Contacts of the strand formed by residues 617 - 621 (chain B) in PDB entry 2O8C


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 617 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    477B  GLY*     3.7    28.7    -      -       -      +
    479B  LYS*     4.2    14.4    -      -       +      +
    518B  THR*     3.7    28.5    -      -       +      -
    519B  LYS*     4.2    25.4    -      -       +      -
    592B  VAL      3.0    18.2    +      -       -      +
    593B  GLN*     3.4    11.5    -      -       +      +
    594B  VAL*     2.8    29.6    +      -       -      +
    615B  CYS      4.7     3.6    -      -       -      +
    616B  SER*     1.3    84.7    -      -       -      +
    618B  GLN*     1.3    64.9    +      -       -      +
    619B  GLU*     4.5     5.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 618 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    594B  VAL*     3.7     7.0    -      -       +      +
    596B  PHE*     4.0    14.6    -      -       +      -
    609B  LEU*     2.7    50.8    +      -       +      +
    610B  LYS*     3.4    30.3    -      -       -      +
    613B  LEU*     3.5     9.3    +      -       -      +
    614B  SER*     4.4     5.4    -      -       -      +
    616B  SER*     3.5    16.0    -      -       -      +
    617B  LEU*     1.3    74.5    -      -       -      +
    619B  GLU*     1.3    70.1    +      -       -      +
    620B  GLY      4.3     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 619 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    422B  ASP*     4.5     4.9    -      -       -      +
    479B  LYS*     3.5    29.4    +      -       -      +
    593B  GLN*     3.0    35.5    +      -       +      +
    594B  VAL      2.9    14.6    +      -       -      +
    595B  LEU*     3.5    22.2    -      -       +      -
    596B  PHE*     3.1    31.0    +      -       -      +
    617B  LEU*     4.5     5.7    -      -       -      +
    618B  GLN*     1.3    82.9    -      -       -      +
    620B  GLY*     1.3    62.1    +      -       -      +
    621B  LEU*     3.7     6.3    +      -       +      +
    690B  TYR*     3.9    13.0    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 620 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    392B  ASP*     5.2     5.2    -      -       -      +
    596B  PHE*     3.7    25.3    -      -       -      -
    598B  LYS*     3.6    19.4    -      -       -      +
    618B  GLN      4.3     0.4    -      -       -      -
    619B  GLU*     1.3    70.9    +      -       -      +
    621B  LEU*     1.3    65.6    +      -       -      +
    622B  ILE*     4.1     1.0    +      -       -      +
    626B  GLN*     4.3     2.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 621 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    595B  LEU*     4.5    14.8    -      -       +      -
    596B  PHE      2.8    17.8    +      -       -      +
    597B  GLU*     3.5     4.2    -      -       -      -
    598B  LYS*     3.0    25.5    +      -       -      -
    619B  GLU*     4.5     9.0    -      -       +      +
    620B  GLY*     1.3    79.2    -      -       -      +
    622B  ILE*     1.3    64.2    +      -       -      +
    623B  PRO      3.3     0.3    -      -       -      -
    626B  GLN*     3.5    14.1    -      -       +      +
    627B  PHE*     3.8    31.4    -      -       +      +
    686B  GLY*     3.6    27.4    -      -       -      +
    689B  PHE*     3.9    26.2    -      -       +      -
    690B  TYR*     4.6    13.7    -      -       +      -
    693B  LYS*     6.4     0.2    -      -       +      -
----------------------------------------------------------
 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