Contacts of the strand formed by residues 177 - 181 (chain C) in PDB entry 3BQM


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 TYR 177 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171C  VAL*     4.5     2.2    -      -       +      -
    172C  GLN      3.4     5.6    -      -       -      +
    173C  PHE*     3.7    11.0    -      -       +      -
    174C  SER      4.8     0.2    -      -       -      -
    175C  THR      3.9    14.1    +      -       -      -
    176C  SER*     1.3    97.8    +      -       -      +
    178C  LYS*     1.3    63.0    +      -       -      +
    179C  THR      4.3     0.2    -      -       -      -
    202C  MET*     4.1     1.1    -      -       -      -
    207C  ASN*     3.4    26.6    +      -       +      +
    210C  GLY*     3.2    29.3    -      -       -      -
    211C  ALA*     3.3    25.1    -      -       +      -
    214C  TYR*     3.7    51.4    +      +       +      -
    244C  ASP*     4.1     0.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 178 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171C  VAL*     3.2     4.2    -      -       -      +
    172C  GLN*     2.9    36.9    +      -       -      +
    177C  TYR*     1.3    74.8    -      -       -      +
    179C  THR*     1.3    71.2    +      -       -      +
    180C  GLU*     3.0    39.4    +      -       -      +
    198C  HIS*     4.0    22.2    +      -       -      +
    199C  VAL*     5.0     0.6    -      -       -      +
    200C  LYS*     5.1     3.8    -      -       -      +
    202C  MET*     3.6    19.5    -      -       +      +
    214C  TYR*     4.5     0.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 179 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170C  ALA      3.7     5.4    -      -       -      +
    171C  VAL*     4.2     7.4    -      -       +      -
    178C  LYS*     1.3    78.2    -      -       -      +
    180C  GLU*     1.3    62.0    +      -       -      +
    181C  PHE*     3.7    27.7    -      -       -      +
    182C  ASP*     3.9    15.7    -      -       +      +
    214C  TYR*     2.6    35.0    +      -       -      -
    218C  GLU      5.1     1.9    +      -       -      -
    219C  VAL*     3.8    13.4    -      -       +      +
    224C  LEU*     5.3     5.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 180 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  PHE*     4.0    14.1    -      -       +      -
    170C  ALA      2.8    14.1    +      -       -      +
    172C  GLN*     3.0    39.6    -      -       -      +
    178C  LYS*     3.0    48.8    +      -       -      +
    179C  THR*     1.3    72.5    -      -       -      +
    181C  PHE*     1.3    62.6    +      -       -      +
    185C  ASP*     5.0     0.2    -      -       -      +
    195C  LEU      4.0     8.3    -      -       -      +
    196C  LEU*     4.3    18.2    -      -       +      -
    198C  HIS*     4.6     0.9    -      -       -      +
    199C  VAL*     3.9    25.4    +      -       +      +
    200C  LYS      4.6     0.5    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 181 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    158C  MET*     3.5    29.8    -      -       +      -
    168C  PHE*     3.5    22.4    -      -       +      -
    169C  ALA*     3.3    10.3    -      -       -      +
    170C  ALA*     2.9    53.1    +      -       +      +
    179C  THR*     3.7     7.4    -      -       -      +
    180C  GLU*     1.3    78.6    -      -       -      +
    182C  ASP*     1.3    70.6    +      -       -      +
    185C  ASP*     3.6    19.1    -      -       +      +
    186C  TYR*     4.1     4.3    -      -       +      -
    195C  LEU*     3.7    49.4    -      -       +      +
    196C  LEU*     3.6    24.7    -      -       +      -
----------------------------------------------------------
 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