Contacts of the strand formed by residues 239 - 243 (chain P) in PDB entry 6F0X


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 239 (chain P).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54P  CYS      3.9    10.9    +      -       -      +
     55P  MET*     3.3    25.4    -      -       -      +
    164P  PHE*     3.3    33.0    -      +       +      -
    166P  GLU*     4.9     1.6    -      -       -      -
    236P  SER      5.8     1.8    -      -       -      -
    237P  ARG*     3.3     3.2    -      -       -      +
    238P  GLY*     1.3    70.8    -      -       -      +
    240P  LYS*     1.3    67.9    +      -       -      +
    241P  LEU*     3.6     5.4    +      -       -      -
    242P  THR*     2.4    50.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 240 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54P  CYS*     4.6     8.7    +      -       -      +
     84P  ARG*     4.4     4.8    -      -       -      +
    163P  GLU*     3.1    46.9    +      -       +      +
    164P  PHE      3.2    15.1    +      -       -      +
    165P  TYR*     3.1    31.9    -      -       +      +
    200P  PHE      6.0     0.4    -      -       -      +
    202P  GLU*     2.6    45.5    +      -       -      +
    238P  GLY*     2.8    11.9    +      -       -      +
    239P  HIS*     1.3    76.7    +      -       -      +
    241P  LEU*     1.3    66.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 241 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54P  CYS*     4.0     9.9    -      -       +      +
     55P  MET*     4.0    11.7    -      -       -      +
     56P  VAL*     3.8    33.4    -      -       +      +
    164P  PHE*     3.8     1.6    +      -       -      -
    165P  TYR*     3.2    26.5    -      -       +      +
    166P  GLU      3.2    18.2    +      -       -      +
    194P  ILE*     5.9     3.1    -      -       +      -
    197P  ALA*     4.9     6.1    -      -       +      +
    199P  ALA*     4.2    24.5    -      -       +      -
    200P  PHE*     6.0     1.3    -      -       +      -
    239P  HIS*     3.5     7.4    -      -       -      -
    240P  LYS*     1.3    84.3    -      -       -      +
    242P  THR*     1.3    80.0    +      -       -      +
    243P  VAL*     3.6    23.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 242 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55P  MET*     3.7    14.4    -      -       +      +
     56P  VAL      3.2    17.0    +      -       -      +
    166P  GLU*     2.6    49.8    +      -       +      +
    168P  ASP*     5.2     2.9    -      -       +      +
    239P  HIS*     2.4    37.1    +      -       -      -
    241P  LEU*     1.3    81.5    -      -       -      +
    243P  VAL*     1.3    62.7    +      -       -      +
    244P  THR*     3.4    19.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 243 (chain P). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56P  VAL*     3.7     6.1    -      -       +      +
     58P  VAL*     4.3    14.8    -      -       +      -
     76P  LEU*     4.6    14.6    -      -       +      -
     80P  ILE*     6.2     1.1    -      -       +      -
    165P  TYR*     5.6     4.5    -      -       +      -
    166P  GLU      2.5    15.1    +      -       -      +
    167P  LEU*     3.3    21.9    -      -       +      +
    168P  ASP*     2.7    33.3    +      -       -      +
    190P  LEU*     4.7    13.2    -      -       +      -
    194P  ILE*     5.1    12.6    -      -       +      -
    241P  LEU*     3.6    27.8    +      -       +      +
    242P  THR*     1.3    71.0    -      -       -      +
    244P  THR*     1.3    64.3    +      -       -      +
    245P  LEU*     5.2     0.7    -      -       +      -
----------------------------------------------------------
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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