Contacts of the strand formed by residues 136 - 140 (chain q) in PDB entry 5GJQ


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 136 (chain q).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185f  ARG*     3.1    35.7    +      -       -      -
     27p  ALA      5.7     0.5    -      -       -      +
     13q  ALA      3.2    15.0    -      -       -      +
     14q  MET*     4.1    13.0    -      -       +      -
    121q  ILE*     3.6     2.9    -      -       -      -
    133q  THR*     2.8    19.3    +      -       -      +
    135q  ASP*     1.3   113.6    +      -       +      +
    137q  VAL*     1.3    66.0    -      -       -      +
    138q  VAL*     4.7     7.0    -      -       +      -
    147q  TYR*     4.2    16.2    -      +       -      -
    150q  CYS*     3.4    53.2    -      -       +      -
    151q  GLU*     3.6    12.8    -      -       +      -
    154q  TRP*     4.1    15.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with VAL 137 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12q  MET*     3.4     1.2    -      -       -      +
     13q  ALA*     2.9    52.6    +      -       +      +
    108q  VAL*     3.9     6.2    -      -       +      +
    121q  ILE*     4.1     8.3    -      -       +      -
    122q  CYS*     3.8    28.5    -      -       -      +
    123q  SER*     4.0    21.1    -      -       -      +
    131q  MET*     4.1    11.0    -      -       +      +
    133q  THR*     3.5    17.9    -      -       +      +
    136q  PHE*     1.3    79.7    -      -       -      +
    138q  VAL*     1.3    71.6    +      -       -      +
    147q  TYR*     6.1     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 138 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22p  GLU*     4.9     7.0    -      -       -      +
     11q  VAL      3.5     5.4    -      -       -      -
     12q  MET*     3.8    13.2    -      -       +      -
    108q  VAL*     4.4     2.5    -      -       -      -
    123q  SER*     4.2     9.4    +      -       -      -
    131q  MET*     5.7     1.2    -      -       -      +
    136q  PHE*     4.7    10.5    -      -       +      -
    137q  VAL*     1.3    83.5    -      -       -      +
    139q  SER*     1.3    73.8    +      -       -      +
    143q  ALA*     4.2     7.9    -      -       +      +
    146q  MET*     3.5    41.1    -      -       +      +
    147q  TYR*     3.5    46.6    +      -       +      +
    150q  CYS*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 139 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22p  GLU*     6.0     1.6    -      -       -      -
     10q  ALA*     3.6     0.3    -      -       -      -
     11q  VAL*     2.9    36.1    +      -       -      +
     54q  ALA*     4.1     6.1    -      -       -      +
    106q  GLU*     3.3    44.0    +      -       -      +
    108q  VAL*     3.9    10.9    -      -       -      +
    123q  SER*     4.2     6.1    -      -       -      -
    124q  LEU      5.0     0.7    +      -       -      -
    138q  VAL*     1.3    85.0    +      -       -      +
    140q  GLY*     1.3    59.4    +      -       -      +
    143q  ALA*     5.3     2.0    -      -       -      -
    146q  MET*     3.4     7.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 140 (chain q). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4q  MET*     6.3     1.1    -      -       -      -
      9q  GLY      3.2    13.7    -      -       -      -
     10q  ALA*     4.4     1.1    -      -       -      -
     54q  ALA*     4.5     3.1    -      -       -      -
    106q  GLU*     4.0    22.1    +      -       -      +
    139q  SER*     1.3    77.5    -      -       -      +
    141q  THR*     1.3    67.2    +      -       -      -
    142q  CYS      3.1     3.7    +      -       -      -
    143q  ALA*     3.5    16.0    +      -       -      +
    146q  MET*     4.1     2.9    -      -       -      +
----------------------------------------------------------
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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