Contacts of the strand formed by residues 162 - 165 (chain E) in PDB entry 1W4R


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 TYR 162 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27E  PRO*     3.5     7.7    -      -       -      +
    130E  ARG*     3.4    29.8    -      -       +      -
    161E  ALA*     1.3   103.4    -      -       +      +
    163E  THR*     1.3    65.3    +      -       -      +
    183E  SER*     3.4     6.6    -      -       -      -
    184E  VAL*     2.9    44.2    +      -       +      +
    185E  CYS*     3.8     9.6    -      -       -      -
    186E  ARG*     3.2    29.9    +      -       +      -
    189E  TYR*     4.2    11.4    -      -       +      -
    141H  PRO      3.3    26.9    -      -       -      -
    142H  LEU      2.7    26.8    +      -       -      -
    143H  ALA      4.0     2.2    -      -       -      -
    144H  GLU*     3.0    25.9    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 163 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27E  PRO*     3.5     4.3    -      -       -      +
     28E  MET*     3.0    59.7    +      -       +      +
    124E  LEU*     4.4     1.7    -      -       -      +
    126E  GLY      5.0     2.2    +      -       -      -
    127E  THR      4.2     4.3    +      -       -      +
    128E  PHE*     3.5    24.3    -      -       -      +
    130E  ARG*     5.3     0.8    -      -       -      +
    162E  TYR*     1.3    75.1    -      -       -      +
    164E  LYS*     1.3    61.4    +      -       -      +
    181E  TYR*     3.7    19.7    -      -       +      -
    182E  HIS      3.5     9.2    -      -       -      +
    184E  VAL*     4.4     2.0    -      -       -      -
    189E  TYR*     3.7     5.9    -      -       -      -
    300E  TTP      3.7    16.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 164 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  PHE      4.9     0.2    -      -       -      -
    155E  GLU*     2.9    36.9    +      -       -      -
    163E  THR*     1.3    72.6    -      -       -      +
    165E  ARG*     1.3    75.3    +      -       -      +
    166E  LEU*     4.6     8.2    -      -       +      +
    181E  TYR*     3.2     8.1    -      -       -      -
    182E  HIS*     2.9    35.8    +      -       +      +
    184E  VAL*     3.9    17.5    -      -       +      +
    188E  CYS      2.8    24.9    +      -       -      +
    189E  TYR*     4.0    27.1    +      -       +      +
    191E  LYS*     4.8    13.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 165 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128E  PHE*     3.4    50.0    +      -       +      +
    164E  LYS*     1.3    83.1    -      -       -      +
    166E  LEU*     1.3    65.4    +      -       -      +
    167E  GLY      3.8    19.2    -      -       -      +
    169E  GLU*     2.8    53.1    +      -       -      +
    171E  GLU      2.6    21.0    +      -       -      -
    172E  VAL      2.7    29.3    +      -       -      -
    174E  VAL*     3.5    16.0    -      -       -      +
    180E  LYS*     3.7    11.4    -      -       +      +
    181E  TYR*     3.0    28.2    +      -       +      -
    300E  TTP      3.7     3.2    +      -       -      -
----------------------------------------------------------
 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