Contacts of the strand formed by residues 195 - 199 (chain A) in PDB entry 2A1I


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 195 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    166A  LEU*     4.0    13.0    -      -       -      +
    167A  ARG      2.8    16.4    +      -       -      -
    168A  VAL*     3.5     9.3    -      -       +      +
    169A  LEU*     2.7    29.2    +      -       -      +
    189A  CYS*     4.9     0.2    -      -       -      -
    194A  CYS*     1.3    72.3    -      -       -      +
    196A  LEU*     1.3    62.3    +      -       -      +
    197A  ILE*     4.0    18.1    +      -       +      -
    212A  TYR*     3.8    22.0    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  LEU*     3.6     2.9    -      -       -      +
    171A  VAL*     4.3    16.6    -      -       +      -
    182A  LEU*     4.5     7.0    -      -       +      +
    185A  LEU*     3.8    14.8    -      -       +      +
    186A  ALA*     3.6    40.6    -      -       +      +
    189A  CYS*     4.1    15.9    -      -       +      -
    194A  CYS      3.6     2.0    +      -       -      +
    195A  THR*     1.3    77.4    -      -       -      +
    197A  ILE*     1.3    76.1    +      -       -      +
    198A  LEU*     3.1    38.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  VAL*     4.0    15.7    -      -       +      -
    169A  LEU      2.9    11.6    +      -       -      +
    170A  LEU*     3.6    13.6    -      -       +      -
    171A  VAL*     2.9    29.6    +      -       -      +
    195A  THR*     4.0     8.3    -      -       +      -
    196A  LEU*     1.3    83.2    -      -       -      +
    198A  LEU*     1.3    64.6    +      -       -      +
    199A  ALA      3.8     0.2    +      -       -      -
    208A  TYR*     3.4    50.7    -      -       +      +
    212A  TYR*     3.8    27.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171A  VAL*     3.6     4.7    -      -       +      +
    173A  VAL*     4.0    18.6    -      -       +      -
    182A  LEU*     4.2    26.9    -      -       +      -
    196A  LEU*     3.1    37.0    -      -       +      +
    197A  ILE*     1.3    75.5    -      -       -      +
    199A  ALA*     1.3    60.1    +      -       -      +
    200A  TRP*     4.1    29.0    +      -       +      +
    204A  GLU*     4.2     1.0    -      -       -      +
    208A  TYR*     3.6    18.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  LEU*     4.1    10.5    -      -       +      -
    171A  VAL      2.8    13.9    +      -       -      +
    172A  GLN*     3.2     7.3    -      -       -      -
    173A  VAL*     2.9    26.0    +      -       -      +
    197A  ILE      3.8     0.6    +      -       -      -
    198A  LEU*     1.3    74.3    -      -       -      +
    200A  TRP*     1.3    63.2    +      -       -      +
    201A  SER      3.4     3.4    -      -       -      +
    204A  GLU*     3.5     7.0    -      -       +      -
    205A  ALA*     3.7    41.1    -      -       +      +
    208A  TYR*     4.2     2.7    -      -       +      -
----------------------------------------------------------
 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