Contacts of the strand formed by residues 96 - 98 (chain F) in PDB entry 4J8W


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 THR 96 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     99C  ARG      3.6    15.0    +      -       -      -
    100C  VAL*     3.4    10.1    -      -       +      +
    101C  THR*     2.7    32.8    +      -       -      -
     65D  ASP*     4.5     4.5    -      -       -      +
     87F  VAL*     5.7     0.7    -      -       +      -
     90F  LEU      4.0     1.4    +      -       -      -
     91F  LYS*     3.9    46.2    +      -       +      +
     94F  GLY*     3.6     3.4    -      -       -      -
     95F  ARG*     1.3    75.6    +      -       -      +
     97F  LEU*     1.3    58.5    +      -       -      +
     98F  TYR*     4.0    27.1    -      -       +      -
    102F  GLY*     4.6     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 97 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101C  THR*     3.4    33.9    -      -       +      +
    103C  ALA*     4.3     5.6    -      -       +      +
     91E  ALA*     3.5    30.7    -      -       +      +
     94E  GLU*     4.4    12.3    -      -       +      -
     95E  ALA*     4.6     5.8    -      -       +      +
     87F  VAL*     4.2    18.0    +      -       +      +
     90F  LEU*     3.7    28.5    -      -       +      +
     95F  ARG      3.4     1.9    +      -       -      +
     96F  THR*     1.3    75.8    -      -       -      +
     98F  TYR*     1.3    67.9    -      -       -      +
     99F  GLY      4.1     0.3    +      -       -      -
    100F  PHE*     3.8    23.1    -      -       +      -
    102F  GLY*     2.6    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 98 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97C  LEU*     3.4    21.7    -      -       +      +
    100C  VAL*     3.6    23.6    -      -       +      -
    101C  THR      2.6    12.6    +      -       -      +
    102C  ILE*     4.4     8.1    -      -       +      -
    103C  ALA*     3.1    29.8    +      -       -      +
     58D  ILE*     3.9    34.2    -      -       +      +
     61D  SER*     3.7    21.8    -      -       -      -
     62D  PHE*     3.6    31.2    -      +       +      -
     65D  ASP*     2.4    45.6    +      -       +      +
     66D  VAL*     5.3     0.2    -      -       -      +
     96F  THR*     4.0    13.2    -      -       +      -
     97F  LEU*     1.3    85.1    -      -       -      +
     99F  GLY*     1.3    58.7    +      -       -      +
    100F  PHE      3.9     0.4    -      -       -      -
    102F  GLY*     3.9     3.4    -      -       -      -
----------------------------------------------------------
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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