Contacts of the strand formed by residues 206 - 208 (chain H) 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 ILE 206 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    195H  VAL*     4.9     2.2    -      -       +      -
    197H  ALA*     3.8    21.8    -      -       +      -
    199H  GLY      3.4     4.9    -      -       -      +
    200H  VAL*     3.8    15.0    -      -       +      -
    201H  VAL*     4.4     0.6    -      -       -      +
    204H  GLY      4.5     2.2    -      -       -      +
    205H  GLY*     1.3    78.0    -      -       -      +
    207H  ILE*     1.3    63.4    +      -       -      +
    208H  ASN*     3.9     8.2    +      -       +      +
    212H  THR*     4.0    24.5    -      -       +      -
    226H  PHE*     4.2     5.4    -      -       +      -
    228H  VAL*     3.7    41.5    -      -       +      -
    274H  ASP*     5.1     0.3    -      -       -      +
    275H  TYR*     3.5     5.2    -      -       -      -
    276H  THR*     2.9    41.5    +      -       -      +
    281H  ILE*     3.8    12.3    -      -       +      -
    284H  LEU*     4.8     2.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 207 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63H  VAL*     3.7    35.0    -      -       +      -
    197H  ALA*     4.4     0.3    -      -       -      +
    198H  GLU*     3.3     6.0    +      -       +      +
    199H  GLY*     2.5    40.3    +      -       -      +
    200H  VAL*     4.7     0.2    -      -       -      +
    201H  VAL*     3.7    28.2    -      -       +      +
    206H  ILE*     1.3    71.4    -      -       -      +
    208H  ASN*     1.3    64.4    +      -       -      +
    236H  VAL*     4.9     2.9    -      -       +      -
    238H  LEU*     5.1     9.6    -      -       +      -
    240H  PRO*     4.8     2.0    -      -       +      -
    246H  VAL*     4.2    22.2    -      -       +      -
    247H  PRO*     5.5     2.9    -      -       +      -
    250H  PHE*     5.6     3.8    -      -       +      -
    273H  VAL*     3.6    23.1    -      -       +      -
    274H  ASP      3.6    10.8    -      -       -      +
    275H  TYR*     4.8     5.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 208 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  HIS*     4.4     4.2    -      -       -      -
    195H  VAL*     3.4    13.7    -      -       -      +
    196H  GLY      2.7    27.2    +      -       -      +
    197H  ALA*     3.6     6.8    -      -       -      +
    198H  GLU*     3.3    34.1    +      -       -      +
    206H  ILE*     3.9     9.8    +      -       +      +
    207H  ILE*     1.3    75.0    -      -       -      +
    209H  LYS*     1.3    69.1    +      -       -      +
    212H  THR*     3.2    31.0    +      -       +      +
    273H  VAL*     3.2     7.4    -      -       -      +
    274H  ASP*     2.9    30.8    +      -       -      +
----------------------------------------------------------
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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