Contacts of the strand formed by residues 549 - 553 (chain A) 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 VAL 549 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    523A  PHE      2.9    14.3    -      -       -      +
    524A  ARG*     3.5     9.6    -      -       -      +
    525A  VAL*     3.2    11.0    +      -       +      +
    526A  THR      4.3     3.8    -      -       -      +
    527A  CYS*     3.8    22.2    -      -       -      -
    528A  LYS      4.8     0.7    -      -       -      +
    529A  GLU*     5.2    12.6    -      -       +      +
    532A  VAL*     5.7     8.5    -      -       +      -
    543A  ASP      4.4     2.5    -      -       -      -
    544A  ILE*     3.9    23.1    -      -       +      -
    548A  GLY*     1.3    77.2    -      -       -      +
    550A  LYS*     1.3    67.8    +      -       -      +
    551A  PHE*     3.3    26.6    -      -       +      -
    995B  GLU*     4.2    17.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 550 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516A  SER*     4.7     4.9    +      -       -      -
    518A  GLN*     5.5     0.8    -      -       -      +
    519A  PHE*     3.4    42.1    -      -       +      -
    522A  TYR*     3.6    48.0    +      -       +      -
    523A  PHE      3.4     4.7    -      -       -      -
    524A  ARG*     4.3    11.0    -      -       +      +
    541A  THR*     4.8     0.5    -      -       -      -
    542A  VAL*     3.6    32.7    +      -       +      +
    543A  ASP*     3.3    23.2    +      -       +      +
    545A  GLN*     4.2    26.9    -      -       +      +
    547A  ASN*     5.4     2.9    -      -       -      +
    548A  GLY      5.7     1.3    -      -       -      -
    549A  VAL*     1.3    77.4    -      -       -      +
    551A  PHE*     1.3    63.6    +      -       -      +
      5E    C      5.2     4.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 551 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    499A  ALA*     6.3     0.9    -      -       +      -
    503A  LEU*     4.3    25.1    -      -       +      -
    511A  ILE*     5.3     1.8    -      -       +      -
    522A  TYR*     4.7     0.8    -      -       -      +
    523A  PHE*     3.1    62.6    +      +       +      +
    525A  VAL*     3.8    28.5    -      -       +      -
    529A  GLU*     6.2     1.8    -      -       +      -
    532A  VAL*     4.5    28.9    -      -       +      -
    539A  PHE*     4.0    24.7    -      +       -      -
    540A  SER      3.4    18.2    -      -       -      +
    541A  THR*     5.4     0.2    -      -       -      -
    542A  VAL*     4.2     3.3    -      -       -      +
    549A  VAL*     3.3    31.6    -      -       +      -
    550A  LYS*     1.3    76.4    -      -       -      +
    552A  THR*     1.3    63.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 552 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    521A  TYR      3.7    23.6    -      -       -      +
    522A  TYR*     4.0    11.0    -      -       +      -
    523A  PHE*     4.2     5.2    -      -       -      -
    539A  PHE*     4.2     4.3    -      -       -      -
    540A  SER*     3.0    34.5    +      -       -      -
    542A  VAL*     4.6    12.6    -      -       +      +
    551A  PHE*     1.3    81.7    -      -       -      +
    553A  ASN*     1.3    63.5    +      -       -      +
    556A  LEU*     3.7    21.3    -      -       +      -
    557A  THR*     3.5    18.3    -      -       -      +
    560A  ASN*     6.0     0.4    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 553 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    495A  THR*     5.6     6.6    +      -       -      +
    499A  ALA*     5.7     4.4    -      -       -      +
    523A  PHE*     4.1    13.7    -      -       -      -
    537A  LYS      5.6     0.2    -      -       -      +
    538A  ASN*     3.4    17.3    -      -       +      +
    539A  PHE*     3.6    25.9    -      -       +      -
    540A  SER*     5.6     1.3    -      -       -      -
    552A  THR*     1.3    75.1    -      -       -      +
    554A  SER*     1.3    63.9    +      -       -      +
    555A  LYS*     3.5    19.9    -      -       -      +
    556A  LEU*     3.0    27.5    +      -       -      +
    557A  THR*     3.2    24.9    +      -       -      +
----------------------------------------------------------
 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