Contacts of the strand formed by residues 287 - 293 (chain F) 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 HIS 287 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  ALA*     3.6    16.2    -      -       +      -
     67B  GLU      3.2    12.2    +      -       -      -
     68B  GLU*     3.2    35.5    -      -       +      -
     69B  ARG*     3.7    17.6    +      -       +      +
    286F  PRO*     1.3    73.8    -      -       -      +
    288F  ILE*     1.3    73.2    +      -       -      +
    289F  GLN*     4.1    22.8    +      -       +      -
    314F  ALA*     4.3    13.6    -      -       +      +
    315F  ALA*     3.1    22.6    +      -       +      -
    343F  LEU*     3.4     4.9    -      -       -      +
    344F  ALA*     3.3     2.9    -      -       -      -
    345F  GLY*     2.8    36.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 288 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26B  PHE*     3.8    33.4    -      -       +      -
    278F  CYS*     5.4     0.4    -      -       -      -
    280F  VAL*     4.0    20.4    -      -       +      -
    286F  PRO*     4.0     5.6    +      -       +      -
    287F  HIS*     1.3    80.4    -      -       -      +
    289F  GLN*     1.3    67.1    +      -       -      +
    290F  TRP*     4.8     2.2    -      -       -      +
    315F  ALA*     2.8    35.0    +      -       +      +
    321F  ASP*     4.9     2.2    -      -       -      +
    324F  ILE*     3.7    39.0    -      -       +      +
    325F  GLU*     4.7     7.0    -      -       +      -
    342F  CYS*     3.9    24.9    -      -       -      -
    343F  LEU      3.3     2.9    -      -       -      +
    344F  ALA*     4.0    17.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 289 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    287F  HIS*     4.1    19.5    +      -       +      +
    288F  ILE*     1.3    78.8    -      -       -      +
    290F  TRP*     1.3    65.5    +      -       -      +
    291F  ILE*     3.8    16.8    -      -       +      +
    311F  VAL*     3.7    25.9    -      -       +      +
    313F  LYS      3.0    14.6    -      -       -      +
    314F  ALA*     3.9    12.2    -      -       +      +
    324F  ILE*     5.0     0.2    -      -       -      -
    341F  THR      3.8     0.2    -      -       -      +
    342F  CYS*     3.8     1.7    -      -       -      -
    343F  LEU*     3.0    59.5    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 290 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    263F  PRO*     3.7    30.1    -      -       +      -
    276F  PHE*     3.4    42.8    -      +       +      -
    278F  CYS*     3.5    28.7    -      -       +      -
    288F  ILE*     4.8     3.3    -      -       +      +
    289F  GLN*     1.3    77.2    -      -       -      +
    291F  ILE*     1.3    61.8    +      -       -      +
    311F  VAL*     3.6     2.6    -      -       -      +
    312F  LEU*     2.9    28.6    +      -       +      -
    313F  LYS*     2.7    34.4    +      -       +      +
    324F  ILE*     2.9    29.6    +      -       +      -
    325F  GLU*     3.6     5.7    -      -       -      +
    326F  VAL      4.4     0.2    -      -       -      -
    327F  LEU*     3.7    40.1    -      -       +      +
    340F  TYR*     4.9     2.2    -      -       +      -
    341F  THR      3.4    24.7    -      -       -      -
    342F  CYS*     3.7    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 291 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    289F  GLN*     3.8    31.6    -      -       +      +
    290F  TRP*     1.3    81.4    -      -       -      +
    292F  LYS*     1.3    66.1    +      -       -      +
    293F  HIS*     4.4     4.4    +      -       +      +
    309F  LEU*     3.6    36.8    -      -       +      -
    310F  LYS      3.4    11.4    -      -       -      +
    311F  VAL*     4.7     6.1    -      -       +      +
    312F  LEU*     3.5     3.1    -      -       -      -
    339F  GLU      3.9     0.5    -      -       -      +
    340F  TYR*     3.5     3.8    -      -       -      +
    341F  THR*     2.7    52.9    +      -       +      +
    343F  LEU*     4.2    24.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 292 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291F  ILE*     1.3    74.0    -      -       -      +
    293F  HIS*     1.3    63.8    +      -       -      +
    294F  VAL*     3.6    12.6    +      -       +      +
    309F  LEU*     3.6     2.1    -      -       -      -
    310F  LYS*     2.9    30.2    +      -       +      +
    312F  LEU*     3.0    31.8    -      -       +      +
    339F  GLU      3.6     6.5    -      -       -      +
    340F  TYR*     4.5    14.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with HIS 293 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    291F  ILE*     4.4     5.6    +      -       +      -
    292F  LYS*     1.3    75.7    -      -       -      +
    294F  VAL*     1.3    63.0    +      -       -      +
    307F  PRO*     5.6     6.5    -      -       +      -
    308F  TYR      3.5     7.0    -      -       -      +
    309F  LEU*     4.7    16.0    -      -       +      +
    338F  GLY*     5.4     3.5    -      -       -      -
    339F  GLU*     2.8    69.4    +      -       +      +
    341F  THR*     3.0    33.0    -      -       +      -
    354F  SER*     4.4     1.7    +      -       -      -
----------------------------------------------------------
 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