Contacts of the strand formed by residues 33 - 38 (chain E) in PDB entry 3KYM


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 LEU 33 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4E  MET*     4.1    20.2    -      -       +      -
     23E  CYS*     4.4     0.2    -      -       -      -
     29E  VAL*     4.9     0.4    -      -       +      -
     31E  SER      3.2     4.9    +      -       -      -
     32E  TYR*     1.3    76.4    -      -       -      +
     34E  ALA*     1.3    62.2    +      -       -      +
     35E  TRP*     3.3    36.1    -      -       +      +
     49E  TYR*     3.5     0.9    -      -       -      -
     50E  ASP      3.2     8.1    +      -       -      -
     51E  ALA*     2.6    37.4    +      -       +      +
     71E  PHE*     3.7    50.9    -      -       +      -
     88E  CYS*     4.3     5.2    -      -       +      -
     89E  GLN      3.3    29.4    -      -       -      +
     90E  GLN*     4.1     2.2    -      -       +      +
     91E  TYR*     3.8     3.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 34 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33E  LEU*     1.3    77.9    -      -       -      +
     35E  TRP*     1.3    66.1    +      -       -      +
     36E  TYR*     4.0     8.7    -      -       +      +
     46E  LEU*     4.8     0.7    -      -       +      -
     48E  ILE      3.4    10.1    -      -       -      +
     49E  TYR*     4.3     4.5    -      -       +      +
     88E  CYS*     3.2     9.7    -      -       -      +
     89E  GLN*     2.8    59.0    +      -       -      +
     91E  TYR*     3.8    10.1    -      -       +      -
    105F  TYR*     4.2     6.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 35 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6E  GLN*     4.2    18.8    -      -       -      -
     21E  LEU*     4.0    20.9    -      -       +      -
     22E  SER      4.4     1.6    -      -       -      -
     23E  CYS*     3.5    32.8    -      -       +      -
     33E  LEU*     3.3    19.8    -      -       +      +
     34E  ALA*     1.3    78.4    -      -       -      +
     36E  TYR*     1.3    69.3    +      -       -      +
     46E  LEU*     3.8     1.7    -      -       -      +
     47E  LEU*     2.9    35.6    +      -       +      -
     48E  ILE*     2.7    48.8    +      -       +      +
     51E  ALA      4.5     5.3    +      -       -      -
     64E  GLY*     5.0     0.4    -      -       -      -
     65E  SER      5.5     0.2    +      -       -      -
     71E  PHE*     4.2     7.7    -      -       +      +
     72E  THR      4.0    10.1    +      -       -      -
     73E  LEU*     3.7    49.4    -      -       +      +
     86E  TYR*     4.9     4.9    -      -       +      -
     87E  TYR      3.3    16.8    -      -       -      -
     88E  CYS*     4.2     4.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 36 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     34E  ALA*     4.0     8.3    -      -       +      -
     35E  TRP*     1.3    76.9    -      -       -      +
     37E  GLN*     1.3    62.8    +      -       -      +
     44E  PRO*     4.9     5.2    -      -       +      -
     45E  ARG      3.3     7.6    -      -       -      +
     46E  LEU*     3.7    27.9    -      -       +      +
     47E  LEU*     4.3     3.6    -      -       -      -
     85E  VAL      3.9     0.2    -      -       -      +
     86E  TYR*     3.1    10.4    -      -       -      +
     87E  TYR*     2.8    51.7    +      -       +      +
     89E  GLN*     2.8    38.9    +      -       +      -
     98E  PHE*     4.2    14.1    -      +       -      -
     45F  LEU*     6.2     1.3    -      -       +      -
    105F  TYR*     3.4     4.2    -      -       -      +
    106F  PHE*     2.8    49.2    +      +       -      +
    109F  TRP*     3.5    30.1    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 37 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36E  TYR*     1.3    73.6    -      -       -      +
     38E  GLN*     1.3    63.5    +      -       -      +
     39E  LYS*     3.6    30.4    +      -       -      +
     43E  ALA      4.3     1.2    -      -       -      +
     44E  PRO*     3.4     2.3    -      -       -      +
     45E  ARG*     2.5    72.3    +      -       +      +
     47E  LEU*     3.4    23.1    -      -       +      +
     62E  PHE*     4.6     5.1    -      -       -      -
     81E  GLU      4.2     3.6    +      -       -      -
     82E  ASP*     4.1     9.1    +      -       -      +
     84E  ALA*     4.1     4.4    -      -       +      +
     85E  VAL      3.5     4.0    -      -       -      -
     86E  TYR*     2.9    36.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 38 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37E  GLN*     1.3    75.7    -      -       -      +
     39E  LYS*     1.3    67.4    -      -       -      +
     40E  PRO*     4.0     1.7    -      -       +      +
     42E  GLN      4.4     5.0    +      -       -      +
     43E  ALA      4.9     1.1    -      -       -      -
     44E  PRO*     3.5    30.4    -      -       +      +
     84E  ALA*     3.7     3.3    -      -       -      +
     85E  VAL*     2.7    40.1    +      -       +      +
     87E  TYR*     2.8    43.7    +      -       +      -
     39F  GLN*     3.6    12.2    +      -       -      +
     45F  LEU*     5.0     1.4    -      -       -      +
     95F  TYR*     3.4    24.2    +      -       -      -
----------------------------------------------------------
 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