Contacts of the strand formed by residues 194 - 198 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    162B  ASN*     2.7    22.4    +      -       -      +
    163B  SER*     3.4     1.2    -      -       -      -
    164B  PHE      3.2    24.4    +      -       -      -
    193B  ALA*     1.3    75.2    -      -       -      +
    195B  ILE*     1.3    62.1    +      -       -      +
    196B  LEU*     3.5    10.5    -      -       +      +
    249B  PRO*     6.0     0.2    -      -       -      -
    251B  TYR*     4.4    11.0    -      -       +      -
    391B  ILE*     3.6    28.9    -      -       +      +
    392B  PHE*     3.8    32.8    -      -       +      -
    475B  PRO*     4.1    15.5    -      -       +      -
    478B  LEU*     4.1    22.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  PHE      3.8     3.6    -      -       -      +
    166B  VAL*     4.9     1.8    -      -       +      -
    185B  PHE*     3.6    64.8    -      -       +      +
    188B  LEU*     3.8    30.1    -      -       +      -
    189B  LYS*     4.3     5.8    -      -       -      +
    193B  ALA      3.6     8.2    +      -       -      +
    194B  VAL*     1.3    74.8    -      -       -      +
    196B  LEU*     1.3    67.5    +      -       -      +
    197B  VAL*     4.5     2.0    -      -       +      -
    248B  CYS*     4.0    12.8    -      -       +      -
    249B  PRO      3.9    24.5    +      -       -      +
    250B  VAL*     3.8     2.4    -      -       +      +
    251B  TYR*     2.8    28.6    +      -       -      +
    479B  TYR*     5.3     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    107B  HIS*     3.9    22.4    -      -       +      +
    138B  HIS*     4.0    21.1    -      -       +      +
    163B  SER*     4.2    10.8    -      -       -      -
    164B  PHE      2.8    15.3    +      -       -      +
    165B  GLN*     3.2    11.7    -      -       +      -
    166B  VAL*     2.9    26.9    +      -       -      +
    194B  VAL*     3.5    31.9    -      -       +      +
    195B  ILE*     1.3    76.3    -      -       -      +
    197B  VAL*     1.3    65.7    +      -       -      +
    251B  TYR*     3.4    26.9    -      -       +      -
    253B  THR*     3.6    19.7    -      -       +      -
    277B  GLU*     5.1     1.1    -      -       -      +
    392B  PHE*     4.2     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    165B  GLN*     4.4     2.2    -      -       -      -
    166B  VAL*     3.4    13.0    -      -       +      +
    168B  MET*     3.5    36.3    -      -       +      -
    185B  PHE*     3.8    27.1    -      -       +      -
    195B  ILE*     4.5     2.0    -      -       +      +
    196B  LEU*     1.3    81.7    -      -       -      +
    198B  HIS*     1.3    68.2    +      -       -      +
    199B  ALA*     3.5     8.0    +      -       +      +
    239B  ALA*     4.4     5.6    -      -       +      -
    250B  VAL*     3.9    20.2    -      -       +      -
    251B  TYR      3.0     8.2    +      -       -      +
    252B  ILE*     4.2     9.0    -      -       +      +
    253B  THR*     3.0    27.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  TYR*     5.7     0.7    -      -       -      -
    165B  GLN*     3.8    12.9    -      -       -      +
    166B  VAL      2.9     8.9    +      -       -      +
    167B  TYR*     3.6    38.1    -      +       +      -
    168B  MET*     2.9    27.0    +      -       -      +
    169B  ALA*     4.2     9.4    -      -       +      +
    170B  TYR*     3.5    25.4    +      +       -      -
    197B  VAL*     1.3    72.5    -      -       -      +
    199B  ALA*     1.3    57.3    +      -       -      +
    200B  GLU*     2.9    35.0    +      -       +      +
    253B  THR*     4.0     5.6    -      -       -      +
    254B  LYS*     4.2    19.9    +      -       -      -
    304B  SER      3.5    18.3    +      -       -      -
    305B  PRO*     4.3     4.9    -      -       +      -
----------------------------------------------------------
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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