Contacts of the strand formed by residues 416 - 421 (chain A) in PDB entry 4BBZ


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 ALA 416 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    317A  ILE*     3.3    26.9    -      -       +      -
    406A  THR*     4.0    21.1    -      -       +      -
    409A  PHE*     5.3     0.7    -      -       +      -
    410A  SER*     4.2    12.8    -      -       -      -
    414A  ASN      3.5     1.2    +      -       -      +
    415A  ASN*     1.3    76.6    -      -       -      +
    417A  PHE*     1.3    61.8    +      -       -      +
    492A  VAL*     3.3     9.4    -      -       -      +
    493A  PHE*     2.7    40.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 417 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    316A  GLN*     5.1     0.4    -      -       +      -
    317A  ILE      2.9    16.3    +      -       -      +
    318A  LEU*     3.4     4.3    -      -       +      -
    319A  VAL*     2.8    34.4    +      -       -      +
    406A  THR*     5.5     0.7    -      -       -      -
    415A  ASN*     4.0    24.0    -      -       +      -
    416A  ALA*     1.3    77.8    -      -       -      +
    418A  PHE*     1.3    56.9    +      -       -      +
    474A  PHE*     4.4     8.3    -      +       -      -
    478A  GLY      3.9    14.6    -      -       -      -
    479A  ASN*     3.7    13.9    -      -       -      -
    480A  PRO*     3.5    37.9    -      -       +      -
    481A  GLN*     4.0     0.2    -      -       -      -
    490A  TRP*     3.5    39.7    -      +       +      +
    491A  PRO      3.5    14.6    -      -       -      -
    492A  VAL*     3.7    27.1    -      -       +      -
    493A  PHE*     4.5     1.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 418 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    319A  VAL*     3.1    20.9    -      -       +      -
    320A  GLY*     4.0     9.6    -      -       -      -
    321A  VAL*     4.2     8.7    -      -       +      -
    402A  ALA*     3.9    18.4    -      -       +      -
    403A  LEU*     3.8    28.5    -      -       +      -
    406A  THR*     3.5    32.1    -      -       +      -
    417A  PHE*     1.3    72.7    -      -       -      +
    419A  TYR*     1.3    90.4    +      -       -      +
    490A  TRP*     3.0    15.8    +      -       -      +
    491A  PRO      5.1     0.4    +      -       -      -
    493A  PHE*     3.7    28.2    -      +       +      +
    499A  LYS      4.5     1.6    +      -       -      +
    500A  TYR*     3.4    15.5    -      -       +      -
    501A  LEU      2.9    21.8    +      -       -      -
    514A  LEU*     3.9    20.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 419 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222A  LEU      4.8     0.2    -      -       -      -
    223A  GLN*     3.2    37.2    -      -       +      +
    224A  SER*     4.4     0.7    +      -       -      -
    318A  LEU*     3.6    24.7    -      -       +      -
    319A  VAL*     2.9    24.1    +      -       -      -
    320A  GLY*     3.2    30.1    -      -       -      -
    321A  VAL*     3.4    20.9    +      -       -      -
    322A  ASN*     4.5     2.1    +      -       -      -
    418A  PHE*     1.3    96.7    -      -       -      +
    420A  TYR*     1.3    62.5    +      -       -      +
    421A  PHE*     3.6    20.4    -      +       +      -
    441A  GLU*     4.4    10.6    +      -       +      +
    471A  TRP*     3.8    17.3    -      +       -      -
    490A  TRP*     3.6    14.4    -      +       +      -
    500A  TYR*     4.6     0.7    -      -       -      -
    501A  LEU*     3.2    11.2    -      -       +      +
    503A  LEU*     3.9    21.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 420 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321A  VAL*     3.5    17.5    -      -       +      -
    322A  ASN      4.3     0.4    -      -       -      -
    323A  LYS*     3.2    23.8    -      -       +      +
    399A  ILE*     4.8     1.1    -      -       +      -
    419A  TYR*     1.3    74.9    -      -       -      +
    421A  PHE*     1.3    63.5    +      -       -      +
    422A  GLU*     3.4    45.0    +      -       +      +
    500A  TYR*     3.6    32.1    -      +       +      -
    501A  LEU      2.9     7.9    +      -       -      +
    502A  THR*     3.4     4.9    -      -       +      -
    503A  LEU      3.0    22.3    +      -       -      -
    514A  LEU*     3.5    31.4    -      -       +      -
    515A  ARG*     2.9    28.2    +      -       -      -
    701A  SO4      2.7    30.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 421 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    321A  VAL      2.9     9.9    +      -       -      +
    322A  ASN*     3.2    28.8    -      -       -      +
    323A  LYS*     2.9    26.9    +      -       -      +
    419A  TYR*     3.6    13.0    -      +       +      -
    420A  TYR*     1.3    70.9    -      -       -      +
    422A  GLU*     1.3    57.9    +      -       -      +
    423A  HIS*     3.1    33.4    -      -       +      -
    436A  VAL*     3.7    14.3    -      -       +      +
    440A  TYR      3.7     6.5    -      -       -      -
    441A  GLU*     3.6    32.1    -      -       +      -
    444A  PHE*     4.0    18.8    -      +       +      -
    463A  LEU*     4.4    11.4    -      -       +      -
    467A  ILE*     3.9    21.3    -      -       +      -
    503A  LEU*     4.0    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