Contacts of the strand formed by residues 336 - 339 (chain A) in PDB entry 4JUO


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 336 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    332A  ILE*     3.5     4.8    -      -       -      +
    333A  ASP*     2.9    31.7    +      -       -      +
    334A  ASN*     2.7    24.4    +      -       +      +
    335A  PHE*     1.3    82.7    -      -       +      +
    337A  PRO*     1.3    81.1    +      -       -      +
    338A  ARG*     3.6     3.6    +      -       -      +
    639C  PHE*     4.5    19.5    -      -       +      -
    640C  THR      4.6     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 337 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ILE*     3.5    34.1    -      -       +      -
     30A  LEU*     4.4     1.1    -      -       +      -
    174A  TYR*     3.8    46.6    +      -       +      +
    330A  VAL*     4.2     9.9    -      -       +      -
    331A  ALA      3.5     6.5    -      -       -      +
    332A  ILE*     3.6     5.8    -      -       +      -
    335A  PHE      4.6     0.2    -      -       -      +
    336A  THR*     1.3    97.9    +      -       -      +
    338A  ARG*     1.3    61.4    +      -       -      +
    639C  PHE*     4.5    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 338 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  ILE*     5.8     0.2    -      -       +      -
    174A  TYR*     6.5     0.2    -      -       -      -
    330A  VAL*     3.2     8.0    -      -       -      +
    331A  ALA      2.9    35.0    +      -       -      +
    333A  ASP*     3.2    32.0    +      -       +      +
    336A  THR*     4.9     3.8    -      -       -      +
    337A  PRO*     1.3    77.4    -      -       -      +
    339A  GLN*     1.3    66.6    +      -       -      +
    340A  VAL*     3.6    17.8    +      -       +      +
    344A  PRO*     1.5    77.6    +      -       -      +
    347A  SER*     5.0     0.4    +      -       -      -
    348A  SER*     4.3     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 339 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231A  THR*     3.0    26.7    -      -       -      +
    232A  GLY*     4.6     3.4    -      -       -      -
    233A  LYS*     3.2    40.6    -      -       -      +
    328A  ASN*     4.5     5.6    -      -       -      +
    329A  MET      3.4    11.2    -      -       -      +
    330A  VAL*     4.3    12.9    -      -       +      +
    338A  ARG*     1.3    80.2    +      -       -      +
    340A  VAL*     1.3    64.0    +      -       -      +
    344A  PRO*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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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