Contacts of the strand formed by residues 493 - 497 (chain A) in PDB entry 2JGN


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 ILE 493 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    434A  LEU*     3.7    39.3    -      -       +      -
    443A  THR*     3.5     8.3    -      -       +      +
    445A  VAL*     3.8    27.4    -      -       +      -
    460A  LEU*     4.3    14.8    -      -       +      -
    465A  TYR*     3.9    28.7    -      -       +      -
    466A  ALA      3.9     6.6    +      -       -      +
    467A  CYS*     3.2    17.0    -      -       +      +
    468A  THR*     2.9    27.7    +      -       -      -
    486A  PHE*     4.2     1.8    -      -       -      -
    491A  SER      3.1     3.2    -      -       -      +
    492A  PRO*     1.3    88.9    -      -       +      +
    494A  LEU*     1.3    65.8    +      -       -      +
    495A  VAL*     4.4     2.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 494 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    443A  THR      3.1     6.9    +      -       -      -
    444A  LEU*     3.5    14.5    -      -       +      +
    445A  VAL*     2.9    25.1    +      -       -      +
    468A  THR*     3.5    13.5    -      -       -      +
    469A  SER      4.7     0.9    -      -       -      -
    470A  ILE*     4.0    33.4    -      -       +      +
    482A  ALA      5.4     0.7    -      -       -      +
    483A  LEU*     5.2     2.2    -      -       +      -
    486A  PHE*     3.4    50.4    -      -       +      -
    493A  ILE*     1.3    73.4    -      -       -      +
    495A  VAL*     1.3    81.5    +      -       -      +
    496A  ALA*     3.6    14.8    -      -       +      -
    506A  ILE*     4.1    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 495 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    445A  VAL*     3.4    21.8    -      -       +      +
    447A  VAL*     4.1    15.0    -      -       +      -
    453A  ALA*     3.7    35.3    -      -       +      +
    456A  LEU*     4.3    10.8    -      -       +      -
    457A  GLU*     4.8     7.4    -      -       -      +
    460A  LEU*     4.2    24.9    -      -       +      -
    467A  CYS*     5.4     0.9    -      -       +      -
    468A  THR      2.8    17.5    +      -       -      +
    469A  SER*     3.0    12.6    -      -       -      -
    470A  ILE      2.8    26.7    +      -       -      +
    493A  ILE*     4.4     3.6    -      -       +      -
    494A  LEU*     1.3    75.1    -      -       -      +
    496A  ALA*     1.3    61.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 496 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    444A  LEU*     4.2    13.0    -      -       +      -
    445A  VAL      2.9     6.9    +      -       -      -
    446A  PHE*     3.3    16.5    -      -       +      -
    447A  VAL*     2.9    28.0    +      -       -      -
    453A  ALA*     4.9     0.7    -      -       -      -
    470A  ILE*     3.5    11.9    -      -       +      +
    494A  LEU*     3.6    17.7    +      -       +      +
    495A  VAL*     1.3    76.6    -      -       -      +
    497A  THR*     1.3    70.4    +      -       -      +
    506A  ILE*     6.0     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 497 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    446A  PHE*     4.1     7.3    -      -       -      -
    447A  VAL*     3.6    10.1    -      -       +      +
    448A  GLU      5.0     2.0    -      -       -      -
    449A  THR*     3.5    28.5    -      -       -      +
    450A  LYS*     2.9    47.1    +      -       +      +
    453A  ALA*     4.0     4.7    -      -       +      -
    470A  ILE      3.4    11.0    +      -       -      +
    471A  HIS*     3.8     8.6    -      -       +      -
    496A  ALA*     1.3    85.5    -      -       -      +
    498A  ALA*     1.3    74.3    +      -       -      +
----------------------------------------------------------
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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