Contacts of the strand formed by residues 562 - 566 (chain A) in PDB entry 6Q6Q


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 CYS 562 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  LYS*     4.3     6.1    -      -       -      +
    561A  HIS*     1.3    75.6    -      -       -      +
    563A  SER*     1.3    72.3    +      -       -      +
    564A  THR*     4.6    11.2    -      -       -      -
   1245A  PRO      5.1     0.7    -      -       -      +
   1246A  THR      2.8    11.1    +      -       -      +
   1247A  GLU*     3.4    22.8    -      -       +      -
   1248A  LEU*     3.0    24.6    +      -       -      +
   1249A  HIS*     5.1     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 563 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ARG*     3.8    30.6    -      -       -      +
    159A  ASP*     3.6    21.1    +      -       -      -
    162A  LYS*     4.8     5.8    +      -       -      +
    561A  HIS      5.5     0.2    +      -       -      -
    562A  CYS*     1.3    82.1    -      -       -      +
    564A  THR*     1.3    67.3    +      -       -      +
    565A  LEU*     5.2     7.0    -      -       -      +
   1248A  LEU*     3.2    13.5    -      -       -      -
   1249A  HIS*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 564 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562A  CYS*     4.6     9.0    -      -       -      -
    563A  SER*     1.3    80.5    -      -       -      +
    565A  LEU*     1.3    67.5    +      -       -      +
   1248A  LEU      3.1     4.4    +      -       -      -
   1249A  HIS*     2.3    47.3    +      -       +      +
   1250A  ILE      3.1    23.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 565 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155A  ARG*     3.5    40.4    -      -       -      +
    159A  ASP*     5.5     0.2    -      -       -      +
    199A  PRO      4.2    14.0    -      -       -      +
    201A  LEU*     3.6    25.6    -      -       +      -
    563A  SER*     5.2     4.0    -      -       -      +
    564A  THR*     1.3    89.1    -      -       -      +
    566A  LYS*     1.3    60.3    +      -       -      +
    567A  TYR*     4.4     3.8    -      -       +      -
   1201A  ILE*     3.9    21.5    -      -       +      -
   1205A  GLU*     4.0    14.4    -      -       -      +
   1248A  LEU*     5.3     3.1    -      -       +      +
   1250A  ILE*     3.3    25.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 566 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    565A  LEU*     1.3    74.5    -      -       -      +
    567A  TYR*     1.3    69.7    +      -       -      +
    979A  GLU*     5.4     5.2    -      -       -      +
    983A  MET*     6.2     1.8    -      -       -      -
   1201A  ILE*     4.9     1.8    -      -       -      +
   1250A  ILE      2.9     7.7    +      -       -      +
   1251A  ALA*     3.5    21.9    -      -       +      -
   1252A  LEU*     2.9    29.5    +      -       -      +
----------------------------------------------------------
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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