Contacts of the strand formed by residues 431 - 436 (chain A) in PDB entry 1JEQ


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 GLY 431 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  PHE*     3.9     3.1    -      -       -      -
    368A  VAL      3.7     9.2    -      -       -      -
    369A  TYR*     5.0     0.2    -      -       -      -
    382A  PHE*     3.8    11.0    -      -       -      -
    386A  LEU*     3.2    22.0    -      -       -      +
    416A  GLN*     2.8    34.8    +      -       -      +
    430A  PRO*     1.3    74.4    -      -       -      +
    432A  PHE*     1.3    64.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 432 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    367A  PHE*     3.6     8.3    -      -       -      -
    368A  VAL*     2.7    49.9    +      -       +      +
    382A  PHE*     3.5    29.2    -      +       -      -
    385A  LEU*     4.0    10.5    -      -       +      -
    386A  LEU*     3.5    41.7    -      -       +      -
    389A  CYS*     4.1    14.4    -      -       -      -
    396A  ALA*     5.4     3.1    -      -       +      -
    413A  LEU*     3.5    38.1    -      -       +      -
    414A  VAL      3.4     0.4    -      -       -      -
    415A  PRO*     3.5    35.7    -      -       +      -
    416A  GLN*     4.9     0.2    -      -       -      -
    431A  GLY*     1.3    72.8    -      -       -      -
    433A  GLN*     1.3    61.1    +      -       -      +
    434A  LEU      3.5     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 433 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    365A  SER*     2.9    33.7    +      -       -      -
    366A  LEU      3.6     6.3    -      -       -      +
    367A  PHE*     4.9     2.2    -      -       +      +
    412A  ALA      3.0     5.2    -      -       -      +
    413A  LEU*     3.3     1.4    -      -       -      -
    414A  VAL*     2.8    55.6    +      -       +      +
    416A  GLN*     4.0    16.9    -      -       +      +
    432A  PHE*     1.3    70.3    -      -       -      +
    434A  LEU*     1.3    61.3    +      -       -      +
    435A  VAL*     3.1    17.2    +      -       -      +
    353B  ARG*     3.8    13.2    -      -       -      +
    354B  ARG*     3.3    42.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 434 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    273A  ILE*     4.1    19.7    -      -       +      -
    345A  LEU*     4.2     6.5    -      -       +      -
    365A  SER*     3.2     8.1    -      -       -      -
    366A  LEU*     2.9    47.3    +      -       +      +
    368A  VAL*     3.8    14.4    -      -       +      -
    400A  TYR*     3.7    31.6    -      -       +      -
    411A  VAL*     3.8    20.0    -      -       +      -
    413A  LEU*     3.6    17.9    -      -       +      -
    432A  PHE      3.5     2.6    +      -       -      -
    433A  GLN*     1.3    69.2    -      -       -      +
    435A  VAL*     1.3    61.8    +      -       -      +
    436A  PHE*     3.7    28.0    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 435 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    356A  LEU*     6.2     0.9    -      -       +      -
    365A  SER*     3.7     5.4    -      -       -      +
    411A  VAL*     3.0     6.0    -      -       -      -
    412A  ALA*     2.6    50.1    +      -       +      +
    414A  VAL*     4.0    12.1    -      -       +      -
    433A  GLN*     3.1    44.0    -      -       -      +
    434A  LEU*     1.3    74.4    -      -       -      +
    436A  PHE*     1.3    75.9    +      -       -      +
    437A  LEU*     3.6     6.9    +      -       +      -
    353B  ARG*     3.6    33.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 436 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    360A  HIS      4.1    10.0    -      -       -      +
    362A  LEU*     4.1    22.1    +      -       +      +
    363A  ARG*     2.7    67.3    +      -       +      +
    364A  PRO      3.6     7.4    -      -       -      -
    365A  SER*     4.9     0.8    +      -       -      -
    366A  LEU*     4.1    11.0    -      -       +      -
    400A  TYR*     3.9    34.8    -      +       -      -
    409A  TYR*     4.4    20.9    -      +       +      -
    410A  PHE      4.2     0.2    -      -       -      -
    411A  VAL*     4.1    13.2    -      -       +      -
    434A  LEU*     3.7    19.3    -      -       +      -
    435A  VAL*     1.3    85.3    -      -       -      +
    437A  LEU*     1.3    61.0    +      -       -      +
    353B  ARG*     4.3     0.7    +      -       -      -
----------------------------------------------------------
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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