Contacts of the strand formed by residues 194 - 198 (chain A) in PDB entry 1KCX


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 VAL 194 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162A  ASN*     2.7    20.4    +      -       -      +
    163A  SER*     3.3     0.9    -      -       -      -
    164A  PHE      3.1    26.0    +      -       -      +
    188A  LEU*     5.8     0.2    -      -       -      +
    193A  ALA*     1.3    73.4    -      -       -      +
    195A  ILE*     1.3    59.7    +      -       -      +
    196A  LEU*     3.6     9.6    -      -       +      +
    251A  TYR*     4.5    11.0    -      -       +      -
    275A  PHE*     6.5     0.2    -      -       +      -
    391A  ILE*     3.7    28.7    -      -       +      +
    392A  PHE*     3.7    35.4    -      -       +      -
    475A  PRO*     4.0    17.3    -      -       +      -
    478A  LEU*     4.2    21.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  PHE      3.7     3.4    -      -       -      +
    166A  VAL*     5.1     2.0    -      -       +      -
    185A  PHE*     3.7    64.4    -      -       +      +
    188A  LEU*     3.8    31.9    -      -       +      -
    189A  LYS*     4.2     5.6    -      -       -      +
    193A  ALA      3.7     7.8    +      -       -      +
    194A  VAL*     1.3    73.3    -      -       -      +
    196A  LEU*     1.3    64.7    +      -       -      +
    197A  VAL*     4.5     1.3    -      -       +      -
    248A  CYS*     3.9    12.6    -      -       +      -
    249A  PRO*     3.9    24.8    +      -       -      +
    250A  VAL*     4.3     1.5    -      -       +      +
    251A  TYR*     2.8    33.3    +      -       -      +
    478A  LEU*     5.8     0.2    -      -       -      +
    479A  TYR*     5.3     0.7    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  VAL      5.3     0.4    -      -       -      +
    107A  HIS*     3.8    24.0    -      -       +      +
    138A  HIS*     3.8    21.1    -      -       +      +
    163A  SER*     4.0    12.1    -      -       -      -
    164A  PHE      2.7    18.2    +      -       -      +
    165A  GLN*     3.2    11.6    -      -       +      -
    166A  VAL*     3.0    26.0    +      -       -      +
    194A  VAL*     3.6    30.7    -      -       +      +
    195A  ILE*     1.3    74.2    -      -       -      +
    197A  VAL*     1.3    68.5    +      -       -      +
    251A  TYR*     3.4    23.8    -      -       +      -
    253A  THR*     3.8    17.7    -      -       +      -
    277A  GLU*     5.4     0.9    -      -       -      +
    392A  PHE*     4.1     7.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165A  GLN*     4.3     2.2    -      -       -      -
    166A  VAL*     3.5    11.2    -      -       +      +
    168A  MET*     3.5    37.0    -      -       +      -
    185A  PHE*     3.9    19.3    -      -       +      -
    195A  ILE*     4.5     1.6    -      -       +      -
    196A  LEU*     1.3    81.1    -      -       -      +
    198A  HIS*     1.3    65.1    +      -       -      +
    199A  ALA*     3.5     8.7    +      -       +      +
    239A  ALA*     4.5     4.0    -      -       +      -
    250A  VAL*     3.9    27.8    -      -       +      -
    251A  TYR      3.0    10.6    +      -       -      +
    252A  ILE*     4.3     8.5    -      -       +      -
    253A  THR*     2.7    34.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  TYR*     5.7     0.7    -      -       -      -
    165A  GLN*     3.8    11.8    -      -       -      +
    166A  VAL      3.1     5.9    +      -       -      -
    167A  TYR*     3.6    38.4    -      +       +      -
    168A  MET*     3.0    25.5    +      -       -      +
    169A  ALA*     4.0    11.5    +      -       +      +
    170A  TYR*     3.6    23.0    +      +       -      -
    197A  VAL*     1.3    73.3    -      -       -      +
    199A  ALA*     1.3    59.4    +      -       -      +
    200A  GLU*     3.2    30.4    +      -       +      +
    253A  THR*     3.9     5.2    -      -       -      -
    254A  LYS*     4.2    17.4    +      -       -      -
    304A  SER      3.1    25.8    +      -       -      -
    305A  PRO*     4.0     9.4    -      -       +      +
----------------------------------------------------------
 Back to top of page


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