Contacts of the strand formed by residues 73 - 78 (chain A) in PDB entry 2A4X


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 PHE 73 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  VAL*     4.2     6.7    -      -       +      -
     71A  HIS*     3.1    27.4    -      -       +      +
     72A  ARG*     1.3    91.0    -      -       +      +
     74A  ALA*     1.3    78.8    +      -       -      +
     75A  ILE*     3.8    24.7    -      -       +      -
    121A  ASN*     3.5    43.7    -      -       +      -
    122A  VAL*     4.0     5.7    +      -       -      +
    209B  ALA      3.0    15.7    -      -       -      +
    210B  VAL*     4.1     1.6    -      -       +      +
    211B  VAL*     4.6     1.8    -      -       -      +
    272B  ARG*     4.0    12.3    -      -       +      -
    273B  PHE*     3.4    64.6    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  HIS*     4.8     2.0    -      -       +      +
     73A  PHE*     1.3    80.6    -      -       -      +
     75A  ILE*     1.3    64.5    +      -       -      +
     76A  ALA*     4.1     0.6    +      -       -      -
    122A  VAL*     3.2    26.2    -      -       +      +
    124A  ASP*     3.5    20.2    -      -       -      +
    700A  BLM      4.2     7.9    -      -       +      -
    207B  LEU*     4.0     0.9    -      -       -      +
    208B  PHE*     3.6     3.6    -      -       -      -
    209B  ALA*     2.9    39.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 75 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10A  VAL*     4.1    14.4    -      -       +      -
     22A  TYR*     3.8    27.6    -      -       +      +
     49A  LEU*     4.8     6.3    -      -       +      -
     73A  PHE*     3.8    24.2    -      -       +      -
     74A  ALA*     1.3    75.6    -      -       -      +
     76A  ALA*     1.3    61.6    +      -       -      +
     77A  PHE*     3.6    24.0    -      -       +      -
    121A  ASN*     6.0     0.4    -      -       +      -
    122A  VAL      3.1     9.3    +      -       -      +
    123A  VAL*     3.2    14.4    -      -       +      +
    124A  ASP*     2.9    21.4    +      -       -      -
    205B  ILE*     4.0    20.0    -      -       +      -
    207B  LEU      3.7     5.6    -      -       -      +
    208B  PHE*     3.8    26.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 76 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74A  ALA      4.1     0.6    -      -       -      -
     75A  ILE*     1.3    73.4    -      -       -      +
     77A  PHE*     1.3    63.2    +      -       -      +
    112A  TYR*     4.7     3.1    -      -       -      +
    124A  ASP*     3.4    24.5    -      -       +      +
    126A  PHE*     3.9    19.5    -      -       +      -
    205B  ILE*     3.9     3.1    -      -       -      +
    206B  SER*     2.9    24.8    +      -       -      -
    207B  LEU*     2.9    38.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  TYR*     3.8    27.4    -      +       -      -
     25A  LEU*     3.7    40.8    -      -       +      -
     27A  VAL*     3.9     9.2    -      -       +      -
     75A  ILE*     3.6    18.8    -      -       +      -
     76A  ALA*     1.3    76.8    -      -       -      +
     78A  GLU*     1.3    60.5    +      -       -      +
     79A  PHE*     3.6    17.9    -      -       +      -
    123A  VAL*     3.6    30.1    -      -       +      -
    124A  ASP      2.8    12.3    +      -       -      +
    125A  LEU*     3.6     2.5    -      -       +      -
    126A  PHE*     2.9    30.6    +      -       -      +
    203B  ALA*     4.7     1.8    -      -       +      -
    204B  ARG*     3.4     7.9    -      -       -      +
    205B  ILE*     3.4    37.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76A  ALA      4.1     0.6    +      -       -      -
     77A  PHE*     1.3    73.3    -      -       -      +
     79A  PHE*     1.3    72.7    +      -       -      +
    126A  PHE*     3.4    22.3    -      -       +      +
    128A  PRO*     3.9    20.0    -      -       +      +
    700A  BLM      3.6    26.1    +      -       -      -
    202B  SER      3.6     1.9    -      -       -      +
    203B  ALA*     3.3     6.2    -      -       -      -
    204B  ARG*     2.8    65.5    +      -       +      +
    206B  SER*     3.7    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