Contacts of the strand formed by residues 437 - 441 (chain A) in PDB entry 1H7B


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 437 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  SER*     5.8     8.1    -      -       -      -
    393A  GLY*     3.7    22.1    -      -       -      +
    395A  SER      3.6    20.4    +      -       -      +
    396A  SER*     3.4     9.1    -      -       -      -
    397A  VAL*     3.3    20.1    +      -       -      +
    431A  THR*     4.2    10.5    -      -       +      -
    435A  GLY      3.9     1.4    +      -       -      -
    436A  PHE*     1.3    71.8    -      -       -      +
    438A  PHE*     1.3    63.3    +      -       -      +
    439A  SER*     3.6     2.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 438 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    349A  PHE*     4.2     8.7    -      +       -      -
    352A  LEU*     3.7    23.6    -      -       +      -
    353A  MET*     3.7    26.5    -      -       -      -
    356A  ILE*     4.7     0.7    -      -       +      -
    397A  VAL*     3.4    36.1    -      -       +      -
    399A  LEU*     5.7     1.3    -      -       +      -
    427A  LEU*     3.7    27.7    -      -       +      +
    430A  TRP*     3.5    37.7    -      +       +      -
    431A  THR*     3.4    15.4    +      -       -      +
    434A  THR*     3.4    23.3    -      -       -      -
    436A  PHE*     3.1    23.1    +      -       +      -
    437A  ALA*     1.3    72.6    -      -       -      +
    439A  SER*     1.3    61.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 439 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  PHE      4.6     2.0    +      -       -      -
    295A  SER*     6.3     2.9    -      -       -      -
    396A  SER*     4.2    15.3    -      -       -      -
    397A  VAL      2.9    12.1    +      -       -      +
    398A  SER*     3.7     5.2    +      -       -      -
    399A  LEU      3.1    24.8    +      -       -      +
    424A  ASN*     5.4     0.7    -      -       -      -
    427A  LEU*     3.5     9.9    -      -       -      +
    437A  ALA      4.5     1.8    -      -       -      -
    438A  PHE*     1.3    75.0    -      -       -      +
    440A  LEU*     1.3    60.2    +      -       -      +
    441A  TYR*     3.7     0.6    +      -       -      -
    501A  THR*     4.4     8.1    -      -       -      -
    502A  GLY*     3.4    26.6    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 440 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    399A  LEU*     3.7    18.4    -      -       +      +
    401A  TYR*     3.8    20.0    -      -       +      -
    420A  LEU*     3.7    42.2    -      -       +      +
    423A  MET*     3.8    26.5    -      -       +      -
    424A  ASN*     3.6    18.2    +      -       -      +
    427A  LEU*     3.5    11.3    -      -       +      +
    439A  SER*     1.3    72.0    -      -       -      +
    441A  TYR*     1.3    57.6    -      -       -      +
    499A  ILE      3.9    15.3    -      -       -      +
    500A  ALA*     3.5    22.0    -      -       +      -
    501A  THR*     4.6     1.4    +      -       -      +
    502A  GLY*     2.7    29.1    +      -       -      +
    503A  GLY      3.4     2.4    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 441 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    290A  CYS*     5.2     1.9    +      -       -      +
    291A  ARG*     4.0    12.6    +      -       +      +
    292A  SER*     3.7    32.2    +      -       -      -
    314A  VAL*     3.8    40.5    -      -       +      +
    398A  SER*     3.7    24.5    -      -       -      +
    399A  LEU      3.0    10.5    +      -       -      +
    400A  GLY*     3.1    16.9    -      -       -      -
    401A  TYR*     3.3    11.1    -      -       -      -
    439A  SER      4.5     0.2    -      -       -      +
    440A  LEU*     1.3    75.1    -      -       -      +
    442A  SER*     1.3    59.3    +      -       -      +
    443A  THR*     3.0    16.8    +      -       +      -
    444A  PRO*     3.2    38.7    -      -       +      +
    502A  GLY*     3.5    18.8    -      -       -      -
    503A  GLY*     3.8     7.0    -      -       -      -
----------------------------------------------------------
 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