Contacts of the strand formed by residues 568 - 572 (chain E) in PDB entry 1XMI


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 568 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    390E  THR*     3.8    10.8    -      -       +      -
    392E  VAL*     3.6    35.0    -      -       +      -
    471E  ILE*     3.6    30.3    -      -       +      -
    484E  HIS*     4.3     8.1    -      -       +      -
    485E  SER      5.6     0.7    -      -       -      +
    487E  ARG      3.2     4.4    +      -       -      +
    488E  ILE*     3.3    19.4    -      -       +      +
    489E  SER      2.9    25.3    +      -       -      +
    566E  ALA*     3.9     1.6    -      -       -      +
    567E  ASP*     1.3    79.3    -      -       +      +
    569E  TYR*     1.3    70.0    +      -       -      +
    570E  LEU*     3.7    17.9    -      -       +      -
    599E  THR*     3.7    22.4    -      -       +      +
    601E  ILE*     4.3     9.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 569 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    489E  SER*     3.5    18.8    -      -       -      +
    516E  ARG*     3.8     6.2    +      -       -      -
    561E  ALA      3.3    16.6    -      -       -      -
    562E  VAL*     3.9     9.0    +      -       -      -
    564E  LYS      2.6    29.3    +      -       -      -
    565E  ASP*     3.6     2.9    -      -       -      -
    566E  ALA*     3.2    32.7    +      -       +      -
    568E  LEU*     1.3    76.4    -      -       -      +
    570E  LEU*     1.3    64.2    +      -       -      +
    571E  LEU*     3.9     7.5    +      -       +      +
    595E  MET*     3.6    31.2    -      -       +      -
    598E  LYS*     3.6    40.8    -      -       +      -
    599E  THR      3.0    12.9    +      -       -      +
    600E  ARG*     3.3     5.3    -      -       +      +
    601E  ILE      2.9    28.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 570 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468E  LEU*     3.6    43.7    -      -       +      +
    471E  ILE*     4.0    13.7    -      -       +      -
    472E  MET*     3.7    21.5    -      -       +      -
    488E  ILE*     3.8    16.2    -      -       +      -
    489E  SER      2.7    11.8    +      -       -      +
    490E  PHE*     3.4    11.2    -      -       +      -
    491E  CYS      2.8    26.5    +      -       -      -
    568E  LEU*     3.7    25.8    -      -       +      -
    569E  TYR*     1.3    72.9    -      -       -      +
    571E  LEU*     1.3    62.6    +      -       -      +
    572E  ASP      4.0     0.7    -      -       -      -
    601E  ILE*     3.7    29.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 571 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    468E  LEU*     4.5     2.6    -      -       -      +
    489E  SER      5.1     0.9    -      -       -      +
    491E  CYS*     3.7    21.5    -      -       +      +
    558E  LEU*     4.4    18.6    -      -       +      -
    561E  ALA*     4.7     7.2    -      -       +      -
    562E  VAL*     5.5     0.2    -      -       +      -
    569E  TYR*     4.5     9.0    -      -       +      +
    570E  LEU*     1.3    83.8    -      -       -      +
    572E  ASP*     1.3    59.4    +      -       -      +
    573E  SER      3.4     3.3    +      -       -      -
    574E  PRO*     4.3     7.2    -      -       +      -
    591E  VAL*     4.4    20.2    -      -       +      -
    595E  MET*     3.9    25.1    -      -       +      -
    600E  ARG*     4.3    17.0    -      -       +      -
    601E  ILE      2.9    13.8    +      -       -      +
    602E  LEU*     3.4    18.5    -      -       +      +
    603E  VAL*     2.9    26.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 572 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10E   MG      4.1     0.2    -      -       -      -
    465E  THR*     2.6    41.6    +      -       -      +
    468E  LEU*     3.7    18.9    -      -       +      +
    490E  PHE*     4.1     8.6    -      -       +      -
    491E  CYS      2.8    17.9    +      -       -      +
    492E  SER      3.5     2.8    -      -       -      +
    493E  GLN*     3.3    43.4    +      -       +      +
    570E  LEU      4.0     0.4    +      -       -      -
    571E  LEU*     1.3    68.1    -      -       -      +
    573E  SER*     1.3    67.7    +      -       -      +
    574E  PRO*     3.3     1.9    -      -       -      +
    603E  VAL*     3.4    23.6    -      -       -      +
----------------------------------------------------------
 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