Contacts of the strand formed by residues 175 - 178 (chain F) in PDB entry 3STJ


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 175 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162F  LEU*     3.7     1.4    -      -       -      -
    163F  GLY      3.2     8.6    +      -       -      -
    164F  ARG*     2.9    49.2    +      -       +      +
    167F  LEU*     3.6    19.1    -      -       +      -
    169F  LEU*     4.0    18.8    -      -       +      -
    170F  GLU*     4.0    26.7    -      -       +      -
    172F  LEU      5.3     0.7    -      -       -      -
    173F  GLU*     3.7    29.6    -      -       +      -
    174F  ASN*     1.3    78.1    -      -       -      +
    176F  ILE*     1.3    60.3    +      -       -      +
    203F  THR*     4.0    16.2    -      -       +      -
    204F  ALA*     5.0     1.1    -      -       +      -
    217F  PHE*     3.7    22.9    -      -       +      -
    218F  ALA      3.4    19.5    -      -       -      -
    219F  ILE*     3.9    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 176 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132F  SER*     5.6     0.2    -      -       -      -
    135F  LEU*     3.9    13.0    -      -       +      -
    159F  VAL*     3.7    37.2    -      -       +      -
    161F  ALA      3.7     4.3    -      -       -      +
    162F  LEU*     3.9    15.9    -      -       +      +
    163F  GLY      5.8     0.2    -      -       -      +
    174F  ASN      4.9     0.4    -      -       -      +
    175F  PHE*     1.3    75.8    -      -       -      +
    177F  GLN*     1.3    66.9    +      -       -      +
    178F  THR*     4.1     0.9    +      -       -      +
    191F  LEU*     4.3    15.5    -      -       +      -
    199F  ILE      3.2    31.2    -      -       -      +
    200F  GLY*     4.3     3.8    -      -       -      -
    216F  GLY      3.5     0.7    -      -       -      +
    217F  PHE*     3.3     6.1    -      -       -      -
    218F  ALA*     2.9    37.8    +      -       +      +
    220F  PRO*     3.6    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 177 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150E  LEU*     3.8     8.6    -      -       -      +
    153E  THR*     3.2    37.8    +      -       -      +
    159F  VAL*     3.6     3.6    -      -       -      -
    160F  SER*     2.7    32.9    +      -       -      -
    161F  ALA*     2.9    24.7    +      -       +      +
    164F  ARG*     2.9    35.1    +      -       +      -
    175F  PHE      3.9     0.4    +      -       -      -
    176F  ILE*     1.3    75.4    -      -       -      +
    178F  THR*     1.3    59.5    +      -       -      +
    214F  GLY      5.2     0.8    +      -       -      -
    215F  ILE*     3.9    20.5    -      -       +      +
    216F  GLY      3.2     8.1    -      -       -      +
    217F  PHE*     3.5    27.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 178 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141F  ALA*     4.2     7.3    -      -       -      +
    158F  ILE      2.9    23.0    +      -       -      -
    159F  VAL*     4.9     1.6    -      -       -      -
    160F  SER*     3.8     5.4    -      -       -      -
    176F  ILE*     5.1     1.6    -      -       -      +
    177F  GLN*     1.3    74.5    -      -       -      +
    179F  ASP*     1.3    59.3    +      -       -      +
    180F  ALA*     3.2    18.3    +      -       +      +
    182F  ILE*     3.5    30.3    -      -       +      -
    191F  LEU*     3.9    27.6    -      -       +      -
    202F  ASN*     4.9     0.9    -      -       -      +
    214F  GLY      3.4     4.0    -      -       -      +
    215F  ILE*     4.0     0.2    -      -       -      -
    216F  GLY*     2.9    38.4    +      -       -      +
    218F  ALA*     5.5     1.1    -      -       +      -
----------------------------------------------------------
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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