Contacts of the strand formed by residues 188 - 193 (chain E) in PDB entry 1II4


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 188 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186E  MET      4.8     4.0    -      -       -      +
    187E  PRO*     1.3    76.5    -      -       -      +
    189E  MET*     1.3    64.1    +      -       -      +
    190E  ARG*     5.2     7.2    -      -       -      -
    214E  TRP*     4.6     0.4    -      -       -      -
    232E  VAL      3.6     0.9    +      -       -      +
    233E  VAL*     3.1     9.5    -      -       -      +
    234E  GLU*     2.8    49.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 189 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179E  CYS*     3.4    39.9    -      -       +      +
    188E  THR*     1.3    79.6    -      -       -      +
    190E  ARG*     1.3    75.8    +      -       -      +
    191E  TRP*     3.5    29.3    -      -       +      +
    209E  VAL*     5.7     3.8    -      -       +      -
    211E  ASN*     6.0     2.7    -      -       -      +
    214E  TRP*     3.8    39.2    -      -       +      +
    215E  SER      5.6     0.2    -      -       -      +
    231E  CYS*     3.7    11.2    -      -       +      -
    232E  VAL      3.4     4.3    -      -       -      +
    233E  VAL*     3.6    21.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG 190 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188E  THR*     5.2     8.5    -      -       -      +
    189E  MET*     1.3    81.5    -      -       -      +
    191E  TRP*     1.3    67.4    +      -       -      +
    192E  LEU*     4.6    21.6    -      -       +      +
    231E  CYS*     3.3     4.2    -      -       -      -
    232E  VAL*     2.8    55.7    +      -       +      +
    234E  GLU*     3.2    30.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 191 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    177E  PHE*     3.5    47.3    -      +       +      -
    179E  CYS*     4.0     8.3    -      -       -      -
    189E  MET*     3.5    24.4    -      -       +      -
    190E  ARG*     1.3    80.2    -      -       -      +
    192E  LEU*     1.3    69.5    +      -       -      +
    197E  GLU*     4.4     0.2    -      -       -      -
    198E  PHE*     3.4    27.1    +      -       +      +
    207E  TYR*     5.3     4.7    +      +       +      +
    209E  VAL*     4.4    17.9    -      -       +      +
    214E  TRP      3.9    12.8    -      -       -      -
    215E  SER      4.1     7.5    +      -       -      -
    216E  LEU*     3.4    42.0    -      -       +      +
    229E  TYR*     4.6     4.5    -      -       +      -
    230E  THR      3.1    22.7    -      -       -      -
    231E  CYS*     3.6    26.2    -      -       +      -
    244E  TYR*     4.5     9.2    -      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 192 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190E  ARG*     4.6    22.2    -      -       +      +
    191E  TRP*     1.3    87.9    -      -       -      +
    193E  LYS*     1.3    62.0    +      -       -      +
    194E  ASN      3.9     0.4    -      -       -      -
    195E  GLY*     3.8    22.2    -      -       -      +
    196E  LYS*     3.2    24.5    -      -       -      +
    197E  GLU*     3.9     7.6    -      -       +      +
    198E  PHE*     4.3     2.5    -      -       -      -
    228E  ASN      3.4     0.3    -      -       -      +
    229E  TYR*     3.1     9.9    -      -       -      +
    230E  THR*     2.6    49.4    +      -       +      +
    232E  VAL*     4.1    20.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 193 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192E  LEU*     1.3    73.0    -      -       -      +
    194E  ASN*     1.3    91.6    +      -       -      +
    196E  LYS*     2.8    21.7    +      -       -      +
    197E  GLU      5.0     1.1    -      -       -      +
    198E  PHE*     3.7    39.5    -      -       +      +
    202E  HIS*     3.9    26.7    +      -       +      +
    203E  ARG*     5.5     0.6    -      -       -      +
    224E  SER      3.9    15.9    +      -       -      -
    225E  ASP*     4.8     5.1    +      -       -      +
    226E  LYS      4.4    11.2    -      -       -      -
    228E  ASN      3.2     4.9    -      -       -      +
    229E  TYR*     3.7    30.0    +      -       +      +
----------------------------------------------------------
 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