Contacts of the strand formed by residues 64 - 67 (chain A) in PDB entry 2BZG


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 ARG 64 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  GLY      5.5     1.3    -      -       -      +
     63A  LEU*     1.3    72.6    -      -       -      +
     65A  VAL*     1.3    60.9    +      -       -      +
     85A  SER*     3.3    21.0    +      -       -      +
     87A  VAL*     3.7    15.6    -      -       -      +
    131A  TYR*     6.4     0.2    -      -       -      -
    143A  ILE*     2.9    31.3    +      -       -      +
    144A  GLY*     3.8     1.2    -      -       -      -
    145A  LYS      2.9    34.6    +      -       -      +
    146A  PHE*     3.6    31.6    -      -       +      +
    147A  ASP*     2.8    40.5    +      -       -      +
    148A  MSE      3.3     6.1    +      -       -      -
   1247A  B3P      3.7    32.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  LEU*     4.3     7.4    -      -       +      -
     64A  ARG*     1.3    77.2    -      -       -      +
     66A  PHE*     1.3    63.2    +      -       -      +
     67A  PHE*     3.8    24.7    -      -       +      -
     79A  PHE*     4.0    31.6    -      -       +      -
     84A  HIS*     4.1    19.5    -      -       +      -
     85A  SER      2.8    11.3    +      -       -      +
     86A  VAL*     3.4     8.3    -      -       +      +
     87A  VAL      2.9    25.6    +      -       -      +
    146A  PHE*     3.6     4.0    -      -       -      -
    148A  MSE      3.3    33.7    -      -       +      +
    150A  TRP      4.7     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  VAL*     1.3    73.0    -      -       -      +
     67A  PHE*     1.3    62.5    +      -       -      +
     68A  PRO*     3.5    18.0    -      -       +      +
     87A  VAL*     3.3    17.9    -      -       +      -
     88A  GLY      4.3     2.2    -      -       -      -
     89A  VAL*     3.8    18.8    -      -       +      -
    135A  ILE*     3.6    13.5    -      -       +      -
    138A  LEU*     3.6    22.4    -      -       +      -
    143A  ILE*     3.8    18.6    -      -       +      -
    146A  PHE*     3.6    36.3    -      +       +      -
    148A  MSE      2.9    10.4    +      -       -      +
    149A  ILE*     3.3    13.0    -      -       +      -
    150A  TRP      2.9    25.6    +      -       -      -
    170A  MSE      3.6    27.6    -      -       +      -
    173A  LEU*     3.7    14.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  VAL*     3.8    13.2    -      -       +      -
     66A  PHE*     1.3    81.0    -      -       -      +
     68A  PRO*     1.3    69.4    -      -       -      +
     70A  CYS*     3.4    17.2    -      -       +      +
     73A  ALA*     4.0    15.3    -      -       +      -
     75A  GLU*     3.7     7.9    -      -       +      -
     76A  MSE      3.4    44.9    -      -       +      -
     79A  PHE*     3.7    32.8    -      +       -      -
     86A  VAL*     3.8    18.4    -      -       +      -
     87A  VAL      2.8    13.0    +      -       -      +
     88A  GLY*     3.3     0.8    -      -       -      -
     89A  VAL      3.2    20.8    +      -       -      -
    150A  TRP*     3.3    37.5    -      +       +      -
   1246A  SAH      6.1     0.9    -      -       -      -
----------------------------------------------------------
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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