Contacts of the helix formed by residues 168 - 177 (chain B) in PDB entry 1KN0


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 168 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  HIS*     3.6    33.2    +      -       +      +
     70A  ARG*     4.3     7.0    +      -       -      -
    186A  VAL*     5.0     1.6    -      -       -      +
     46B  ARG*     3.9    19.8    +      -       -      +
    165B  CYS*     2.6    22.2    +      -       +      +
    167B  LEU*     1.3    70.6    -      -       -      +
    169B  LYS*     1.3    67.0    +      -       -      +
    170B  ASP*     3.0    25.6    +      -       -      +
    171B  TYR*     3.4    19.8    +      -       +      +
    172B  LEU*     3.1    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 169 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  TYR*     4.8     9.3    +      -       -      -
     67A  GLU*     3.9    28.3    +      -       -      +
     69A  HIS*     5.0     1.6    +      -       -      -
     70A  ARG*     5.9     0.2    -      -       -      +
    167B  LEU      4.1     9.2    -      -       -      +
    168B  ASP*     1.3    71.8    +      -       -      +
    170B  ASP*     1.3    67.5    +      -       -      +
    172B  LEU*     3.2    13.9    +      -       +      +
    173B  ARG*     3.1    30.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 170 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  ARG*     3.9    15.4    +      -       -      -
    183A  PRO*     3.2    17.7    -      -       -      +
    184A  LEU*     3.3    38.7    -      -       +      +
    186A  VAL*     3.2    11.3    -      -       +      +
    168B  ASP*     3.0    14.2    +      -       -      +
    169B  LYS*     1.3    78.8    -      -       -      +
    171B  TYR*     1.3    61.7    +      -       -      +
    173B  ARG*     3.0    29.0    +      -       -      +
    174B  SER*     3.1    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 171 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186A  VAL*     3.3    10.4    -      -       -      +
    188A  LEU*     3.7    18.6    -      -       +      -
     46B  ARG*     3.2    33.4    -      -       +      +
     47B  LEU*     2.6    35.8    +      -       -      +
     52B  ILE*     3.5    20.6    -      -       +      +
    165B  CYS*     3.3    35.0    -      -       +      -
    166B  ILE*     4.1     8.7    -      -       -      -
    168B  ASP*     3.4    26.2    +      -       +      +
    169B  LYS      3.2     0.2    -      -       -      -
    170B  ASP*     1.3    79.9    -      -       -      +
    172B  LEU*     1.3    68.4    +      -       +      +
    174B  SER*     3.1    15.1    +      -       -      -
    175B  LEU*     3.3    36.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 172 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  CYS*     3.9    35.7    -      -       +      +
    166B  ILE*     4.1    20.9    -      -       +      +
    167B  LEU      4.7     3.1    -      -       -      +
    168B  ASP      3.1    16.7    +      -       -      +
    169B  LYS*     3.2    14.6    +      -       +      +
    171B  TYR*     1.3    83.3    -      -       +      +
    173B  ARG*     1.3    59.4    +      -       +      +
    175B  LEU*     2.7    46.3    +      -       +      +
    176B  ASN*     3.3    11.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 173 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183A  PRO*     3.6    17.2    +      -       -      +
    184A  LEU      3.5    16.6    +      -       -      -
    185A  GLU*     4.9     5.1    -      -       -      +
    169B  LYS*     3.1    17.1    +      -       +      +
    170B  ASP*     3.0    37.4    +      -       -      +
    172B  LEU*     1.3    75.3    -      -       +      +
    174B  SER*     1.3    63.4    +      -       -      +
    175B  LEU      3.1     1.2    +      -       -      -
    176B  ASN*     3.1    24.4    +      -       -      +
    177B  LYS*     3.2    44.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 174 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  GLU*     4.7     4.4    -      -       -      +
    186A  VAL*     2.9    51.0    +      -       -      +
    188A  LEU*     3.5    11.0    -      -       -      +
    170B  ASP      3.1     4.7    +      -       -      -
    171B  TYR      3.1    10.7    +      -       -      -
    172B  LEU      3.1     0.4    -      -       -      -
    173B  ARG*     1.3    80.1    +      -       -      +
    175B  LEU*     1.3    60.9    +      -       -      +
    177B  LYS*     3.6    18.3    +      -       -      +
    178B  LEU*     3.4    19.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 175 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188A  LEU*     3.4    20.2    -      -       +      -
     47B  LEU      4.5     0.7    -      -       -      +
     49B  PRO*     3.7    35.8    -      -       +      +
     52B  ILE*     3.8    20.0    -      -       +      -
     64B  CYS*     5.7     1.3    -      -       -      -
    171B  TYR*     3.3    49.1    +      -       +      +
    172B  LEU*     2.7    32.1    +      -       +      +
    174B  SER*     1.3    70.9    -      -       -      +
    176B  ASN*     1.3    65.0    +      -       -      +
    177B  LYS      3.1     0.2    -      -       -      -
    178B  LEU*     3.0    21.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 176 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  LYS*     4.5    15.9    +      -       -      +
    172B  LEU*     3.5    18.6    +      -       -      +
    173B  ARG*     3.1    17.4    +      -       -      +
    175B  LEU*     1.3    72.6    -      -       -      +
    177B  LYS*     1.3    60.2    +      -       +      +
    178B  LEU      2.8    19.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 177 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185A  GLU*     4.9    18.9    +      -       +      +
    173B  ARG*     3.2    39.9    +      -       -      +
    174B  SER*     3.8    14.4    -      -       -      +
    175B  LEU      3.1     0.8    -      -       -      -
    176B  ASN*     1.3    76.4    -      -       +      +
    178B  LEU*     1.3    66.3    +      -       -      +
    179B  PRO*     4.7     0.5    -      -       -      +
----------------------------------------------------------
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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