Contacts of the helix formed by residues 727 - 738 (chain E) in PDB entry 3RTR


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 HIS 727 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    725E  LEU      4.3     0.2    +      -       -      -
    726E  LYS*     1.3    70.1    -      -       -      +
    728E  GLN*     1.3    65.7    +      -       +      +
    730E  LEU*     3.0     7.0    +      -       -      +
    731E  LEU*     2.8    54.9    +      -       +      +
    750E  LYS*     4.3    26.6    +      -       +      -
    753E  ILE*     4.6    12.8    -      -       +      +
    770E  ASP*     2.9    41.9    +      -       +      +
    772E  TYR*     3.3    37.8    +      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 728 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    726E  LYS*     3.3     3.0    -      -       +      +
    727E  HIS*     1.3    84.7    -      -       +      +
    729E  GLN*     1.3    57.0    +      -       -      +
    731E  LEU*     3.1    27.0    +      -       -      +
    732E  GLY*     3.0    30.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 729 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    722E  ARG*     5.2     3.2    -      -       -      +
    725E  LEU*     3.1    33.7    -      -       +      +
    726E  LYS*     3.1    22.5    +      -       +      +
    728E  GLN*     1.3    76.3    -      -       -      +
    730E  LEU*     1.3    62.5    +      -       -      +
    732E  GLY*     4.2     0.8    -      -       -      +
    733E  GLU*     3.0    45.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 730 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    715E  ILE*     3.8    32.1    -      -       +      -
    718E  ILE*     3.7    32.1    -      -       +      -
    719E  MET*     3.8    18.4    -      -       +      -
    725E  LEU*     3.7    10.5    -      -       +      +
    726E  LYS      2.9    11.9    +      -       -      +
    727E  HIS*     3.2    10.1    -      -       -      +
    729E  GLN*     1.3    77.2    -      -       -      +
    731E  LEU*     1.3    62.1    +      -       -      +
    733E  GLU*     3.4     1.4    +      -       -      +
    734E  VAL*     3.1    34.3    +      -       +      +
    749E  ILE*     6.0     0.2    -      -       +      -
    753E  ILE*     3.9    25.6    -      -       +      -
    762E  LEU*     5.5     1.8    -      -       +      -
    772E  TYR*     3.9    19.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 731 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    727E  HIS*     2.8    40.5    +      -       +      +
    728E  GLN*     3.1    27.6    +      -       -      +
    730E  LEU*     1.3    80.4    -      -       -      +
    732E  GLY*     1.3    60.7    +      -       -      +
    734E  VAL*     3.6     5.2    +      -       -      +
    735E  LEU*     3.1    35.0    +      -       +      +
    746E  VAL*     4.2    35.2    -      -       +      +
    749E  ILE*     3.8    34.1    -      -       +      -
    750E  LYS*     6.2     1.3    -      -       +      +
    753E  ILE*     5.9     2.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 732 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    728E  GLN*     3.0    19.3    +      -       -      +
    729E  GLN*     4.2     1.6    -      -       -      -
    731E  LEU*     1.3    77.7    -      -       -      +
    733E  GLU*     1.3    60.7    +      -       -      +
    735E  LEU*     3.1    25.2    +      -       -      +
    736E  THR*     3.3    15.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 733 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    718E  ILE*     3.7    32.6    -      -       +      +
    722E  ARG*     3.7    34.7    +      -       -      -
    725E  LEU*     4.4     5.8    -      -       +      -
    729E  GLN*     3.0    38.0    +      -       +      +
    730E  LEU      3.6     4.9    -      -       -      +
    731E  LEU      3.4     0.2    -      -       -      -
    732E  GLY*     1.3    75.9    -      -       -      +
    734E  VAL*     1.3    60.7    +      -       -      +
    736E  THR*     3.8     7.3    +      -       -      -
    737E  GLN*     3.8    25.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 734 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    711E  ILE*     4.6    11.2    -      -       +      -
    714E  ALA*     4.3     9.0    -      -       +      -
    715E  ILE*     3.7    24.2    -      -       +      +
    718E  ILE*     3.4    20.0    -      -       +      -
    730E  LEU*     3.1    22.2    +      -       +      +
    731E  LEU      3.9     5.4    -      -       -      +
    732E  GLY      3.2     0.2    -      -       -      -
    733E  GLU*     1.3    75.4    -      -       -      +
    735E  LEU*     1.3    65.3    +      -       -      +
    736E  THR      3.2     0.9    +      -       -      -
    737E  GLN*     3.7     1.6    +      -       -      +
    738E  LEU*     3.4    42.1    +      -       +      +
    744E  PRO*     5.0     2.5    -      -       +      -
    749E  ILE*     4.3    22.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 735 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    731E  LEU*     3.1    25.8    -      -       +      +
    732E  GLY*     3.1    15.0    +      -       -      +
    734E  VAL*     1.3    78.9    -      -       -      +
    736E  THR*     1.3    52.3    +      -       -      +
    738E  LEU      3.6     0.7    -      -       -      -
    739E  SER*     2.8    35.0    +      -       -      -
    743E  LYS*     4.3    16.8    +      -       -      +
    744E  PRO*     4.4    27.3    -      -       +      +
    746E  VAL*     6.0     4.3    -      -       +      -
    749E  ILE*     3.7    26.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 736 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732E  GLY      3.3    12.2    +      -       -      -
    733E  GLU*     4.1     9.4    -      -       -      -
    734E  VAL      3.2     0.6    -      -       -      -
    735E  LEU*     1.3    75.1    -      -       -      +
    737E  GLN*     1.3    66.6    +      -       +      +
    738E  LEU      3.2     2.0    +      -       -      -
    739E  SER*     3.7    15.9    +      -       -      -
    740E  SER*     4.8     1.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 737 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    714E  ALA*     5.2     1.1    -      -       +      -
    717E  ARG*     2.7    47.4    +      -       -      +
    718E  ILE*     3.2    34.2    -      -       -      +
    733E  GLU*     3.8    15.5    +      -       -      +
    734E  VAL      3.7     2.8    +      -       -      +
    736E  THR*     1.3    78.6    -      -       +      +
    738E  LEU*     1.3    69.0    +      -       +      +
    739E  SER      3.5     0.2    -      -       -      -
    740E  SER*     3.8    13.4    +      -       -      -
    741E  ARG*     5.5     3.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 738 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    710E  LEU*     4.1    11.0    -      -       +      +
    711E  ILE*     4.1    27.6    -      -       +      +
    714E  ALA*     3.6    22.4    -      -       +      -
    717E  ARG*     4.9     6.1    -      -       -      +
    734E  VAL*     3.4    21.0    +      -       +      +
    735E  LEU      3.6     0.9    -      -       -      -
    736E  THR      3.2     0.4    -      -       -      -
    737E  GLN*     1.3    88.2    -      -       +      +
    739E  SER*     1.3    56.5    +      -       -      +
    740E  SER      3.1     2.9    +      -       -      -
    741E  ARG*     3.2    16.7    +      -       -      +
    742E  PHE*     2.7    56.3    +      -       +      +
    744E  PRO*     3.9    25.8    -      -       +      -
----------------------------------------------------------
 Back to top of page


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