Contacts of the strand formed by residues 562 - 566 (chain A) in PDB entry 1SQ0


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 SER 562 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556A  VAL*     4.0    11.7    -      -       -      -
    557A  GLU      3.6     3.1    -      -       -      -
    558A  TYR*     4.5     0.9    -      -       -      -
    561A  GLY*     1.3    73.6    +      -       -      -
    563A  HIS*     1.3    65.4    +      -       -      +
    564A  ALA      4.0     0.7    -      -       -      -
    596A  GLU*     4.1     3.8    +      -       -      +
    597A  VAL*     3.6    18.8    +      -       -      +
    600A  TYR*     3.4    45.7    -      -       -      +
    237B  LYS      4.0     1.2    -      -       -      +
    238B  ALA*     3.0    24.3    -      -       -      +
    239B  MET      2.9    14.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 563 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556A  VAL*     3.2     4.4    -      -       -      +
    557A  GLU*     2.6    53.7    +      -       -      +
    559A  HIS*     3.1    38.1    +      +       -      -
    561A  GLY*     4.0     2.5    -      -       -      -
    562A  SER*     1.3    84.1    -      -       -      +
    564A  ALA*     1.3    61.4    +      -       -      +
    565A  TYR*     3.6    14.9    +      -       +      +
    231B  LYS*     6.0     2.2    -      -       +      -
    236B  VAL*     3.8    19.8    -      -       +      +
    238B  ALA*     3.3    25.6    -      -       +      +
    240B  THR*     4.3    11.1    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 564 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555A  VAL      3.4     6.1    -      -       -      +
    556A  VAL*     4.1    15.7    -      -       +      -
    562A  SER      4.0     0.8    -      -       -      -
    563A  HIS*     1.3    71.3    -      -       -      +
    565A  TYR*     1.3    63.5    +      -       -      +
    566A  ILE      4.8     7.2    -      -       -      +
    567A  GLY*     6.1     1.1    -      -       -      -
    600A  TYR*     3.7    24.2    -      -       +      +
    605A  ILE*     6.2     0.2    -      -       +      -
    235B  ASP      3.5     2.6    -      -       -      +
    236B  VAL*     3.5     0.2    -      -       -      -
    237B  LYS*     3.0    39.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 565 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555A  VAL*     2.9    11.6    +      -       +      +
    557A  GLU*     4.1    10.4    +      -       +      -
    563A  HIS*     3.6    23.0    +      -       +      +
    564A  ALA*     1.3    75.5    -      -       -      +
    566A  ILE*     1.3    66.6    +      -       +      +
    570A  ASP*     4.6     3.0    -      -       -      +
    572A  LYS*     5.2     1.0    +      -       -      -
    580A  ILE*     3.3    29.9    -      -       +      +
    583A  GLN*     4.6     4.3    -      -       +      -
    584A  VAL*     3.4    43.2    -      -       +      +
    585A  LYS*     2.9    36.1    +      -       +      +
    234B  VAL      4.8     3.8    -      -       -      -
    235B  ASP*     3.1    28.8    -      -       +      +
    236B  VAL*     3.5    34.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 566 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541A  MET*     4.0    20.0    -      -       +      -
    553A  VAL*     3.9    16.4    -      -       +      +
    554A  ALA*     3.2     6.3    -      -       -      +
    555A  VAL*     3.0    44.1    +      -       +      +
    556A  VAL*     5.2     1.0    -      -       -      +
    564A  ALA*     3.6     7.0    -      -       -      +
    565A  TYR*     1.3    87.0    +      -       -      +
    567A  GLY*     1.3    71.8    +      -       -      +
    570A  ASP*     3.8     7.2    -      -       +      +
    577A  LEU*     3.6    52.3    -      -       +      +
    580A  ILE*     3.5    17.9    -      -       +      -
    581A  ALA      4.2     3.8    -      -       -      +
----------------------------------------------------------
 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