Contacts of the strand formed by residues 69 - 74 (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 GLY 69 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67A  PRO      3.5     1.8    +      -       -      -
     68A  GLY*     1.3    74.5    -      -       -      +
     70A  ILE*     1.3    60.5    +      -       -      +
    100A  GLY      3.2    14.5    +      -       -      -
    101A  THR*     3.5     1.0    -      -       -      +
    102A  THR*     3.0    21.5    +      -       -      -
    103A  MET      3.1     8.1    +      -       -      -
    361A  ARG*     3.4     6.1    -      -       -      -
    362A  MET*     3.6    25.3    -      -       -      -
    384A  THR      3.5    10.1    -      -       -      -
    385A  SER*     4.2     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68A  GLY      4.2     2.7    -      -       -      +
     69A  GLY*     1.3    74.8    -      -       -      +
     71A  ASP*     1.3    61.4    +      -       -      +
     72A  VAL*     3.3     9.8    +      -       +      +
    103A  MET*     3.3    27.8    -      -       +      +
    105A  ILE*     4.4    22.4    -      -       +      -
    329A  THR      4.1     2.6    -      -       -      +
    361A  ARG*     3.2     9.0    +      -       -      +
    384A  THR      2.9    20.2    +      -       -      +
    385A  SER*     3.5    31.2    -      -       -      +
    388A  ALA*     4.2    15.2    -      -       +      +
    389A  ALA*     4.0    13.7    -      -       +      +
    394A  LEU*     5.1     4.5    -      -       +      -
    398A  LYS*     3.8    30.5    -      -       +      -
    399A  GLY      4.4     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  ILE*     1.3    69.9    -      -       -      +
     72A  VAL*     1.3    57.6    +      -       -      +
     73A  ASN      3.0    18.2    +      -       -      +
     74A  THR*     3.6    18.7    -      -       +      +
    101A  THR*     3.9    14.1    -      -       +      -
    103A  MET      2.8    10.9    +      -       -      +
    104A  ILE*     3.4     4.1    -      -       +      +
    105A  ILE      3.0    25.5    +      -       -      +
    329A  THR      4.5     0.2    -      -       -      -
    330A  GLY*     3.3     2.4    -      -       -      -
    331A  SER*     2.8    44.5    +      -       -      -
    358A  ILE*     3.7    10.7    -      -       -      +
    361A  ARG*     3.4    21.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 72 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     70A  ILE*     3.3     4.8    +      -       +      +
     71A  ASP*     1.3    71.2    +      -       -      +
     73A  ASN*     1.3    59.7    +      -       -      +
    105A  ILE*     4.0    15.7    -      -       +      -
    138A  HIS*     2.8    26.9    -      -       -      -
    251A  TYR*     3.2    23.9    +      -       -      +
    277A  GLU*     3.2    18.0    -      -       +      +
    328A  VAL*     4.2     7.4    -      -       +      -
    329A  THR      3.7    19.0    +      -       -      +
    388A  ALA*     3.4    34.3    -      -       +      -
    392A  PHE*     3.9    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 73 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ASP*     3.0    15.0    +      -       -      +
     72A  VAL*     1.3    81.5    -      -       -      +
     74A  THR*     1.3    60.7    +      -       -      +
     75A  TYR*     3.3    26.8    -      -       -      -
    105A  ILE      4.0     0.9    -      -       -      -
    107A  HIS*     3.4    14.9    +      -       -      -
    165A  GLN*     5.2     0.4    +      -       -      -
    253A  THR*     4.1     9.1    -      -       -      +
    254A  LYS*     3.7    19.4    -      -       -      +
    277A  GLU*     2.7    36.2    +      -       -      +
    279A  ILE*     5.1     0.4    -      -       +      -
    330A  GLY*     4.4     3.4    -      -       -      -
    331A  SER*     3.3     2.1    +      -       -      -
    332A  GLY*     2.7    39.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 74 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  ASP*     3.6    25.4    -      -       +      +
     73A  ASN*     1.3    81.8    +      -       -      +
     75A  TYR*     1.3    62.1    +      -       -      +
     76A  LEU*     4.4    11.0    -      -       -      -
    104A  ILE*     3.9    17.7    -      -       +      +
    105A  ILE      3.5     7.2    +      -       -      -
    106A  ASP*     2.9    34.4    +      -       -      +
    107A  HIS*     2.9    32.2    +      -       -      -
    331A  SER*     3.9     2.9    -      -       -      +
    333A  HIS*     4.2     5.6    -      -       +      +
    358A  ILE*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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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