Contacts of the strand formed by residues 78 - 83 (chain B) in PDB entry 3KDM


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 THR 78 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  SER*     5.5     4.7    +      -       -      -
     22B  CYS      3.1    14.8    -      -       -      -
     23B  ALA*     4.0    19.5    -      -       +      -
     29B  PHE*     3.8     5.4    -      -       -      -
     72B  ARG*     3.6     7.8    -      -       -      +
     73B  ASP      3.0    17.0    -      -       -      +
     76B  LYS*     3.6    13.6    -      -       +      +
     77B  ASN*     1.3    84.7    -      -       -      +
     79B  LEU*     1.3    62.1    +      -       -      +
     80B  TYR*     3.0    35.9    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 79 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  SER*     3.5     4.0    -      -       -      -
     22B  CYS*     2.8    36.6    +      -       +      +
     29B  PHE*     3.9    14.3    -      -       +      -
     34B  MET*     3.2    32.8    -      -       +      -
     35B  SER      4.1     2.0    -      -       -      +
     36B  TRP*     3.2    29.6    -      -       +      +
     51B  ILE*     3.7    14.8    -      -       +      -
     70B  ILE*     3.4    28.0    -      -       +      -
     71B  SER      3.2    24.5    -      -       -      +
     72B  ARG*     4.1     3.6    -      -       +      +
     78B  THR*     1.3    72.0    -      -       -      +
     80B  TYR*     1.3    64.9    +      -       -      +
     96B  CYS*     3.9    11.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 80 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  ARG*     4.3    25.1    -      -       +      +
     20B  LEU      3.3     7.2    -      -       -      +
     21B  SER*     4.5    15.3    -      -       -      -
     36B  TRP*     3.3    16.1    +      -       -      -
     69B  THR      4.4     0.2    -      -       -      -
     70B  ILE*     3.5     3.3    -      -       -      +
     71B  SER*     2.8    41.5    +      -       -      +
     73B  ASP*     3.3    35.4    -      -       +      -
     76B  LYS*     2.7    37.8    -      -       +      +
     78B  THR*     3.0    32.3    +      -       -      -
     79B  LEU*     1.3    78.5    -      -       -      +
     81B  LEU*     1.3    61.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 81 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  LEU      3.6     1.4    -      -       -      +
     19B  ARG*     3.2    10.7    -      -       -      -
     20B  LEU*     3.0    35.5    +      -       +      -
     36B  TRP*     3.6    52.3    -      -       +      -
     48B  VAL*     4.4     2.2    -      -       +      -
     49B  SER*     4.6     9.6    -      -       -      +
     68B  PHE*     4.0    30.1    -      -       +      -
     69B  THR      3.4    18.2    -      -       -      +
     70B  ILE*     4.0     7.4    -      -       +      +
     80B  TYR*     1.3    77.1    -      -       -      +
     82B  GLN*     1.4    63.5    +      -       -      +
     83B  MET*     4.0    20.8    -      -       +      +
     94B  TYR*     4.3    10.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 82 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  SER*     3.3    31.9    -      -       -      -
     18B  LEU      3.5    13.4    +      -       -      +
     19B  ARG*     2.4    52.1    +      -       -      +
     67B  ARG      2.9     5.2    -      -       -      +
     68B  PHE*     2.5    36.8    -      -       -      -
     69B  THR*     2.9    30.2    +      -       -      +
     81B  LEU*     1.4    73.8    -      -       -      +
     83B  MET*     1.3    59.6    +      -       -      +
     84B  ASN*     4.0    13.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 83 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16B  GLY      3.0    15.6    -      -       -      +
     17B  SER*     3.1    15.2    -      -       -      -
     18B  LEU*     3.4    18.1    +      -       +      +
     20B  LEU*     3.0    51.4    -      -       +      +
     68B  PHE*     3.0    44.0    -      -       +      -
     81B  LEU*     4.0    14.1    -      -       +      +
     82B  GLN*     1.3    80.8    -      -       -      +
     84B  ASN*     1.3    63.2    +      -       -      +
     86B  LEU*     3.7    13.8    -      -       +      +
     94B  TYR*     4.2    15.5    -      -       -      -
    118B  VAL*     4.5    16.4    -      -       +      -
----------------------------------------------------------
 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