Contacts of the helix formed by residues 718 - 727 (chain E) in PDB entry 6C3P


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 GLY 718 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    695E  THR*     5.8     0.7    -      -       -      -
    696E  LEU*     4.3     5.8    -      -       -      +
    716E  GLY      3.0     4.6    +      -       -      -
    717E  CYS*     1.3    80.0    -      -       -      +
    719E  LYS*     1.3    62.8    +      -       -      +
    721E  SER*     4.0     3.7    -      -       -      -
    722E  LEU*     3.4    17.0    +      -       -      +
    902E  MET*     3.2    16.4    -      -       -      +
    905E  GLY*     4.4     7.6    -      -       -      -
   2004E  ATP      3.0    27.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 719 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711E  ILE*     3.9    28.7    -      -       +      +
    712E  VAL*     3.6     8.3    -      -       -      +
    713E  GLY      3.0    39.1    +      -       -      +
    714E  GLN      3.6    18.2    +      -       -      -
    717E  CYS*     3.6     6.5    -      -       -      -
    718E  GLY*     1.3    77.3    -      -       -      +
    720E  SER*     1.3    66.9    +      -       -      +
    721E  SER      3.5     0.3    +      -       -      -
    722E  LEU*     3.6     2.9    +      -       -      +
    723E  LEU*     3.1    26.6    +      -       -      +
    854E  ASP*     5.0     5.4    -      -       -      +
    886E  VAL*     4.4    15.3    -      -       +      -
    887E  THR      3.7    13.9    +      -       -      -
    888E  HIS*     5.0     7.7    +      -       +      -
    902E  MET*     3.6     9.0    -      -       -      -
   1512E  ASP*     5.4     2.2    -      -       -      +
   2004E  ATP      2.9    36.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 720 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    719E  LYS*     1.3    69.2    -      -       -      +
    721E  SER*     1.3    59.4    +      -       -      +
    723E  LEU*     3.1    10.3    +      -       -      +
    724E  LEU*     2.9    40.9    +      -       -      +
    774E  GLN*     2.7    15.7    +      -       -      -
    853E  ASP*     2.8    24.3    +      -       -      -
   2002E   MG      2.0    31.3    -      -       -      -
   2004E  ATP      2.3    29.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 721 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    688E  TRP*     3.1    16.9    -      -       -      -
    695E  THR*     4.2     9.6    -      -       -      -
    696E  LEU*     4.2     2.2    -      -       -      -
    718E  GLY      4.1     4.0    -      -       -      -
    719E  LYS      3.2     0.2    -      -       -      -
    720E  SER*     1.3    74.6    -      -       -      +
    722E  LEU*     1.3    66.2    +      -       -      +
    724E  LEU*     3.5     3.2    +      -       -      +
    725E  ALA*     2.9    25.1    +      -       -      +
    730E  MET*     3.5    22.9    -      -       -      +
   2004E  ATP      2.5    48.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 722 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681E  ILE*     5.0     5.8    -      -       +      -
    686E  PHE*     4.5     5.4    -      -       +      -
    696E  LEU*     3.4    24.3    -      -       +      +
    699E  ILE*     3.6    30.7    -      -       +      -
    701E  ILE*     3.5    33.2    -      -       +      -
    711E  ILE*     5.9     2.0    -      -       +      -
    718E  GLY      3.4    16.3    +      -       -      +
    719E  LYS      4.0     4.7    -      -       -      +
    720E  SER      3.4     0.4    -      -       -      -
    721E  SER*     1.3    77.6    -      -       -      +
    723E  LEU*     1.3    64.9    +      -       +      +
    725E  ALA*     3.3     2.2    +      -       +      +
    726E  ALA*     2.9    26.9    +      -       +      +
    900E  ILE*     5.2     1.3    -      -       +      -
    902E  MET*     3.6    25.1    -      -       +      -
    907E  ILE*     4.7     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 723 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711E  ILE*     4.4    20.0    -      -       +      -
    719E  LYS      3.1    18.8    -      -       -      +
    720E  SER*     3.4    12.1    -      -       -      +
    721E  SER      3.1     1.0    -      -       -      -
    722E  LEU*     1.3    82.8    -      -       +      +
    724E  LEU*     1.3    68.4    +      -       +      +
    726E  ALA*     2.9    18.8    +      -       +      +
    727E  LEU*     3.0    21.2    +      -       -      +
    851E  PHE*     3.2    42.8    -      -       +      -
    852E  LEU      4.9     0.4    -      -       -      +
    853E  ASP*     5.0     4.0    -      -       -      +
    884E  VAL*     4.9     2.2    -      -       +      -
    886E  VAL*     3.6    31.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 724 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    404E  THR*     5.8     4.9    -      -       +      -
    688E  TRP*     3.9    28.7    -      -       +      -
    720E  SER*     2.9    38.9    +      -       -      +
    721E  SER*     3.9     4.5    -      -       -      +
    723E  LEU*     1.3    77.6    -      -       +      +
    725E  ALA*     1.3    57.8    +      -       -      +
    727E  LEU*     2.9    24.6    +      -       +      -
    729E  GLU*     3.1    37.9    +      -       +      +
    730E  MET*     4.5     2.0    -      -       +      +
    771E  TYR*     3.8    26.7    -      -       +      +
    851E  PHE*     5.7     0.2    -      -       +      -
    853E  ASP*     4.7     4.7    -      -       -      +
   1211E  THR*     5.4    12.3    -      -       +      -
   2004E  ATP      5.8     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 725 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686E  PHE*     3.4    45.6    -      -       +      -
    696E  LEU*     4.4     0.2    -      -       +      -
    721E  SER      2.9    18.6    +      -       -      +
    722E  LEU*     3.4     8.7    -      -       -      +
    724E  LEU*     1.3    75.7    -      -       -      +
    726E  ALA*     1.3    57.2    +      -       -      +
    728E  GLY*     2.9    22.3    +      -       -      -
    730E  MET*     3.6    22.1    +      -       +      +
    737E  VAL*     5.9     1.6    -      -       -      +
    739E  TRP*     5.4     0.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 726 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679E  VAL*     5.0    11.8    -      -       +      +
    681E  ILE*     4.9    16.6    -      -       +      -
    686E  PHE*     5.1     2.1    -      -       -      -
    722E  LEU*     2.9    15.3    +      -       +      +
    723E  LEU*     2.9    15.2    +      -       +      +
    725E  ALA*     1.3    74.1    -      -       -      +
    727E  LEU*     1.3    62.0    +      -       +      +
    728E  GLY      3.2     0.7    -      -       -      -
    737E  VAL*     5.2     7.9    -      -       -      -
    739E  TRP*     3.1    29.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 727 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    723E  LEU      3.0    26.2    +      -       -      +
    724E  LEU*     2.9    15.8    +      -       +      +
    726E  ALA*     1.3    82.8    -      -       +      +
    728E  GLY*     1.3    55.4    +      -       -      -
    729E  GLU*     2.9    30.0    +      -       +      +
    739E  TRP*     5.0     3.4    -      -       -      -
    769E  VAL*     5.3    14.8    -      -       +      -
    771E  TYR*     3.7    33.2    -      -       +      -
    851E  PHE*     4.6    20.0    -      -       +      -
   1211E  THR*     5.2     3.8    -      -       -      +
   1214E  ARG*     5.9     0.2    -      -       -      +
   1215E  ALA*     3.8    25.4    -      -       +      -
----------------------------------------------------------
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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