Contacts of the strand formed by residues 197 - 202 (chain B) in PDB entry 2KH2


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 PHE 197 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    167B  ARG*     3.7    11.0    -      -       -      -
    177B  VAL*     3.9    20.6    -      -       +      -
    178B  ALA*     5.2     0.2    -      -       +      -
    189B  PHE*     3.3    29.0    -      -       +      -
    193B  VAL*     3.5    40.5    +      -       +      -
    195B  GLY*     4.3     8.0    +      -       -      -
    196B  ARG*     1.3    95.8    -      -       +      +
    198B  THR*     1.3    69.7    +      -       -      +
    210B  LEU*     4.3    12.8    -      -       +      -
    211B  GLN      3.4     3.8    -      -       -      +
    212B  MET*     3.7    46.0    -      -       +      -
    215B  LEU*     4.0     4.9    -      -       +      -
    219B  ASP*     3.5    21.8    -      -       -      -
    223B  TYR*     3.8     8.3    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  PHE*     3.9     5.6    -      -       +      -
    195B  GLY      5.0     2.1    +      -       -      -
    197B  PHE*     1.3    79.7    +      -       -      +
    199B  ILE*     1.3    74.4    +      -       +      +
    200B  SER*     4.9     5.1    +      -       -      +
    209B  TYR      3.9     0.2    -      -       -      +
    210B  LEU*     3.7     2.0    -      -       -      +
    211B  GLN*     2.8    50.6    +      -       +      +
    213B  ASN*     4.2     9.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  TRP*     4.2    13.0    -      -       +      +
    178B  ALA*     3.9    20.0    -      -       +      -
    179B  TYR      3.5    15.5    -      -       -      +
    180B  ILE*     3.6    33.7    -      -       +      -
    187B  THR*     3.8    16.8    -      -       +      -
    189B  PHE*     3.5    23.1    -      -       +      -
    198B  THR*     1.3    82.9    -      -       +      +
    200B  SER*     1.3    69.3    +      -       -      +
    209B  TYR      3.6     4.5    -      -       -      +
    210B  LEU*     3.8    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180B  ILE*     3.3    10.4    -      -       -      +
    198B  THR*     4.9     5.7    +      -       -      +
    199B  ILE*     1.3    79.6    +      -       -      +
    201B  ARG*     1.3    59.4    +      -       -      +
    209B  TYR*     2.7    53.6    +      -       -      +
    211B  GLN*     6.0     1.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 201 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  PHE*     3.2    46.0    +      -       +      -
    159B  SER*     5.2     0.8    -      -       -      +
    163B  MET*     3.0    29.5    -      -       -      +
    180B  ILE*     2.8    40.4    +      -       +      +
    181B  SER      2.9    17.5    +      -       -      +
    182B  SER*     3.4    31.4    +      -       -      +
    183B  GLY      5.9     0.9    -      -       -      -
    184B  GLY*     6.2     2.0    -      -       -      -
    200B  SER*     1.3    75.7    -      -       -      +
    202B  ASP*     1.3    61.6    +      -       -      +
    203B  ASN*     4.1     7.8    +      -       -      +
    207B  THR      3.9     3.1    -      -       -      -
    208B  LEU*     4.0     7.9    -      -       +      -
    209B  TYR*     4.7     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 202 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158B  PHE*     3.3     5.4    -      -       -      -
    201B  ARG*     1.3    73.1    -      -       -      +
    203B  ASN*     1.3    58.9    +      -       -      +
    204B  ALA*     2.9    19.5    +      -       -      +
    205B  LYS*     2.9    47.1    +      -       -      +
    206B  ASN      3.1    18.7    +      -       -      -
    207B  THR*     2.9    27.3    +      -       +      +
    209B  TYR*     3.8    20.8    -      -       +      -
----------------------------------------------------------
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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