.3    -      -       -      +
    120B  LEU*     3.5    28.5    -      -       +      -
    134B  PHE*     4.3    11.4    -      -       +      -
    135B  PHE*     1.3    73.8    -      -       -      +
    137B  THR*     1.3    72.3    +      -       -      +
    138B  THR*     4.6     1.9    -      -       -      +
    154B  VAL*     3.7    33.0    -      -       +      -
    158B  MET*     5.0     0.2    -      -       -      -
    161B  VAL*     4.1    26.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83B  PHE      3.7     8.5    -      -       -      -
     84B  MET*     3.8     1.3    -      -       +      -
    115B  HIS*     4.1     8.3    -      -       +      -
    116B  PHE      2.7    30.5    +      -       -      +
    117B  VAL*     3.6     1.0    -      -       -      -
    118B  GLY*     3.1    21.4    +      -       -      -
    119B  ALA      3.3    10.4    +      -       -      +
    135B  PHE*     3.3    32.5    -      -       +      -
    136B  ILE*     1.3    75.5    -      -       -      +
    138B  THR*     1.3    61.0    +      -       -      +
    139B  ALA      3.8    11.9    -      -       -      -
    141B  THR*     3.8    19.1    -      -       +      +
    158B  MET*     3.8     5.4    -      -       -      +
----------------------------------------------------------
 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