Contacts of the strand formed by residues 506 - 511 (chain A) in PDB entry 2HAZ


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 506 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    499A  VAL*     3.7    23.8    -      -       +      -
    500A  GLU      3.4     9.2    -      -       -      +
    501A  PRO*     3.9     6.5    -      -       +      -
    502A  TYR*     4.5     0.9    -      -       -      +
    505A  THR*     1.3    79.0    -      -       -      +
    507A  GLN*     1.3    66.3    +      -       -      +
    552A  VAL      3.7     0.3    -      -       -      +
    553A  THR*     3.3     5.0    -      -       -      +
    554A  ILE*     2.9    46.9    +      -       +      +
    557A  LEU*     4.1     0.4    -      -       +      -
    584A  PHE*     3.9    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 507 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    498A  GLN      3.8     0.2    -      -       -      +
    499A  VAL*     3.3     3.7    -      -       -      -
    500A  GLU*     2.9    62.9    +      -       +      +
    502A  TYR*     4.1    19.0    -      -       +      +
    505A  THR*     4.8     4.8    +      -       -      -
    506A  ALA*     1.3    75.0    -      -       -      +
    508A  VAL*     1.3    63.3    +      -       -      +
    509A  GLN      3.6     1.8    +      -       -      -
    551A  ILE*     3.3    31.4    -      -       +      +
    552A  VAL      3.7     3.4    -      -       -      -
    553A  THR*     3.1    40.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 508 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496A  ILE*     4.0    38.8    -      -       +      -
    498A  GLN      3.9     2.2    -      -       -      -
    499A  VAL*     4.2    13.2    -      -       +      +
    507A  GLN*     1.3    73.3    -      -       -      +
    509A  GLN*     1.3    61.7    +      -       -      +
    510A  PHE*     3.7     3.3    +      -       -      -
    551A  ILE*     3.1     6.6    -      -       -      +
    552A  VAL*     2.8    50.2    +      -       +      +
    554A  ILE*     4.0    33.9    -      -       +      -
    565A  VAL*     4.3    13.2    -      -       +      -
    567A  LEU*     4.5    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 509 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496A  ILE*     3.5     6.1    -      -       -      +
    497A  ASP*     2.7    41.8    +      -       +      +
    498A  GLN*     2.8    51.2    +      -       -      +
    500A  GLU*     2.8    30.6    +      -       -      +
    507A  GLN      3.6     0.6    +      -       -      -
    508A  VAL*     1.3    70.5    -      -       -      +
    510A  PHE*     1.3    54.3    +      -       -      +
    550A  GLY      3.5     6.3    -      -       -      +
    551A  ILE*     3.9    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 510 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494A  PRO*     4.3     3.4    -      -       +      -
    495A  SER      3.0    13.5    -      -       -      +
    496A  ILE*     4.4     1.8    -      -       +      -
    497A  ASP*     4.2     3.8    -      -       -      +
    508A  VAL*     3.9    10.5    -      -       +      +
    509A  GLN*     1.3    75.3    -      -       -      +
    511A  ASP*     1.3    82.9    +      -       -      +
    512A  GLU*     4.2     7.9    +      -       +      +
    524A  TYR*     3.5    36.6    -      +       -      -
    546A  ALA*     3.6    44.6    -      -       +      -
    547A  SER*     4.2     2.2    -      -       -      -
    550A  GLY*     3.1    32.1    +      -       -      +
    551A  ILE      3.9    11.0    -      -       -      -
    552A  VAL*     4.2     6.1    -      -       +      -
    567A  LEU*     3.4    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 511 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    101A   NA      2.3    30.7    -      -       -      -
    494A  PRO*     3.3     5.4    -      -       -      +
    495A  SER*     2.6    44.4    +      -       -      -
    497A  ASP*     3.1    13.6    -      -       -      +
    510A  PHE*     1.3    82.9    -      -       -      +
    512A  GLU*     1.3    74.9    +      -       -      +
----------------------------------------------------------
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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