Contacts of the strand formed by residues 351 - 355 (chain A) in PDB entry 5JXG


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 351 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122A  TRP*     4.8     1.3    -      -       +      -
    123A  TYR*     3.5    36.8    -      -       +      +
    201A  GLU*     3.4    34.5    -      -       +      +
    341A  TYR      4.0    18.6    -      -       -      +
    342A  SER*     4.1    14.8    -      -       -      -
    350A  GLN*     1.3    79.6    -      -       -      +
    352A  VAL*     1.3    66.4    +      -       -      +
    361A  THR      3.9     0.9    -      -       -      +
    362A  GLU*     3.4     8.1    -      -       -      -
    363A  SER      3.5     0.2    +      -       -      -
    364A  HIS*     3.0    50.5    +      -       +      +
    369A  ALA*     4.0    15.7    -      -       +      -
    373A  LEU*     4.1     7.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  LYS*     3.9    28.7    -      -       +      +
    120A  GLN*     3.7    28.3    -      -       +      +
    121A  GLN*     3.1    33.0    +      -       +      +
    123A  TYR*     2.9    18.2    +      -       -      +
    200A  GLY      5.7     0.2    -      -       -      +
    201A  GLU*     5.3     2.3    -      -       -      +
    211A  CYS*     4.7     2.0    -      -       -      -
    212A  GLY      5.1     0.2    -      -       -      +
    350A  GLN      4.2     7.4    -      -       -      +
    351A  ILE*     1.3    74.8    -      -       -      +
    353A  THR*     1.3    67.6    +      -       -      +
    360A  CYS*     4.4     5.8    -      -       -      -
    361A  THR      3.3     9.9    -      -       -      +
    362A  GLU*     4.0    25.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121A  GLN*     5.2     0.4    -      -       -      +
    197A  ARG*     2.7    37.7    +      -       +      +
    200A  GLY*     3.3     5.0    -      -       -      -
    201A  GLU*     3.2    23.1    +      -       -      -
    211A  CYS*     3.4    14.8    -      -       -      -
    212A  GLY      6.0     0.2    -      -       -      +
    351A  ILE*     4.7     0.2    -      -       -      -
    352A  VAL*     1.3    78.0    -      -       -      +
    354A  THR*     1.3    69.7    +      -       -      +
    361A  THR*     2.8    53.2    +      -       +      +
    364A  HIS*     3.9    16.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 354 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  HIS*     3.6    21.1    -      -       +      +
    162A  ASP*     3.5    36.1    -      -       +      +
    163A  LEU*     4.1     9.5    -      -       +      +
    196A  THR*     2.8    27.3    +      -       -      +
    197A  ARG*     3.1    26.2    +      -       -      +
    200A  GLY*     3.1    21.1    +      -       -      -
    204A  ALA*     4.3     3.4    -      -       +      -
    211A  CYS*     4.5     4.3    -      -       -      -
    353A  THR*     1.3    80.5    +      -       -      +
    355A  ASP*     1.3    59.6    +      -       -      +
    359A  LYS      3.8     4.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 355 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160A  HIS*     3.1    22.7    +      -       -      -
    193A  ARG*     3.7    16.0    +      -       -      +
    196A  THR*     3.9     5.8    -      -       -      -
    197A  ARG*     2.9    42.4    +      -       -      +
    354A  THR*     1.3    75.3    -      -       -      +
    356A  LEU*     1.3    88.9    +      -       -      +
    359A  LYS*     2.8    32.9    +      -       +      +
    360A  CYS      4.2     0.6    -      -       -      +
    361A  THR*     3.8    16.6    -      -       -      +
----------------------------------------------------------
 Back to top of page


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