Contacts of the helix formed by residues 390 - 395 (chain F) in PDB entry 6O81


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 ALA 390 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249C  THR*     4.0     3.1    +      -       -      +
    311C  PRO*     3.7    33.2    -      -       +      +
    386F  LEU*     3.4    32.1    -      -       +      +
    387F  LEU*     3.5     5.6    +      -       +      +
    388F  ILE      3.4     0.2    -      -       -      -
    389F  PRO*     1.3    76.9    -      -       +      +
    391F  ALA*     1.3    59.1    +      -       -      +
    392F  SER      3.2     2.2    -      -       -      -
    393F  TYR*     3.0    23.2    +      -       +      +
    394F  VAL      3.0    12.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 391 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    253C  THR*     5.8     0.4    -      -       -      +
    334F  LEU*     5.4     0.4    -      -       +      -
    361F  VAL*     4.2     8.3    -      -       +      -
    386F  LEU*     4.8     0.4    -      -       -      -
    387F  LEU      3.3     9.1    +      -       -      +
    388F  ILE*     3.4    22.0    -      -       -      +
    389F  PRO      3.2     0.4    -      -       -      -
    390F  ALA*     1.3    78.2    -      -       -      +
    392F  SER*     1.3    60.0    +      -       -      +
    394F  VAL*     3.5     9.7    -      -       +      +
    395F  LEU*     3.2    33.9    +      -       +      +
    423F  LEU*     3.8    28.9    -      -       +      -
    426F  VAL*     4.7     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 392 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250C  GLY*     5.6     0.2    -      -       -      -
    252C  HIS*     3.5    28.8    -      -       -      -
    253C  THR*     3.8    15.7    +      -       -      -
    314C  ASP*     2.8    28.1    +      -       -      -
    388F  ILE      4.5     0.8    +      -       -      -
    389F  PRO      3.0    10.7    +      -       -      -
    391F  ALA*     1.3    76.8    -      -       -      +
    393F  TYR*     1.3    59.8    +      -       -      +
    396F  PRO*     3.4     9.1    -      -       -      +
    426F  VAL*     3.9    15.1    -      -       -      +
    430F  HIS*     3.4    18.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 393 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    338B  SER      5.1     0.3    -      -       -      -
    339B  ARG*     2.5    86.6    +      -       +      +
    340B  HIS*     5.0     2.6    +      +       -      -
    286C  HIS*     3.5    44.4    -      +       +      -
    288C  PHE*     3.2    33.2    -      +       -      -
    309C  HIS*     5.4     8.7    -      +       +      -
    311C  PRO*     4.1    15.0    -      -       +      -
    314C  ASP*     5.4     3.8    -      -       -      +
    386F  LEU*     5.3     3.1    -      -       +      -
    389F  PRO      5.3     0.4    -      -       -      +
    390F  ALA*     3.0    21.0    +      -       +      +
    392F  SER*     1.3    81.7    +      -       -      +
    394F  VAL*     1.3    63.2    +      -       +      +
    396F  PRO*     3.5     9.1    -      -       -      +
    397F  GLU*     5.3     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 394 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    339B  ARG*     4.1     0.7    -      -       -      +
    332F  VAL*     5.8     0.2    -      -       +      -
    334F  LEU*     4.0    18.4    -      -       +      -
    357F  ARG*     5.7     2.5    -      -       -      +
    359F  VAL*     3.9    24.7    -      -       +      -
    361F  VAL*     5.0     0.7    -      -       +      -
    384F  SER*     5.8     1.1    -      -       -      +
    386F  LEU*     3.6    22.4    -      -       +      -
    390F  ALA      3.0    11.7    +      -       -      +
    391F  ALA*     3.5    15.5    -      -       -      +
    393F  TYR*     1.3    79.9    -      -       +      +
    395F  LEU*     1.3    56.6    +      -       -      +
    396F  PRO      3.3     0.2    -      -       -      -
    397F  GLU*     2.7    48.0    +      -       +      +
    398F  VAL*     3.2    20.2    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 395 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    334F  LEU*     4.0     8.3    -      -       +      -
    391F  ALA      3.2    21.6    +      -       -      +
    394F  VAL*     1.3    73.7    -      -       -      +
    396F  PRO*     1.3    70.6    -      -       +      +
    397F  GLU      3.2     0.2    -      -       -      -
    398F  VAL*     3.3    33.4    -      -       +      +
    401F  VAL*     3.9    21.3    -      -       +      -
    423F  LEU*     4.6    13.2    -      -       +      +
    426F  VAL*     3.7    25.1    -      -       +      -
    427F  ALA*     3.8    18.4    -      -       +      +
    430F  HIS*     3.7    16.2    -      -       +      +
    432F  VAL*     3.6    34.0    -      -       +      +
----------------------------------------------------------
 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