Contacts of the strand formed by residues 704 - 709 (chain B) 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 ILE 704 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    695B  CYS*     3.6    25.6    -      -       +      +
    696B  ALA*     3.9    26.8    -      -       +      +
    699B  CYS*     4.5     4.1    -      -       +      +
    702B  SER*     3.3     6.2    +      -       -      +
    703B  ALA*     1.3    83.2    -      -       -      +
    705B  LEU*     1.3    64.0    +      -       -      +
    706B  PRO*     3.7     7.3    -      -       -      +
    738B  ILE*     3.6    31.2    -      -       +      -
    739B  GLN      3.7     3.6    -      -       -      +
    740B  ILE*     3.8    12.8    -      -       +      -
    751B  CYS*     3.5    33.9    -      -       +      -
    762B  LEU*     4.6     1.1    -      -       +      -
    822B  ARG*     4.0    11.6    +      -       -      -
   3234B  SF4      3.5    18.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 705 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    702B  SER      5.8     0.9    -      -       -      +
    703B  ALA      4.2     0.4    -      -       -      -
    704B  ILE*     1.3    75.4    -      -       -      +
    706B  PRO*     1.3    80.6    -      -       +      +
    707B  VAL*     3.5     3.4    +      -       +      +
    739B  GLN*     2.9    41.1    +      -       +      +
    741B  ASN*     6.2     0.4    -      -       +      -
    778B  LEU*     4.3    15.7    -      -       +      -
    781B  ALA*     3.7    41.1    -      -       +      +
    782B  ALA*     4.0     9.6    -      -       +      +
    786B  VAL*     4.9    17.5    -      -       +      -
    804B  PRO*     5.9     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 706 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    693B  ASN*     3.5    27.8    -      -       -      +
    696B  ALA*     3.5    23.8    -      -       +      -
    704B  ILE      3.7     8.3    -      -       -      +
    705B  LEU*     1.3    98.4    -      -       +      +
    707B  VAL*     1.3    59.8    +      -       -      +
    708B  LEU      4.2     0.7    +      -       -      -
    736B  PHE*     4.5     1.3    -      -       +      -
    737B  ARG      3.5     7.0    -      -       -      +
    738B  ILE*     4.0     9.9    -      -       +      -
    786B  VAL*     6.0     1.0    -      -       -      +
    800B  GLN*     3.6    22.0    -      -       +      +
    801B  PHE*     4.0    19.9    -      -       +      -
    822B  ARG*     5.4     2.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 707 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    705B  LEU*     3.7    14.6    -      -       +      +
    706B  PRO*     1.3    77.8    -      -       -      +
    708B  LEU*     1.3    62.6    +      -       -      +
    709B  ALA*     4.0    13.7    -      -       +      -
    714B  LEU*     5.1     0.2    -      -       +      -
    721B  PHE*     4.3    13.7    -      -       +      -
    735B  LYS      5.2     0.7    -      -       -      +
    736B  PHE*     3.4    11.7    -      -       -      -
    737B  ARG*     2.7    45.2    +      -       +      +
    739B  GLN*     4.1     5.8    -      -       +      -
    781B  ALA*     3.7    29.6    -      -       +      +
    784B  ILE*     3.5    31.9    -      -       +      -
    801B  PHE*     4.8     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 708 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    706B  PRO      4.1     1.0    +      -       -      -
    707B  VAL*     1.3    73.0    -      -       -      +
    709B  ALA*     1.3    59.9    +      -       -      +
    726B  ALA*     4.2    14.1    -      -       +      -
    731B  LEU*     4.0    16.4    -      -       +      -
    734B  TYR*     3.6    36.6    -      -       +      -
    735B  LYS      3.5     3.8    -      -       -      +
    736B  PHE*     4.5     7.2    -      -       +      -
    784B  ILE*     4.1     3.9    -      -       -      +
    785B  PRO      4.2     0.9    -      -       -      +
    787B  LYS*     2.8    46.6    +      -       +      +
    790B  VAL*     3.6    31.0    -      -       +      -
    801B  PHE*     3.8    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 709 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707B  VAL*     4.2     6.7    -      -       +      -
    708B  LEU*     1.3    74.8    -      -       -      +
    710B  LYS*     1.3    65.0    +      -       -      +
    713B  GLU*     3.4    10.5    -      -       +      +
    714B  LEU*     3.4    34.5    -      -       +      -
    734B  TYR*     3.4     8.6    -      -       -      -
    735B  LYS*     2.7    41.7    +      -       +      +
    784B  ILE*     4.2    11.9    -      -       +      -
    787B  LYS*     4.1     0.4    -      -       -      +
----------------------------------------------------------
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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