Contacts of the strand formed by residues 832 - 836 (chain A) in PDB entry 1KEK


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 MET 832 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    824A  ILE*     3.7    30.5    -      -       +      +
    825A  THR*     4.4     6.7    -      -       +      -
    828A  PHE*     3.4     9.2    +      -       -      +
    829A  GLY*     3.4    29.4    +      -       -      +
    830A  GLU      3.6     0.2    -      -       -      -
    831A  ARG*     1.3    80.4    -      -       -      +
    833A  PHE*     1.4    60.7    +      -       -      +
    834A  ILE*     3.8    20.0    -      -       +      -
    862A  PRO*     3.6    25.9    -      -       +      +
    863A  ALA      3.0    22.9    +      -       -      -
    956A  SER*     3.2    11.2    -      -       -      +
    958A  TRP*     3.6    28.7    -      -       +      -
    960A  PHE*     3.9     9.2    -      -       +      -
    210B  PRO*     3.4    11.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 833 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    832A  MET*     1.4    78.6    -      -       -      +
    834A  ILE*     1.3    64.5    +      -       -      +
    863A  ALA*     3.5     8.3    -      -       +      -
    879A  MET*     4.0    26.5    -      -       +      -
    883A  MET*     3.8    24.2    -      -       +      -
    886A  ARG*     6.3     0.2    -      -       -      -
    955A  LYS*     3.6    37.7    -      -       +      -
    956A  SER      2.9     7.2    +      -       -      +
    957A  VAL*     4.1    22.7    -      -       +      -
    958A  TRP*     2.8    25.4    +      -       -      +
     77B  ALA*     4.2    13.9    -      -       +      -
    208B  MET*     3.3    48.0    -      -       +      -
    209B  ASN*     4.2     4.0    -      -       -      -
    210B  PRO*     3.8    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 834 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    825A  THR*     5.4     0.4    -      -       +      -
    832A  MET*     3.8    22.4    -      -       +      -
    833A  PHE*     1.3    78.4    -      -       -      +
    835A  ALA*     1.3    63.2    +      -       -      +
    836A  ASN*     4.0     7.2    -      -       -      +
    853A  TYR*     3.7    22.9    -      -       +      -
    862A  PRO*     3.6    26.0    -      -       +      -
    863A  ALA      2.9    10.2    +      -       -      +
    864A  TRP*     3.6    21.7    -      -       +      -
    865A  GLY*     3.0    25.6    +      -       -      +
    879A  MET*     4.1     6.4    -      -       -      +
    958A  TRP*     3.3     3.8    -      -       +      +
    960A  PHE*     3.7    42.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 835 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834A  ILE*     1.3    69.5    -      -       -      +
    836A  ASN*     1.3    59.9    +      -       -      +
    865A  GLY      3.7     4.3    -      -       -      -
    872A  ALA*     3.4    26.7    -      -       -      +
    875A  TYR*     3.8    12.6    -      -       +      -
    876A  GLY*     3.4    25.6    -      -       -      +
    879A  MET*     3.9     7.6    -      -       +      +
    958A  TRP      2.9     9.8    +      -       -      +
    959A  ILE*     3.3     4.6    -      -       +      +
    960A  PHE      2.9    24.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 836 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    834A  ILE*     3.8     1.3    -      -       +      +
    835A  ALA*     1.3    73.0    -      -       -      +
    837A  ALA*     1.3    82.0    +      -       -      +
    841A  SER*     2.6    35.3    +      -       -      -
    842A  SER*     3.6     2.5    +      -       -      -
    844A  TRP*     5.8     0.2    -      -       -      -
    853A  TYR*     4.4     2.0    +      -       -      -
    864A  TRP*     3.2    50.1    -      -       +      +
    865A  GLY      2.8    12.1    +      -       -      +
    866A  ASN*     3.0    19.8    -      -       -      +
    867A  SER      4.3     2.3    +      -       -      -
    868A  LEU      4.4     0.5    -      -       -      +
    872A  ALA*     4.1     2.9    -      -       -      +
    875A  TYR*     4.9     0.8    -      -       -      -
    960A  PHE*     3.4    30.9    -      -       -      +
----------------------------------------------------------
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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