Contacts of the helix formed by residues 730 - 738 (chain D) in PDB entry 4AY6


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 ASP 730 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    570A  MET*     5.5     4.6    -      -       -      +
   1000A  LYS*     3.5    49.4    +      -       +      +
    728D  GLY*     3.2     0.6    -      -       -      -
    729D  ILE*     1.3    94.1    -      -       -      +
    731D  LEU*     1.3    64.2    +      -       -      +
    732D  LYS      3.3     3.3    +      -       -      -
    733D  ALA*     3.4    14.0    +      -       +      +
    734D  PHE*     3.3    19.9    +      -       -      +
    792D  PHE*     4.3     6.6    -      -       +      -
    815D  ARG*     4.2    12.5    -      -       -      +
    816D  THR*     5.5     3.0    +      -       -      +
    817D  ILE*     4.4     9.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 731 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707D  LYS*     4.7     8.7    -      -       +      +
    708D  LYS*     4.0     9.0    -      -       -      +
    709D  ALA*     3.7    23.6    -      -       +      +
    726D  LEU*     3.5    42.4    -      -       +      +
    727D  ASN*     4.3     3.6    -      -       -      -
    728D  GLY*     3.3    21.4    +      -       -      +
    729D  ILE      3.3     1.0    +      -       -      -
    730D  ASP*     1.3    77.9    -      -       -      +
    732D  LYS*     1.3    58.5    +      -       -      +
    734D  PHE*     3.2    15.5    +      -       +      +
    735D  LEU*     2.9    40.9    +      -       +      +
    765D  PRO*     6.0     0.4    -      -       +      -
    817D  ILE*     4.3    21.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 732 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707D  LYS*     6.2     7.6    -      -       +      +
    729D  ILE      4.9     2.6    +      -       -      +
    730D  ASP      3.3     0.8    -      -       -      -
    731D  LEU*     1.3    78.4    -      -       -      +
    733D  ALA*     1.3    62.1    +      -       -      +
    735D  LEU*     3.1    15.9    +      -       +      +
    736D  ASP*     2.9    51.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 733 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1000A  LYS*     6.0     3.4    -      -       +      -
    730D  ASP*     3.4    15.2    +      -       +      +
    732D  LYS*     1.3    79.0    -      -       -      +
    734D  PHE*     1.3    58.7    +      -       -      +
    736D  ASP*     3.5    12.9    +      -       -      +
    737D  SER*     3.3    15.4    +      -       -      -
    792D  PHE*     3.5    21.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 734 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    726D  LEU*     4.6     9.6    -      -       +      -
    730D  ASP      3.3     3.3    +      -       -      +
    731D  LEU*     3.2    18.5    +      -       +      +
    733D  ALA*     1.3    76.3    -      -       -      +
    735D  LEU*     1.3    69.4    +      -       +      +
    737D  SER*     2.7    25.4    +      -       -      -
    738D  LEU*     3.5    30.5    +      -       +      +
    767D  ILE*     4.5    11.2    -      -       +      -
    772D  ILE*     5.1     4.5    -      -       +      -
    776D  VAL*     5.8     2.7    -      -       +      -
    789D  ILE*     3.4    41.7    -      -       +      -
    792D  PHE*     3.6    35.8    -      +       +      -
    794D  ILE*     4.2    18.6    -      -       +      -
    817D  ILE*     3.7    26.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 735 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    709D  ALA*     4.1    15.9    -      -       +      -
    731D  LEU*     2.9    29.0    +      -       +      +
    732D  LYS*     3.1    14.8    +      -       +      +
    734D  PHE*     1.3    81.8    -      -       +      +
    736D  ASP*     1.3    63.9    +      -       -      +
    738D  LEU*     3.2    25.2    +      -       +      +
    741D  VAL*     3.4    23.9    -      -       +      +
    743D  ILE*     5.9     0.7    -      -       +      -
    765D  PRO*     3.4    34.5    -      -       +      -
    767D  ILE*     3.8    35.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 736 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732D  LYS*     2.9    43.6    +      -       -      +
    733D  ALA*     3.6    12.7    -      -       -      +
    734D  PHE      3.1     0.4    -      -       -      -
    735D  LEU*     1.3    77.1    -      -       -      +
    737D  SER*     1.3    62.8    +      -       -      +
    738D  LEU      3.5     4.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 737 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    733D  ALA      3.3     6.4    +      -       -      -
    734D  PHE*     2.7    26.2    +      -       -      -
    736D  ASP*     1.3    76.5    -      -       -      +
    738D  LEU*     1.3    61.0    +      -       -      +
    739D  PRO*     4.0     2.8    -      -       -      +
    790D  ASN*     2.8    36.0    +      -       -      +
    792D  PHE*     4.0    18.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 738 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    734D  PHE*     3.5    31.4    -      -       +      +
    735D  LEU*     3.2    24.6    +      -       +      +
    736D  ASP      3.9     5.0    -      -       -      +
    737D  SER*     1.3    90.7    +      -       -      +
    739D  PRO*     1.3    76.7    -      -       +      +
    740D  ASP      3.6     1.1    +      -       -      +
    741D  VAL*     3.9    11.4    -      -       +      +
    767D  ILE*     3.7    42.8    -      -       +      -
    772D  ILE*     3.9    32.3    -      -       +      -
    789D  ILE*     4.7     0.2    -      -       +      -
    790D  ASN*     4.2     7.9    -      -       -      +
----------------------------------------------------------
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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