Contacts of the strand formed by residues 84 - 89 (chain A) in PDB entry 1PJX


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 GLN 84 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  CYS*     3.7     2.9    -      -       -      -
     79A  ASP*     2.9    57.5    +      -       +      +
     82A  ALA*     3.0    19.0    +      -       +      +
     83A  ASN*     1.3    74.5    +      -       -      +
     85A  LEU*     1.3    65.6    +      -       -      +
     86A  PHE*     4.0     4.6    -      -       +      -
     96A  VAL*     3.4    16.4    -      -       +      +
     97A  VAL      3.5     7.9    -      -       -      +
     98A  GLN*     2.9    36.9    +      -       -      +
     99A  THR*     5.5     1.1    -      -       -      +
    461A  PEG      3.5    28.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 85 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  VAL*     4.1    19.7    -      -       +      -
     26A  ASP*     4.6    12.1    -      -       +      -
     32A  TYR*     3.9    38.1    -      -       +      -
     48A  ILE*     4.7    13.7    -      -       +      -
     61A  ILE*     5.5     1.8    -      -       +      -
     76A  CYS*     5.0     3.4    -      -       +      -
     77A  GLN      3.5     2.7    -      -       -      +
     78A  CYS*     4.0    30.7    -      -       +      -
     83A  ASN      6.1     0.2    -      -       -      -
     84A  GLN*     1.3    75.9    -      -       -      +
     86A  PHE*     1.3    64.3    +      -       -      +
     87A  VAL*     3.9    16.4    +      -       +      -
     95A  LEU      3.7     0.2    -      -       -      +
     96A  VAL*     3.3     4.9    -      -       -      +
     97A  VAL*     2.8    48.5    +      -       +      +
     98A  GLN      6.3     0.4    -      -       -      -
     99A  THR*     6.3     2.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 86 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  GLY      3.8     0.3    -      -       -      +
     76A  CYS*     3.2     5.7    -      -       -      +
     77A  GLN      2.8    37.3    +      -       -      +
     79A  ASP*     3.8    30.1    -      -       +      -
     84A  GLN*     4.0     7.4    -      -       +      -
     85A  LEU*     1.3    74.1    -      -       -      +
     87A  VAL*     1.3    61.0    +      -       -      +
     88A  ALA      4.2     0.4    -      -       -      -
     94A  LEU*     4.1     4.9    -      -       +      -
     95A  LEU      3.4     3.8    -      -       -      -
     96A  VAL*     3.3    28.9    -      -       +      -
    106A  ILE*     3.9    13.0    -      -       +      -
    122A  CYS*     3.9     4.8    -      -       -      -
    124A  PHE*     3.7    19.3    -      +       +      -
    130A  LEU*     3.8    29.6    -      -       +      -
    158A  PHE*     4.3     4.0    -      +       -      -
    422A  EDO      3.1    35.0    -      -       -      -
    461A  PEG      3.9    15.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 87 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34A  VAL*     4.5     1.3    -      -       +      -
     48A  ILE*     4.3    11.4    -      -       +      -
     73A  PRO*     3.7    30.3    -      -       +      -
     75A  GLY      3.2     9.9    -      -       -      +
     76A  CYS*     4.0    19.3    -      -       -      -
     85A  LEU*     4.0    14.8    -      -       +      +
     86A  PHE*     1.3    80.7    -      -       -      +
     88A  ALA*     1.3    66.2    +      -       -      +
     89A  ASP      3.6     0.5    +      -       -      -
     94A  LEU*     3.5     6.1    -      -       -      +
     95A  LEU*     2.8    52.6    +      -       +      +
     97A  VAL*     3.8    22.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     73A  PRO*     3.7     1.2    -      -       -      +
     74A  ALA*     2.8    31.9    +      -       -      -
     75A  GLY      2.8    12.8    +      -       -      +
     86A  PHE      4.2     0.4    -      -       -      -
     87A  VAL*     1.3    71.0    -      -       -      +
     89A  ASP*     1.3    54.7    +      -       -      +
     93A  GLY      3.6     5.6    -      -       -      -
     94A  LEU*     4.3     4.3    -      -       +      +
    119A  CYS*     3.6    15.4    -      -       +      +
    120A  ASN      3.5    29.6    -      -       -      +
    121A  ASP*     3.6    14.6    -      -       -      +
    122A  CYS*     4.6     5.5    -      -       -      -
    132A  ILE*     4.7     2.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  PRO*     4.1     0.7    -      -       -      +
     71A  GLY*     3.3     9.4    -      -       -      -
     72A  ILE      2.9    31.1    +      -       -      -
     73A  PRO*     3.2    15.6    -      -       +      +
     87A  VAL      5.0     0.2    -      -       -      -
     88A  ALA*     1.3    73.7    -      -       -      +
     90A  MET*     1.3    59.0    +      -       -      +
     91A  ARG*     2.8    27.5    +      -       -      -
     92A  LEU*     2.9    22.4    +      -       +      +
     93A  GLY      2.8    35.8    +      -       -      +
     95A  LEU*     3.8    22.7    -      -       +      +
    119A  CYS      2.9    14.3    +      -       -      -
----------------------------------------------------------
 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