Contacts of the strand formed by residues 88 - 92 (chain A) in PDB entry 1F6A


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 88 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  PHE*     4.1     2.0    -      -       -      -
     86A  ASP*     3.5    13.6    +      -       -      +
     87A  TRP*     1.3    90.1    -      -       -      +
     89A  LEU*     1.3    62.9    +      -       -      +
    107A  CYS*     3.8    22.4    -      -       -      -
    108A  HIS      3.7     3.4    -      -       -      +
    109A  GLY*     3.7    11.4    -      -       -      +
    115A  VAL*     3.4    30.1    -      -       +      -
    151A  CYS      4.7     0.7    -      -       -      +
    152A  THR*     4.1     2.5    -      -       -      -
    153A  GLY*     3.7    32.1    -      -       -      +
    155A  VAL*     4.2     3.8    -      -       +      -
    160A  TYR*     3.9    22.2    -      -       +      +
    161A  GLU      4.6     2.4    +      -       -      -
    162A  SER*     3.6    30.8    -      -       -      +
    163A  GLU      4.4     2.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ARG*     3.3    34.5    -      -       +      +
     16A  ILE*     3.8     9.4    -      -       -      -
     17A  PHE*     3.3    24.7    -      -       +      +
     84A  PHE*     3.3    52.9    -      -       +      -
     86A  ASP*     6.1     1.3    -      -       +      -
     88A  LEU*     1.3    73.8    -      -       -      +
     90A  LEU*     1.3    66.6    +      -       -      +
     91A  GLN*     3.4    22.7    -      -       +      +
    106A  ARG      3.5     0.5    -      -       -      +
    107A  CYS*     3.8     1.2    -      -       -      -
    108A  HIS*     2.9    35.5    +      -       +      +
    151A  CYS*     4.8     0.7    -      -       -      -
    162A  SER*     4.3     2.0    -      -       -      -
    163A  GLU      5.8     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  ARG*     3.0    27.9    +      -       -      +
     89A  LEU*     1.3    72.8    -      -       -      +
     91A  GLN*     1.3    63.7    +      -       -      +
    105A  LEU*     4.6    11.2    -      -       +      -
    106A  ARG      3.6     9.2    -      -       -      +
    120A  TYR*     3.7    35.4    -      -       +      -
    149A  TYR*     3.9    29.4    -      -       +      +
    150A  TYR*     4.0     2.5    -      -       -      +
    151A  CYS*     4.0    13.5    -      -       +      +
    162A  SER*     3.9    18.2    -      -       -      +
    163A  GLU      4.6     4.9    +      -       -      +
    165A  LEU*     3.5    39.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  TRP*     3.4    40.7    -      -       +      +
     15A  ARG*     3.0    32.6    +      -       -      +
     16A  ILE*     3.6    12.1    -      -       -      +
     20A  GLU*     4.0     7.5    +      -       -      -
     89A  LEU*     3.4    23.6    -      -       +      +
     90A  LEU*     1.3    76.8    -      -       -      +
     92A  ALA*     1.3    62.7    +      -       -      +
    104A  PHE      3.6     0.7    -      -       -      +
    105A  LEU*     3.5     5.7    -      -       -      +
    106A  ARG*     3.0    61.2    +      -       +      +
    108A  HIS*     3.7    11.8    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  TRP*     3.5    19.7    -      -       -      -
     14A  ASN*     4.3    10.6    +      -       -      -
     15A  ARG*     4.8     4.7    -      -       -      +
     90A  LEU      4.2     0.8    +      -       -      -
     91A  GLN*     1.3    75.5    -      -       -      +
     93A  SER*     1.3    65.4    +      -       -      +
     94A  ALA*     3.3    18.0    +      -       -      +
     95A  GLU*     5.0     3.7    -      -       +      +
    103A  LEU*     5.0     1.3    -      -       +      -
    104A  PHE      3.2     8.1    -      -       -      +
    105A  LEU*     4.2    11.9    -      -       +      -
    165A  LEU*     4.0    22.7    -      -       +      +
    167A  ILE*     4.5     6.3    -      -       +      -
----------------------------------------------------------
 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