Contacts of the strand formed by residues 158 - 163 (chain C) in PDB entry 6KQH


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 TYR 158 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148C  PHE*     5.4     0.7    -      -       +      -
    149C  THR      3.3    15.9    -      -       -      +
    150C  PRO*     3.8    17.0    -      -       +      -
    151C  ASP*     4.1     0.9    -      -       -      +
    156C  GLY*     3.4    28.5    +      -       -      -
    157C  ARG*     1.3    78.3    -      -       -      +
    159C  ILE*     1.3    71.1    +      -       -      +
    160C  ALA      4.1     0.2    -      -       -      -
    174C  LEU      4.1     3.6    -      -       -      +
    175C  GLU*     4.4     6.2    -      -       -      +
    176C  VAL*     4.7     5.1    +      -       -      +
    310C  LEU*     3.6    22.7    -      -       +      +
    313C  LEU*     3.4    57.7    +      -       +      +
    314C  THR*     3.9    17.2    +      -       -      -
    322C  VAL*     3.9    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 159 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147C  TYR      3.9     0.2    -      -       -      +
    148C  PHE*     3.4     5.3    -      -       -      -
    149C  THR*     2.9    42.5    +      -       -      +
    150C  PRO      4.9     0.9    -      -       -      +
    151C  ASP*     3.5    39.3    -      -       +      +
    152C  PRO*     5.3     2.7    -      -       +      -
    158C  TYR*     1.3    75.6    -      -       -      +
    160C  ALA*     1.3    68.4    +      -       -      +
    161C  SER*     4.0     6.8    +      -       -      +
    173C  ASP*     3.6    27.4    -      -       +      +
    174C  LEU      3.7     4.9    -      -       -      +
    175C  GLU*     3.6    32.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 160 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147C  TYR      3.4     5.2    -      -       -      -
    148C  PHE*     3.5    28.7    -      -       +      -
    158C  TYR      4.1     1.2    +      -       -      -
    159C  ILE*     1.3    72.7    -      -       -      +
    161C  SER*     1.3    64.0    +      -       -      +
    162C  ILE*     4.3     0.9    -      -       +      -
    172C  ILE      3.7     0.2    -      -       -      +
    173C  ASP*     3.2     6.8    -      -       -      +
    174C  LEU*     2.9    51.2    +      -       +      +
    306C  THR*     4.2    13.0    -      -       +      -
    310C  LEU*     4.4     8.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 161 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  ARG*     5.5     2.5    -      -       -      -
    145C  GLY      3.5     2.6    -      -       -      +
    146C  VAL*     3.4     3.7    -      -       -      +
    147C  TYR*     2.9    49.0    +      -       -      +
    149C  THR*     4.7     6.3    +      -       -      +
    159C  ILE*     4.0    12.5    +      -       -      +
    160C  ALA*     1.3    78.1    +      -       -      +
    162C  ILE*     1.3    62.3    +      -       -      +
    163C  ILE*     3.9    16.6    -      -       -      -
    171C  TRP*     6.0     2.5    -      -       -      -
    172C  ILE      3.3     4.5    -      -       -      -
    173C  ASP*     3.4    14.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 162 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145C  GLY      3.6     6.5    -      -       -      +
    146C  VAL*     4.3    14.8    -      -       +      -
    160C  ALA      5.5     0.4    -      -       -      -
    161C  SER*     1.3    74.9    -      -       -      +
    163C  ILE*     1.3    61.4    +      -       -      +
    164C  PRO*     3.8     3.0    -      -       -      +
    170C  PRO      4.0     0.9    -      -       -      +
    171C  TRP*     3.5     4.9    -      -       -      -
    172C  ILE*     2.9    49.9    +      -       +      +
    174C  LEU*     4.8     6.1    -      -       +      -
    267C  TYR*     3.7     8.9    +      -       -      +
    269C  LEU*     4.7     5.8    -      -       +      -
    290C  LEU*     3.7    36.6    -      -       +      -
    302C  VAL*     4.1    17.5    -      -       +      -
    303C  PHE*     4.7    15.7    -      -       +      -
    306C  THR*     4.1    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 163 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142C  ARG*     3.7    38.1    -      -       +      +
    143C  SER      4.7     2.0    -      -       -      +
    144C  PRO*     3.1    11.9    -      -       +      +
    145C  GLY      2.9    40.7    +      -       -      +
    147C  TYR*     4.3     9.0    -      -       +      -
    161C  SER*     4.5    16.4    -      -       -      +
    162C  ILE*     1.3    77.1    -      -       -      +
    164C  PRO*     1.3    73.7    -      -       -      +
    171C  TRP*     3.6    57.2    -      -       +      +
    269C  LEU*     3.4     6.4    -      -       -      +
----------------------------------------------------------
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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