Contacts of the helix formed by residues 864 - 873 (chain C) in PDB entry 1X86


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 ILE 864 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    788C  ARG*     4.0    14.4    -      -       -      +
    792C  ILE*     3.7    36.8    -      -       +      -
    795C  LEU*     5.0     3.4    -      -       +      -
    796C  PHE*     3.7    21.3    -      -       +      -
    852C  VAL*     4.8     3.1    -      -       +      -
    861C  ILE*     4.2    11.9    -      -       +      -
    863C  GLN*     1.3    74.1    -      -       -      +
    865C  GLY*     1.3    69.6    +      -       -      +
    866C  GLU      3.4     1.8    -      -       -      -
    867C  ASP*     3.0    21.9    +      -       +      +
    868C  LEU*     3.0    43.2    +      -       +      +
    871C  TRP*     4.6     7.0    -      -       +      -
    947C  ILE*     4.6     7.6    -      -       +      -
    956C  GLU*     2.9    16.3    +      -       -      +
    960C  VAL*     4.9     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 865 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    863C  GLN      4.0     0.2    -      -       -      -
    864C  ILE*     1.3    74.0    -      -       -      +
    866C  GLU*     1.3    63.1    +      -       -      +
    868C  LEU*     2.9    18.3    +      -       -      +
    869C  LEU*     3.0    18.3    +      -       -      +
    956C  GLU*     2.9    27.5    +      -       -      +
    959C  LYS*     4.3    10.9    -      -       -      +
    960C  VAL*     4.2    14.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 866 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    864C  ILE      3.4     0.8    -      -       -      -
    865C  GLY*     1.3    74.2    -      -       -      +
    867C  ASP*     1.3    58.3    +      -       -      +
    869C  LEU*     3.4    15.4    +      -       -      +
    870C  THR*     2.9    31.6    +      -       -      -
    959C  LYS*     3.2    38.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 867 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    852C  VAL*     4.0     9.2    -      -       -      +
    855C  ARG*     3.0    39.4    +      -       -      -
    863C  GLN      3.8     9.5    -      -       -      +
    864C  ILE*     3.0    13.2    +      -       +      +
    866C  GLU*     1.3    75.6    -      -       -      +
    868C  LEU*     1.3    67.7    +      -       -      +
    870C  THR*     3.2     8.8    +      -       -      -
    871C  TRP*     2.9    51.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 868 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    795C  LEU*     4.0    19.5    -      -       +      -
    864C  ILE*     3.0    34.2    +      -       +      +
    865C  GLY      2.9     6.4    +      -       -      +
    867C  ASP*     1.3    75.0    -      -       -      +
    869C  LEU*     1.3    54.7    +      -       -      +
    871C  TRP*     2.7    52.2    +      -       +      +
    872C  PHE*     3.0    29.2    +      -       +      -
    944C  LEU*     4.1    13.2    -      -       +      -
    947C  ILE*     4.7     5.2    -      -       +      -
    960C  VAL*     3.8    35.0    -      -       +      -
    963C  ALA*     3.7    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 869 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    865C  GLY      3.0    12.8    +      -       -      +
    866C  GLU*     3.7    25.4    -      -       -      +
    868C  LEU*     1.3    77.5    -      -       -      +
    870C  THR*     1.3    56.5    +      -       -      +
    872C  PHE*     4.4     0.9    -      -       -      +
    873C  SER*     2.9    45.2    +      -       -      +
    959C  LYS*     3.6    45.1    -      -       +      +
    962C  LYS*     3.6    39.9    -      -       -      +
    963C  ALA*     3.6    19.3    -      -       -      +
    966C  HIS*     4.7     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 870 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    848C  GLN*     3.7    21.8    -      -       -      +
    866C  GLU*     2.9    22.8    +      -       -      +
    867C  ASP*     3.3    14.1    +      -       -      -
    869C  LEU*     1.3    76.5    -      -       -      +
    871C  TRP*     1.3    63.2    +      -       +      +
    873C  SER      4.3     1.1    -      -       -      +
    875C  PRO*     5.8     0.2    -      -       -      +
    876C  GLY*     3.9    15.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with TRP 871 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    795C  LEU*     4.6     1.3    -      -       +      -
    796C  PHE*     3.9    16.2    -      +       -      -
    845C  LEU*     3.6    22.3    -      -       +      +
    848C  GLN*     3.2    44.6    +      -       +      +
    849C  MET*     3.6    44.9    -      -       +      -
    852C  VAL*     3.7    19.5    -      -       +      -
    864C  ILE*     4.6     4.5    -      -       +      -
    867C  ASP*     2.9    42.1    +      -       +      +
    868C  LEU*     2.7    41.9    +      -       +      +
    870C  THR*     1.3    78.6    -      -       -      +
    872C  PHE*     1.3    75.5    +      +       +      +
    873C  SER      3.9     0.4    -      -       -      -
    876C  GLY*     3.7    18.6    -      -       -      +
    877C  GLU*     4.9     0.2    -      -       -      -
    880C  LEU*     4.9     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 872 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    795C  LEU*     5.5     1.3    -      -       +      -
    845C  LEU*     4.4     8.7    -      -       +      -
    849C  MET*     5.1     3.1    -      -       +      -
    868C  LEU*     3.0    37.2    +      -       +      +
    869C  LEU*     4.9     0.7    -      -       -      -
    871C  TRP*     1.3   105.8    -      +       +      +
    873C  SER*     1.3    58.8    +      -       -      +
    877C  GLU*     3.2    22.8    -      -       -      +
    880C  LEU*     4.2    23.3    -      -       +      -
    940C  TYR*     3.8    34.3    -      +       -      -
    944C  LEU*     3.8    25.6    -      -       +      -
    963C  ALA*     4.3     9.6    -      -       +      +
    966C  HIS*     3.4    18.5    -      -       +      +
    967C  CYS*     3.4    28.0    -      -       -      -
    970C  ILE*     4.4     4.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 873 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    869C  LEU*     2.9    37.2    +      -       -      +
    870C  THR*     4.3     1.6    -      -       -      +
    872C  PHE*     1.3    79.6    -      -       -      +
    874C  GLY*     1.3    70.6    +      -       -      +
    875C  PRO*     3.1     3.5    -      -       -      +
    876C  GLY*     2.9    13.0    +      -       -      -
    877C  GLU*     3.6     5.4    -      -       -      -
    962C  LYS*     4.5     7.8    +      -       -      -
    966C  HIS*     3.7    21.7    +      -       -      -
----------------------------------------------------------
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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