Contacts of the strand formed by residues 226 - 228 (chain E) in PDB entry 6CU0


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 TRP 226 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101E  LEU*     5.3     0.5    -      -       -      +
    102E  LEU*     4.6    12.3    +      -       +      +
    149E  LEU*     3.8    11.9    -      -       +      -
    150E  ARG      3.3    28.5    -      -       -      -
    151E  ARG*     3.4    24.0    -      -       +      +
    156E  GLU      4.1     4.2    +      -       -      -
    157E  GLY*     3.4    34.0    +      -       -      -
    158E  SER      4.4     0.4    -      -       -      -
    161E  VAL*     6.1     0.2    -      -       +      -
    185E  LEU*     3.7    47.2    -      -       +      +
    186E  PRO*     3.8    37.7    -      -       +      -
    188E  ALA*     5.2     2.9    -      -       +      -
    193E  ARG      4.2     3.1    -      -       -      -
    194E  ASN      3.9     3.6    -      -       -      -
    195E  SER*     3.7    34.3    -      -       -      -
    222E  ALA      4.8     2.5    -      -       -      -
    223E  ARG*     3.0    21.9    +      -       -      +
    224E  HIS      3.3     1.6    -      -       -      +
    225E  ALA*     1.3    84.4    -      -       +      +
    227E  GLN*     1.3    70.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 227 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    100E  VAL*     3.3    28.3    -      -       -      +
    101E  LEU*     3.6    22.2    -      -       +      +
    102E  LEU*     5.2     2.2    -      -       -      +
    149E  LEU*     3.4     9.7    -      -       -      +
    150E  ARG*     2.8    33.9    +      -       +      +
    152E  VAL*     3.7    33.5    -      -       +      +
    224E  HIS      4.9     2.5    +      -       -      +
    226E  TRP*     1.3    79.2    -      -       -      +
    228E  LEU*     1.3    66.7    +      -       -      +
     67H  GLN      5.2     2.9    -      -       -      +
     69H  LYS      3.1    27.3    +      -       -      +
     70H  GLY*     3.9     4.8    -      -       -      -
     71H  VAL      4.2     1.6    -      -       -      +
     72H  PHE*     3.9    12.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 228 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97E  ALA*     5.2     2.0    -      -       +      -
     99E  ASN*     3.3    48.1    -      -       +      +
    100E  VAL*     2.9    21.6    +      -       -      +
    101E  LEU      4.7     2.7    -      -       -      +
    102E  LEU*     5.3     3.9    -      -       +      +
    147E  LEU*     3.3    34.5    -      -       +      -
    148E  GLU      3.8     2.5    -      -       -      -
    149E  LEU*     3.6    12.7    -      -       +      +
    150E  ARG*     5.5     0.2    -      -       -      -
    161E  VAL*     5.2     0.2    -      -       +      -
    216E  LEU*     4.7    26.0    -      -       +      -
    227E  GLN*     1.3    79.0    -      -       -      +
    229E  THR*     1.3    65.8    +      -       -      +
    230E  GLN*     3.5     4.3    +      -       -      +
    233E  THR*     3.6    18.8    -      -       +      +
----------------------------------------------------------
 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