Contacts of the strand formed by residues 574 - 577 (chain A) in PDB entry 1PJR


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 VAL 574 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339A  ARG*     4.4     7.6    -      -       -      +
    349A  ARG*     3.8    30.7    -      -       +      +
    353A  ASP      3.0     9.3    +      -       -      +
    354A  PHE*     3.5    40.5    -      -       +      -
    355A  ALA      3.2    23.0    +      -       -      +
    572A  PHE*     3.9     1.2    -      -       -      +
    573A  PRO*     1.3    78.6    -      -       +      +
    575A  VAL*     1.3    63.1    +      -       -      +
    576A  PHE*     4.1    12.3    -      -       +      -
    614A  GLU*     3.4    25.6    -      -       +      +
    616A  VAL*     4.3    11.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 575 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  ALA*     3.5     5.2    -      -       +      +
    357A  LEU*     3.8    19.7    -      -       +      -
    572A  PHE*     3.9    24.2    -      -       +      -
    574A  VAL*     1.3    76.9    -      -       -      +
    576A  PHE*     1.3    64.2    +      -       -      +
    577A  LEU*     3.6    28.3    -      -       +      -
    607A  GLY      4.2     6.1    -      -       -      +
    610A  ARG*     4.0     5.8    -      -       +      -
    611A  ALA*     3.8    35.2    -      -       +      +
    614A  GLU      3.1     6.3    +      -       -      -
    615A  LEU*     3.5     6.0    -      -       +      +
    616A  VAL*     3.0    25.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 576 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    335A  PHE*     4.8     2.5    -      +       -      -
    336A  VAL*     3.8    32.1    -      -       +      -
    339A  ARG*     4.0    32.8    -      -       +      -
    340A  ILE*     4.0    17.3    -      -       +      -
    354A  PHE*     3.8    30.5    -      +       +      -
    355A  ALA      3.0    20.1    +      -       -      +
    356A  VAL*     3.5     8.9    -      -       +      -
    357A  LEU*     2.9    27.7    +      -       -      +
    574A  VAL*     4.1     7.2    -      -       +      -
    575A  VAL*     1.3    75.1    -      -       -      +
    577A  LEU*     1.3    59.9    +      -       -      +
    578A  ILE*     3.7    14.9    +      -       +      -
    616A  VAL*     3.3    42.4    -      -       +      +
    618A  THR*     5.2     0.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 577 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    357A  LEU*     3.6    20.6    -      -       +      +
    564A  LEU*     4.5    14.1    -      -       +      -
    575A  VAL*     3.6    25.8    -      -       +      -
    576A  PHE*     1.3    70.4    -      -       -      +
    578A  ILE*     1.3    62.1    +      -       -      +
    580A  MET*     3.9    29.9    -      -       +      +
    585A  PHE*     4.1    17.3    -      -       +      -
    604A  ALA*     4.9     4.7    -      -       +      +
    607A  GLY*     4.0    17.0    -      -       -      +
    608A  ILE*     5.0     4.5    -      -       +      +
    615A  LEU*     4.0    11.4    -      -       +      -
    616A  VAL      2.9     8.1    +      -       -      -
    617A  LEU*     3.6    19.1    -      -       +      -
    618A  THR*     3.4    21.9    +      -       -      +
----------------------------------------------------------
 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