Contacts of the strand formed by residues 428 - 433 (chain A) in PDB entry 5CHG


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 428 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    387A  MET*     3.8    27.4    -      -       +      -
    392A  ALA*     3.9    25.4    -      -       +      +
    395A  ILE*     3.9    31.6    -      -       +      -
    396A  GLU      4.9     0.9    -      -       -      +
    414A  ALA*     4.7    11.0    -      -       +      -
    416A  GLY*     6.0     0.2    -      -       -      -
    418A  TYR*     6.1     3.6    -      -       +      -
    425A  CYS*     5.8     0.2    -      -       -      -
    427A  ASP*     1.3    79.5    -      -       -      +
    429A  ASP*     1.3    65.0    +      -       -      +
    430A  VAL*     3.8    21.8    -      -       +      -
    488A  ARG      3.1     6.6    +      -       -      +
    489A  LEU*     3.4     7.6    -      -       +      +
    490A  ASP      3.0    25.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 429 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    414A  ALA*     3.3     3.0    -      -       -      +
    415A  CYS*     2.5    42.8    +      -       -      +
    416A  GLY*     3.4    20.4    -      -       -      +
    418A  TYR*     6.4     0.2    -      -       -      +
    427A  ASP*     3.1    13.2    -      -       -      +
    428A  VAL*     1.3    76.0    -      -       -      +
    430A  VAL*     1.3    58.3    +      -       -      +
    431A  ALA      4.0     0.2    +      -       -      -
    490A  ASP*     3.0    27.3    -      -       -      +
    506A  PHE*     3.6    23.3    -      -       +      -
      5P    A      3.7     2.6    -      -       -      +
      6P    C      3.0    36.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 430 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    396A  GLU*     4.6    16.8    -      -       +      -
    399A  VAL*     4.2    20.2    -      -       +      -
    412A  CYS*     4.3    10.8    -      -       +      -
    413A  VAL      3.5     9.2    -      -       -      +
    414A  ALA*     4.7     4.0    -      -       -      +
    428A  VAL*     3.8    21.8    -      -       +      -
    429A  ASP*     1.3    75.9    -      -       -      +
    431A  ALA*     1.3    72.0    +      -       -      +
    432A  ILE*     4.1    12.3    -      -       +      -
    489A  LEU*     4.1    13.2    -      -       +      -
    490A  ASP      2.9    12.1    +      -       -      +
    491A  ILE*     3.5     9.4    -      -       +      +
    492A  ILE*     3.1    28.2    +      -       -      +
    506A  PHE*     4.7     1.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 431 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    411A  LEU      3.6     0.5    -      -       -      +
    412A  CYS*     3.3     4.3    -      -       -      -
    413A  VAL*     2.7    34.9    +      -       +      +
    415A  CYS*     3.7    22.4    -      -       -      -
    429A  ASP      4.0     1.0    +      -       -      -
    430A  VAL*     1.3    73.7    -      -       -      +
    432A  ILE*     1.3    61.3    +      -       -      +
    492A  ILE*     3.7    18.2    -      -       +      -
    494A  VAL*     6.0     1.1    -      -       +      -
    499A  PHE*     4.4    10.8    -      -       +      -
    502A  ALA*     5.6     4.7    -      -       +      -
    503A  LEU*     4.2    17.0    -      -       +      +
    506A  PHE*     5.1     3.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 432 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399A  VAL*     4.1     9.4    -      -       +      -
    403A  ALA*     4.7     1.6    -      -       +      -
    410A  LEU*     4.5    15.5    -      -       +      -
    411A  LEU      3.2     7.0    -      -       -      +
    412A  CYS*     3.8    25.8    -      -       -      -
    430A  VAL*     4.1     7.9    -      -       +      +
    431A  ALA*     1.3    80.6    -      -       -      +
    433A  THR*     1.3    69.3    +      -       -      +
    443A  ILE*     5.2     8.1    -      -       +      -
    447A  LEU*     3.5    31.2    -      -       +      -
    491A  ILE*     4.0    13.9    -      -       +      -
    492A  ILE      2.9    15.4    +      -       -      +
    493A  VAL*     3.4    19.0    -      -       +      +
    494A  VAL*     3.0    28.3    +      -       -      +
    499A  PHE*     5.2     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 433 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    410A  LEU*     3.6     8.5    -      -       -      +
    411A  LEU*     2.7    50.9    +      -       +      +
    432A  ILE*     1.3    77.1    -      -       -      +
    434A  HIS*     1.3    65.1    +      -       -      +
    440A  HIS*     4.6     3.8    -      -       -      -
    494A  VAL*     3.0    19.7    +      -       -      -
    495A  PRO*     4.2     0.2    -      -       -      +
    496A  TYR*     3.3    29.8    +      -       +      -
    499A  PHE*     3.5    46.9    -      -       +      -
----------------------------------------------------------
 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