Contacts of the strand formed by residues 165 - 170 (chain A) in PDB entry 1CKQ


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 165 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90A  PRO*     5.0     0.6    -      -       +      +
    109A  VAL*     3.5    31.8    -      -       +      +
    111A  GLU*     2.8    37.6    +      -       +      +
    146A  SER      4.7     1.6    +      -       -      -
    149A  ASN*     3.4    30.5    -      -       +      +
    150A  ILE*     3.7    27.9    -      -       +      +
    153A  ILE*     4.0    18.4    -      -       +      -
    163A  PHE*     3.1    34.5    +      +       +      +
    164A  PRO*     1.3    74.8    -      -       -      +
    166A  VAL*     1.3    75.0    +      -       -      +
    167A  LEU*     4.5     7.4    -      -       +      -
    235A  ALA*     3.7     8.6    -      -       +      -
    236A  SER*     2.9    29.3    +      -       -      +
    258A  ILE*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    108A  LEU*     3.6    29.6    -      -       +      -
    109A  VAL      2.9     7.5    +      -       -      +
    110A  ALA*     3.4     4.4    -      -       +      -
    111A  GLU*     2.9    28.6    +      -       -      +
    164A  PRO      3.9     1.8    -      -       -      +
    165A  TYR*     1.3    78.3    -      -       -      +
    167A  LEU*     1.3    61.1    +      -       -      +
    168A  PHE*     3.9    32.0    -      -       +      -
    236A  SER*     3.6     2.0    -      -       -      +
    238A  TYR*     4.1    17.7    -      -       +      -
    254A  ILE*     4.3     3.1    -      -       +      -
    255A  MET*     4.8     4.0    -      -       +      -
    258A  ILE*     3.3    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    111A  GLU*     3.4    21.1    -      -       +      +
    113A  LYS*     3.7    28.3    -      -       +      -
    146A  SER*     4.3    12.6    -      -       -      +
    150A  ILE*     4.6    12.6    -      -       +      -
    165A  TYR*     4.2    11.2    +      -       +      -
    166A  VAL*     1.3    74.5    -      -       -      +
    168A  PHE*     1.3    66.5    +      -       -      +
    169A  LEU*     3.8    12.3    -      -       +      +
    204A  LEU*     3.9    35.9    -      -       +      -
    235A  ALA*     5.8     1.3    -      -       +      -
    236A  SER      3.0    11.7    +      -       -      +
    237A  ILE*     3.8    12.7    -      -       +      -
    238A  TYR*     2.9    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35A  VAL*     4.5     9.6    -      -       +      -
    110A  ALA*     5.1     1.1    -      -       +      -
    111A  GLU      2.9    19.7    +      -       -      +
    112A  ALA*     3.4     8.9    -      -       +      +
    113A  LYS*     2.9    28.2    +      -       -      +
    114A  HIS*     5.7     0.2    -      -       -      -
    166A  VAL*     3.9    21.1    -      -       +      -
    167A  LEU*     1.3    74.1    -      -       -      +
    169A  LEU*     1.3    61.2    +      -       -      +
    238A  TYR*     3.4    11.4    -      +       +      -
    246A  TRP*     3.6    38.1    -      +       +      +
    251A  MET*     3.9    42.0    -      -       +      -
    254A  ILE*     3.9    28.7    -      -       +      -
    255A  MET*     3.8    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  LYS*     3.7     5.2    -      -       +      -
    143A  ILE*     3.9    20.4    -      -       +      -
    167A  LEU*     3.8    17.3    -      -       +      +
    168A  PHE*     1.3    80.1    -      -       -      +
    170A  GLU*     1.3    60.0    +      -       -      +
    174A  PHE*     3.8    21.5    -      -       +      -
    201A  LEU*     4.8     2.2    -      -       +      -
    204A  LEU*     3.5    26.7    -      -       +      -
    237A  ILE*     3.4    28.9    -      -       +      -
    238A  TYR      2.9    24.5    +      -       -      +
    239A  THR*     3.9    14.4    -      -       -      +
    240A  GLN      3.4    12.3    +      -       -      -
    246A  TRP*     2.8    25.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 170 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113A  LYS      3.2     4.9    +      -       -      -
    114A  HIS*     3.3    37.1    +      -       +      +
    115A  GLN      3.1    22.5    +      -       -      -
    169A  LEU*     1.3    78.7    -      -       -      +
    171A  GLY*     1.3    63.0    +      -       -      +
    174A  PHE*     3.5    10.9    -      -       -      -
    240A  GLN*     5.0     4.9    -      -       -      -
    243A  GLY      5.3     1.1    -      -       -      +
    244A  ARG      3.8    15.9    -      -       -      +
    245A  GLU*     3.5    32.7    -      -       -      +
    246A  TRP*     3.1    31.4    +      -       +      +
----------------------------------------------------------
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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