Contacts of the strand formed by residues 566 - 570 (chain B) in PDB entry 1D0N


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 ALA 566 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541B  VAL*     2.8    32.9    +      -       +      +
    565B  ASP*     1.3    72.9    -      -       -      +
    567B  PHE*     1.3    67.5    +      -       -      +
    577B  LEU*     4.7     3.6    -      -       +      -
    578B  TRP      3.4    10.8    -      -       -      +
    579B  VAL*     4.4    11.4    -      -       +      +
    583B  ALA*     4.7     2.5    -      -       +      -
    587B  GLU*     3.7    36.5    -      -       +      +
    588B  LYS*     4.4     3.4    -      -       -      +
    591B  ALA*     4.2    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 567 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538B  LEU*     4.1    22.9    -      -       +      -
    539B  PHE      3.2     5.4    -      -       -      -
    540B  GLN*     3.5    35.7    -      -       +      -
    541B  VAL*     5.1     0.2    -      -       -      -
    554B  ILE*     5.8     2.0    -      -       +      -
    560B  ALA*     3.6    16.4    -      -       +      -
    561B  LEU*     3.7    19.1    -      -       +      -
    562B  ASN      3.3    35.7    -      -       -      -
    565B  ASP*     3.2    32.8    -      -       -      -
    566B  ALA*     1.3    78.4    -      -       -      +
    568B  VAL*     1.3    63.6    +      -       -      +
    577B  LEU*     3.6     7.3    -      -       -      +
    578B  TRP*     2.7    58.4    +      +       +      +
    614B  PHE*     5.9     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 568 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    537B  ARG      3.6     1.0    -      -       -      +
    538B  LEU*     3.2     6.3    -      -       -      +
    539B  PHE*     2.8    42.5    +      -       +      +
    541B  VAL*     4.7     1.6    -      -       +      -
    567B  PHE*     1.3    79.4    -      -       -      +
    569B  LEU*     1.3    67.8    +      -       -      +
    570B  LYS*     4.8     2.2    -      -       +      +
    575B  ALA*     5.7     0.2    -      -       +      -
    576B  TYR      3.3     5.2    -      -       -      +
    577B  LEU*     4.0     7.0    -      -       +      -
    591B  ALA*     3.7    37.5    -      -       +      +
    594B  LEU*     4.1    22.9    -      -       +      -
    595B  LEU*     3.5    28.5    -      -       +      -
    598B  LEU*     4.6     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 569 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536B  THR*     3.8    22.4    -      -       +      -
    537B  ARG      3.3    17.7    -      -       -      +
    538B  LEU*     4.3    11.9    -      -       +      -
    556B  PRO*     4.9     0.7    -      -       +      -
    568B  VAL*     1.3    74.8    -      -       -      +
    570B  LYS*     1.3    60.4    +      -       -      +
    571B  THR*     4.0     8.7    -      -       +      -
    574B  ALA      3.9     0.7    -      -       -      +
    575B  ALA*     3.2     6.2    -      -       -      +
    576B  TYR*     2.8    61.9    +      -       +      +
    578B  TRP*     6.2     0.4    -      -       -      +
    614B  PHE*     4.2    18.6    -      -       +      +
    617B  ALA*     4.2    16.8    -      -       +      -
    618B  LEU*     3.2    34.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 570 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535B  SER      3.4     5.8    +      -       -      +
    536B  THR*     3.0     6.6    -      -       -      +
    537B  ARG*     2.8    61.4    +      -       +      +
    539B  PHE*     5.3     1.3    -      -       +      -
    568B  VAL*     5.3     1.8    -      -       +      -
    569B  LEU*     1.3    72.9    -      -       -      +
    571B  THR*     1.3    82.6    +      -       -      +
    572B  PRO*     4.3     6.5    +      -       -      +
    574B  ALA      4.0     1.3    -      -       -      -
    575B  ALA*     4.5    15.0    -      -       +      +
    598B  LEU*     4.9    25.6    -      -       +      -
    600B  ALA*     4.7    14.1    -      -       +      -
----------------------------------------------------------
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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