Contacts of the strand formed by residues 133 - 137 (chain F) in PDB entry 3GTL


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 VAL 133 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1443A  VAL*     5.1     0.4    -      -       -      -
   1444A  MET*     2.6    52.1    +      -       +      +
   1445A  ILE      4.1     9.6    -      -       -      +
    132F  LEU*     1.3    76.9    -      -       -      +
    134F  ILE*     1.3    67.2    +      -       -      +
    135F  ARG*     3.4     3.7    +      -       -      +
    145F  ASP*     3.9    22.0    -      -       +      +
    146F  TRP      3.4    31.9    -      -       -      +
    147F  SER*     3.5     7.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 134 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1441A  PHE*     3.8    30.5    -      -       +      -
   1442A  ASP      4.1     1.3    -      -       -      -
   1443A  VAL*     3.8     7.9    -      -       +      -
     85F  MET*     5.4     0.2    -      -       +      -
     89F  GLU*     3.5    27.4    -      -       +      +
     93F  ILE*     3.3    36.1    -      -       +      -
    132F  LEU      4.2     0.8    -      -       -      -
    133F  VAL*     1.3    72.4    -      -       -      +
    135F  ARG*     1.3    61.3    +      -       -      +
    136F  ARG*     3.5    31.0    -      -       +      +
    144F  GLU      3.6     0.3    -      -       -      +
    145F  ASP*     3.3     6.2    -      -       -      -
    146F  TRP*     3.0    37.9    +      -       +      +
    148F  VAL*     4.9     2.4    -      -       +      +
    151F  LEU*     4.7    14.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 135 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1441A  PHE*     3.4     3.5    -      -       -      +
   1442A  ASP*     3.0    35.5    +      -       +      +
   1444A  MET*     4.3    31.2    -      -       +      +
     73F  ALA*     6.0     0.8    -      -       -      +
    133F  VAL*     4.1     5.6    -      -       -      +
    134F  ILE*     1.3    74.5    -      -       -      +
    136F  ARG*     1.3    58.0    +      -       -      +
    137F  TYR*     3.1    45.2    +      -       +      -
    143F  PHE*     3.0    37.9    -      -       +      -
    144F  GLU      3.2     4.9    -      -       -      -
    145F  ASP*     2.8    36.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 136 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    852A  TYR*     3.1    46.5    -      -       +      -
   1441A  PHE*     4.3     1.6    -      -       +      -
     81F  THR*     3.1    26.0    +      -       +      -
     82F  THR*     2.6    31.8    +      -       -      -
     84F  TYR      3.0    17.0    +      -       -      -
     86F  THR*     4.4     5.3    -      -       -      +
     89F  GLU*     2.5    28.5    +      -       -      -
    134F  ILE*     3.5    14.3    -      -       +      +
    135F  ARG*     1.3    70.5    -      -       -      +
    137F  TYR*     1.3    63.3    +      -       -      +
    138F  LEU*     3.6     3.0    +      -       -      +
    143F  PHE*     3.2     5.4    -      -       -      -
    144F  GLU*     2.8    41.6    +      -       +      +
    146F  TRP*     3.3    35.4    -      -       +      +
    151F  LEU*     3.8     4.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 137 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    851A  HIS*     4.7     8.7    +      -       -      -
    852A  TYR*     4.0    19.9    -      -       -      +
   1440A  ALA      4.3    15.4    +      -       -      +
   1441A  PHE*     4.8     1.8    -      -       -      -
   1442A  ASP*     3.2    28.8    +      -       -      +
    135F  ARG*     3.1    54.8    +      -       +      -
    136F  ARG*     1.3    72.1    -      -       -      +
    138F  LEU*     1.3    65.6    +      -       -      +
    139F  PRO*     4.2     1.0    -      -       -      +
    141F  GLY*     4.6    18.4    -      -       -      -
    142F  SER      4.0     2.2    -      -       -      -
    143F  PHE*     4.3    11.4    -      +       +      -
----------------------------------------------------------
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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