Contacts of the helix formed by residues 3769 - 3781 (chain F) in PDB entry 6X34


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 GLY3769 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3695F  HIS*     3.8    13.9    +      -       -      -
   3698F  VAL*     3.5    20.0    -      -       -      +
   3699F  LEU*     5.5     6.1    -      -       -      +
   3768F  ARG*     1.3    74.4    -      -       -      +
   3770F  ALA*     1.3    60.1    +      -       -      -
   3771F  ALA      3.5     2.0    -      -       -      -
   3772F  GLU*     3.8    15.9    +      -       -      +
   3773F  MET*     3.6    16.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA3770 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3698F  VAL*     4.0    11.8    -      -       +      +
   3725F  MET*     5.2     7.0    -      -       -      -
   3765F  LEU*     3.3    42.0    -      -       +      +
   3768F  ARG*     3.1     6.2    +      -       +      -
   3769F  GLY*     1.3    75.3    -      -       -      +
   3771F  ALA*     1.3    65.1    +      -       -      +
   3772F  GLU      3.2     0.4    -      -       -      -
   3773F  MET*     3.4    12.5    +      -       -      +
   3774F  VAL*     3.5    19.6    +      -       -      +
   3795F  LEU*     5.3     5.1    -      -       +      +
   3799F  ILE*     6.1     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA3771 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3765F  LEU      4.6     3.1    +      -       -      +
   3766F  HIS*     5.4     7.2    -      -       -      +
   3768F  ARG      4.6     2.1    +      -       -      +
   3769F  GLY*     3.5     0.6    -      -       -      -
   3770F  ALA*     1.3    78.7    -      -       -      +
   3772F  GLU*     1.3    65.0    +      -       +      +
   3774F  VAL*     3.3    22.8    -      -       -      +
   3775F  LEU*     3.5    13.5    -      -       -      +
   3799F  ILE*     6.1     0.9    -      -       +      -
   3807F  VAL*     3.9    28.5    -      -       +      -
   3810F  LYS*     4.9    15.0    -      -       +      -
   3811F  MET*     4.4    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU3772 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3769F  GLY*     3.8    16.7    +      -       -      +
   3770F  ALA      3.2     0.6    -      -       -      -
   3771F  ALA*     1.3    78.8    -      -       +      +
   3773F  MET*     1.3    64.2    +      -       -      +
   3775F  LEU*     3.5     5.7    +      -       -      +
   3776F  GLN*     3.3    37.0    +      -       -      +
   3810F  LYS*     3.1    39.2    -      -       -      +
   3813F  ASP*     4.7     0.7    -      -       -      +
   3814F  TYR*     3.2    43.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET3773 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3698F  VAL*     4.3    17.3    -      -       -      +
   3701F  PHE*     5.4     9.6    -      -       +      -
   3702F  SER*     5.7     5.4    -      -       -      +
   3718F  TYR*     4.4    11.7    +      -       +      +
   3769F  GLY      3.6    11.3    +      -       -      +
   3770F  ALA*     3.4    11.3    +      -       -      +
   3771F  ALA      3.3     0.6    -      -       -      -
   3772F  GLU*     1.3    80.4    -      -       -      +
   3774F  VAL*     1.3    63.3    +      -       +      +
   3776F  GLN*     3.6     7.3    +      -       -      +
   3777F  MET*     3.3    25.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL3774 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3718F  TYR*     5.3     5.2    -      -       -      +
   3770F  ALA      3.5    13.2    -      -       -      +
   3771F  ALA*     3.3    22.9    -      -       -      +
   3773F  MET*     1.3    78.3    -      -       +      +
   3775F  LEU*     1.3    69.2    +      -       +      +
   3777F  MET*     4.2     4.1    -      -       -      +
   3778F  ILE*     3.2    27.0    +      -       -      +
   3792F  THR*     4.7    20.1    -      -       +      +
   3795F  LEU*     3.9    26.5    -      -       +      -
   3796F  GLY*     4.9    12.8    -      -       -      -
   3799F  ILE*     6.3     1.1    -      -       +      -
   3811F  MET*     4.5     8.3    -      -       +      -
   3823F  PHE*     4.8     0.2    -      -       -      -
   3882F  PHE*     5.3     6.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU3775 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3771F  ALA      3.5    15.9    +      -       -      +
   3772F  GLU*     3.5    10.4    +      -       -      +
   3773F  MET      3.2     0.4    -      -       -      -
   3774F  VAL*     1.3    92.7    -      -       +      +
   3776F  GLN*     1.3    63.4    +      -       -      +
   3777F  MET      3.3     0.4    -      -       -      -
   3778F  ILE      3.5     0.7    +      -       -      -
   3779F  SER*     3.5     9.0    +      -       -      -
   3811F  MET*     3.8    51.4    -      -       +      +
   3814F  TYR*     4.5    17.5    -      -       +      -
   3815F  LEU*     4.4    20.4    -      -       +      -
   3823F  PHE*     3.2    47.8    -      -       +      -
   3882F  PHE*     5.2     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN3776 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    462F  GLU*     4.1    17.4    +      -       -      +
   3702F  SER*     4.1    22.4    -      -       -      -
   3705F  ALA*     4.4     7.2    -      -       +      +
   3706F  LEU*     3.4    33.3    -      -       +      +
   3772F  GLU*     3.3    26.3    +      -       -      +
   3773F  MET*     3.6     5.1    +      -       -      +
   3775F  LEU*     1.3    76.1    -      -       -      +
   3777F  MET*     1.3    60.3    +      -       -      +
   3779F  SER*     3.5     6.9    +      -       -      -
   3780F  ALA*     3.1    26.2    +      -       -      +
   3814F  TYR*     2.9    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET3777 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3701F  PHE      5.9     0.7    -      -       -      +
   3704F  THR*     5.8     2.2    -      -       -      -
   3705F  ALA*     4.5    15.6    -      -       +      +
   3712F  LEU*     5.8     4.3    -      -       +      -
   3718F  TYR*     3.8    22.0    -      -       +      +
   3773F  MET      3.3    17.8    +      -       -      +
   3774F  VAL      4.6     2.9    -      -       -      +
   3775F  LEU      3.3     0.4    -      -       -      -
   3776F  GLN*     1.3    76.3    -      -       -      +
   3778F  ILE*     1.3    64.4    +      -       -      +
   3780F  ALA*     3.2    26.5    +      -       +      -
   3781F  CYS*     3.4    14.9    +      -       +      +
   3788F  MET*     3.7    29.6    -      -       +      +
   3789F  VAL*     6.5     0.7    -      -       +      -
   3792F  THR*     3.7    32.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE3778 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3774F  VAL      3.2    18.8    -      -       -      +
   3775F  LEU      3.5     0.6    +      -       -      -
   3776F  GLN      3.3     0.4    -      -       -      -
   3777F  MET*     1.3    77.4    -      -       +      +
   3779F  SER*     1.3    61.3    +      -       -      +
   3781F  CYS*     3.2    19.0    -      -       -      -
   3789F  VAL*     4.8    11.7    -      -       +      -
   3792F  THR*     4.0    19.3    -      -       -      +
   3793F  LEU*     3.8    33.0    -      -       +      -
   3823F  PHE*     3.8    31.6    -      -       +      +
   3826F  SER*     3.1    31.6    +      -       -      +
   3827F  ILE*     4.8     7.0    -      -       +      -
   3830F  LEU*     5.4     7.4    -      -       +      -
   3882F  PHE*     6.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER3779 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3775F  LEU      3.5     8.9    +      -       -      -
   3776F  GLN*     3.5     9.7    +      -       -      -
   3777F  MET      3.3     0.4    -      -       -      -
   3778F  ILE*     1.3    78.9    -      -       -      +
   3780F  ALA*     1.3    61.4    +      -       -      +
   3781F  CYS      3.3     0.4    +      -       -      -
   3782F  LYS*     3.6    10.9    +      -       -      +
   3821F  VAL      4.6     2.6    +      -       -      -
   3822F  GLY*     3.7    26.7    -      -       -      +
   3823F  PHE*     3.7    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA3780 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3705F  ALA*     3.9    25.1    -      -       +      +
   3710F  SER      4.5     3.5    -      -       -      +
   3711F  LYS      2.9    20.1    -      -       -      +
   3776F  GLN      3.1    17.6    +      -       -      +
   3777F  MET*     3.2    25.2    +      -       +      +
   3779F  SER*     1.3    76.3    -      -       -      +
   3781F  CYS*     1.3    61.6    +      -       -      +
   3782F  LYS*     3.2     4.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with CYS3781 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3711F  LYS*     4.1    10.1    -      -       -      +
   3712F  LEU*     5.2     5.1    -      -       +      +
   3777F  MET*     3.4    13.2    +      -       +      +
   3778F  ILE*     3.2    22.4    -      -       -      +
   3779F  SER      3.3     1.2    -      -       -      -
   3780F  ALA*     1.3    78.9    -      -       -      +
   3782F  LYS*     1.3    64.5    +      -       -      +
   3783F  GLY*     3.2    18.6    +      -       -      -
   3784F  GLU*     3.4    39.6    +      -       +      +
   3789F  VAL*     4.4    19.5    -      -       +      -
   3826F  SER*     3.7    11.0    -      -       -      -
   3830F  LEU*     5.3     5.8    -      -       -      -
----------------------------------------------------------
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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