Contacts of the strand formed by residues 156 - 161 (chain I) 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 ASP 156 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132I  MET*     5.3     1.9    -      -       -      +
    155I  ARG*     1.3    78.7    +      -       -      +
    157I  PHE*     1.3    63.6    +      -       -      +
    158I  ILE*     3.8    23.8    +      -       +      +
    170I  MET*     6.2     1.6    -      -       +      -
    171I  ALA      3.5     8.3    -      -       -      +
    172I  ASN*     3.4    19.7    -      -       -      +
    196I  HIS      3.5     9.7    -      -       -      +
    197I  THR*     3.7    11.6    -      -       -      +
    199I  LEU*     2.9    30.6    +      -       -      +
    200I  VAL*     4.6     7.1    -      -       -      -
    201I  ASP*     4.7     5.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 157 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228A  LEU*     3.6    28.7    -      -       +      -
    231A  PHE*     3.6    41.1    -      +       +      -
    155I  ARG*     4.2     8.7    -      -       -      -
    156I  ASP*     1.3    72.1    -      -       -      +
    158I  ILE*     1.3    60.4    +      -       -      +
    159I  GLY      4.0     0.6    +      -       -      -
    169I  PHE*     4.5     5.2    -      +       +      -
    170I  MET*     3.2     4.0    -      -       -      -
    171I  ALA*     2.9    44.9    +      -       +      +
    172I  ASN      5.2     0.4    -      -       -      -
    173I  GLU*     4.0    33.7    -      -       +      -
    176I  LEU*     6.2     2.0    -      -       +      -
    179I  GLU      5.5     1.8    -      -       -      -
    180I  LEU*     5.6     4.5    -      -       +      -
    195I  PHE*     4.4    17.7    -      -       +      -
    196I  HIS      3.4     4.7    -      -       -      +
    197I  THR*     3.3    31.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 158 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132I  MET*     3.8    33.4    -      -       +      -
    156I  ASP*     3.9    29.6    -      -       +      +
    157I  PHE*     1.3    79.3    -      -       -      +
    159I  GLY*     1.3    64.2    +      -       -      +
    160I  VAL*     3.8     5.0    +      -       +      +
    167I  LEU*     4.9    11.0    -      -       +      -
    169I  PHE      3.5     8.5    -      -       -      +
    170I  MET*     3.7    22.0    -      -       +      -
    171I  ALA      4.9     0.2    -      -       -      +
    194I  ARG      3.6     1.7    -      -       -      +
    195I  PHE*     3.4     3.7    -      -       -      -
    196I  HIS*     2.9    37.4    +      -       -      +
    199I  LEU*     3.8    29.8    -      -       +      -
    265I  SER*     5.4     3.6    -      -       -      +
    267I  ILE*     5.8     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 159 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158I  ILE*     1.3    72.3    -      -       -      +
    160I  VAL*     1.3    59.7    +      -       -      -
    167I  LEU*     4.0     1.0    -      -       -      +
    168I  LEU*     2.9    24.6    +      -       -      -
    169I  PHE      2.8    23.0    +      -       -      +
    193I  ILE*     3.7    13.0    -      -       -      -
    194I  ARG      3.4     7.0    -      -       -      -
    195I  PHE*     3.6    25.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 160 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158I  ILE*     3.8     6.0    +      -       +      +
    159I  GLY*     1.3    74.6    -      -       -      -
    161I  ASP*     1.3    70.4    +      -       -      +
    164I  GLY*     4.0    28.5    -      -       -      +
    165I  LYS      4.1     3.1    -      -       -      +
    166I  ARG      3.3    22.0    -      -       -      +
    167I  LEU*     3.9     7.9    -      -       +      +
    168I  LEU*     4.4     1.1    -      -       -      -
    193I  ILE*     3.6     6.4    -      -       -      -
    194I  ARG*     2.9    44.0    +      -       +      +
    196I  HIS*     3.8    24.5    -      -       +      +
    265I  SER*     4.4    10.1    -      -       -      +
    267I  ILE*     5.6     7.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 161 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    160I  VAL*     1.3    81.1    -      -       -      +
    162I  SER*     1.3    80.4    +      -       -      +
    163I  THR*     3.1    21.7    +      -       -      +
    164I  GLY*     2.8    22.5    +      -       -      -
    166I  ARG*     2.9    30.7    +      -       +      +
    168I  LEU*     3.9    13.2    -      -       +      +
    190I  HIS*     3.2    39.8    +      -       +      +
    191I  PRO*     5.9     0.9    -      -       -      +
    192I  ARG*     3.7    10.2    -      -       -      +
    194I  ARG*     5.0     0.9    -      -       -      +
----------------------------------------------------------
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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