Contacts of the strand formed by residues 67 - 74 (chain C) in PDB entry 3KDH


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 67 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60C  PRO*     4.9     3.8    -      -       +      -
     61C  GLU*     3.8    46.0    -      -       +      +
     64C  LYS*     4.2    22.4    +      -       +      +
     65C  HIS      3.2    10.3    -      -       -      +
     66C  PHE*     1.3    79.9    -      -       -      +
     68C  LYS*     1.3    63.7    +      -       -      +
     69C  ARG      3.7    25.4    -      -       -      +
     70C  CYS*     4.7     3.1    -      -       +      -
     85C  VAL*     3.7    23.8    -      -       +      -
     86C  THR      3.6     2.7    -      -       -      -
     87C  VAL*     5.5     2.0    -      -       +      -
     88C  ILE*     5.1     1.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 68 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61C  GLU*     5.8     1.2    -      -       -      +
     66C  PHE      3.9     1.2    +      -       -      -
     67C  VAL*     1.3    74.9    -      -       -      +
     69C  ARG*     1.3    89.7    +      -       -      +
     86C  THR*     2.8    26.0    +      -       +      +
     88C  ILE*     4.2    29.3    -      -       +      +
     93C  ALA*     5.1     6.8    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 69 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61C  GLU*     6.1     0.9    -      -       -      -
     67C  VAL*     3.7    10.3    -      -       -      +
     68C  LYS*     1.3   109.7    -      -       -      +
     70C  CYS*     1.3    64.5    +      -       -      +
     84C  GLU      4.6     0.2    -      -       -      -
     86C  THR*     2.8    54.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 70 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58C  ASP*     3.6    19.9    -      -       -      +
     59C  ASN*     5.3     0.7    -      -       -      +
     60C  PRO*     3.5    37.9    -      -       +      -
     61C  GLU*     5.7     1.1    -      -       +      +
     67C  VAL*     4.7     2.7    -      -       +      -
     69C  ARG*     1.3    80.9    -      -       -      +
     71C  ARG*     1.3    67.1    +      -       -      +
     83C  ARG*     3.8    25.6    -      -       -      -
     84C  GLU      3.3    13.7    -      -       -      +
     85C  VAL*     3.9     5.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 71 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  GLY*     2.7    47.5    +      -       -      -
     58C  ASP*     5.2     3.4    -      -       -      -
     70C  CYS*     1.3    77.3    -      -       -      +
     72C  LEU*     1.3    70.8    +      -       -      +
     73C  ILE*     3.6    10.6    -      -       +      +
     83C  ARG*     3.3     4.1    -      -       -      -
     84C  GLU*     2.8    65.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 72 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    138A  SER*     5.5     0.5    -      -       -      -
    140A  LYS*     3.7    23.1    -      -       -      +
     57C  PHE*     4.0    17.7    -      -       +      -
     58C  ASP*     3.7    32.8    -      -       +      +
     71C  ARG*     1.3    81.8    +      -       -      +
     73C  ILE*     1.3    60.6    -      -       -      +
     74C  SER      4.3     1.1    -      -       -      +
     75C  GLY      3.7    18.2    -      -       -      +
     76C  ASP*     3.6     9.4    -      -       -      -
     77C  GLY*     3.5    31.0    -      -       -      +
     81C  SER*     4.6     2.9    -      -       -      +
     82C  VAL      3.4     7.2    -      -       -      +
     83C  ARG*     3.8    20.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 73 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  PRO*     4.5     6.1    -      -       +      -
    139A  GLY      3.8     6.1    -      -       -      +
    140A  LYS*     3.2    13.2    -      -       -      +
    141A  VAL*     2.9    51.6    +      -       +      +
     71C  ARG*     3.6    25.3    +      -       +      +
     72C  LEU*     1.3    74.3    -      -       -      +
     74C  SER*     1.3    60.7    +      -       -      +
     82C  VAL*     2.8    40.7    +      -       +      +
     84C  GLU*     3.5    48.7    -      -       +      +
     97C  THR*     4.2     7.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 74 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  HIS*     2.8    27.9    +      -       -      +
     45A  ALA*     3.3     9.3    -      -       -      +
     46A  PRO*     3.9    21.8    -      -       -      -
    140A  LYS*     4.6     4.2    -      -       -      +
    141A  VAL*     4.5     6.0    +      -       -      -
     72C  LEU*     3.5     2.7    -      -       -      +
     73C  ILE*     1.3    82.1    -      -       -      +
     75C  GLY*     1.3    66.2    +      -       -      +
     80C  GLY      5.0     3.3    +      -       -      -
     81C  SER*     3.3     3.7    -      -       -      -
     82C  VAL*     2.9    38.0    +      -       -      +
----------------------------------------------------------
 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