Contacts of the strand formed by residues 589 - 596 (chain A) in PDB entry 4DAY


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 CYS 589 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  LYS*     3.2    31.9    -      -       -      -
    512A  ALA      3.4    14.8    -      -       -      +
    513A  PHE*     4.1    12.8    -      -       +      -
    587A  ASP      3.6     3.6    +      -       -      -
    588A  LEU*     1.3    79.3    -      -       -      +
    590A  CYS*     1.3    67.4    +      -       -      +
    610A  ASP*     4.8     1.9    -      -       -      +
     59B  TRP*     4.5     9.0    -      -       -      -
     61B  GLN*     5.2     0.9    -      -       -      -
    103B  MET*     5.1     3.6    -      -       -      -
    123B  THR*     4.1     4.9    -      -       +      -
    125B  LEU*     3.8    28.6    -      -       +      +
    131B  HIS*     3.7    17.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 590 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    511A  LYS*     3.8    14.1    -      -       -      +
    512A  ALA      3.0    27.6    +      -       -      +
    588A  LEU*     4.1    16.8    -      -       -      -
    589A  CYS*     1.3    79.9    -      -       -      +
    591A  LEU*     1.3    75.6    +      -       -      +
    592A  MET*     3.5     4.3    +      -       -      +
    608A  LEU*     3.8    27.8    -      -       -      -
    609A  GLN      3.2    15.3    -      -       -      +
    610A  ASP*     4.2    14.8    -      -       -      +
    611A  VAL*     4.1     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 591 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    490A  PRO*     4.1     1.8    -      -       +      +
    491A  PHE*     3.8    25.8    -      -       +      -
    509A  LYS*     3.8    26.7    -      -       +      +
    510A  VAL      3.0     9.2    -      -       -      +
    511A  LYS*     3.7    16.8    -      -       +      -
    590A  CYS*     1.3    75.6    -      -       -      +
    592A  MET*     1.3    59.4    +      -       -      +
    593A  THR      4.1     0.4    -      -       -      -
    608A  LEU*     3.3     4.9    -      -       -      -
    609A  GLN*     2.8    49.1    +      -       +      +
    611A  VAL*     3.6    25.3    -      -       +      +
    615A  HIS*     3.3    42.4    -      -       +      +
    134B  MET*     6.4     0.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 592 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    508A  VAL      3.4     0.2    -      -       -      +
    509A  LYS*     3.4     4.9    -      -       -      -
    510A  VAL*     2.7    30.4    +      -       +      +
    512A  ALA*     3.6    40.8    -      -       +      +
    513A  PHE*     4.5     3.1    -      -       -      +
    514A  ILE*     4.8     0.2    -      -       +      -
    534A  VAL*     4.6    18.2    -      -       +      -
    545A  PHE*     5.7     2.7    -      -       +      -
    588A  LEU*     3.7    30.1    -      -       +      -
    590A  CYS*     3.9     4.9    -      -       -      +
    591A  LEU*     1.3    74.0    -      -       -      +
    593A  THR*     1.3    63.8    +      -       -      +
    594A  ILE*     3.0    25.2    +      -       +      +
    605A  VAL*     4.4    18.6    -      -       +      -
    607A  ALA      3.6     6.1    -      -       -      +
    608A  LEU*     3.3    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 593 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    507A  THR*     4.1    20.4    -      -       +      -
    508A  VAL      3.3     5.6    -      -       -      +
    509A  LYS*     3.6    18.9    -      -       -      +
    591A  LEU      4.1     1.6    -      -       -      -
    592A  MET*     1.3    69.6    -      -       -      +
    594A  ILE*     1.3    56.4    +      -       -      +
    605A  VAL*     3.7     2.9    -      -       -      +
    606A  LEU*     2.8    54.6    +      -       +      -
    607A  ALA*     3.2    30.9    +      -       +      +
    609A  GLN*     5.0     4.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 594 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494A  LEU*     5.2     4.5    -      -       +      -
    506A  THR      3.7     0.7    -      -       -      +
    507A  THR*     3.6     4.5    -      -       -      +
    508A  VAL*     3.0    44.9    +      -       +      +
    510A  VAL*     3.5    28.0    -      -       +      -
    534A  VAL*     4.7     6.3    -      -       +      -
    541A  LEU*     4.1    20.4    -      -       +      -
    543A  VAL*     4.5     6.5    -      -       +      -
    592A  MET*     3.0    22.6    +      -       +      +
    593A  THR*     1.3    77.7    -      -       -      +
    595A  SER*     1.3    63.5    +      -       -      +
    596A  PHE*     4.2     4.0    -      -       +      +
    603A  ALA*     3.6    25.4    -      -       +      -
    604A  MET      4.1     3.1    -      -       -      +
    605A  VAL*     4.1    12.6    -      -       +      -
    606A  LEU*     4.6     3.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 595 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    505A  VAL*     3.9    21.0    -      -       -      +
    506A  THR      3.5     5.0    +      -       -      -
    507A  THR*     4.7     4.6    +      -       -      +
    594A  ILE*     1.3    70.4    -      -       -      +
    596A  PHE*     1.3    61.1    +      -       -      +
    597A  ASN      3.6     1.0    +      -       -      -
    603A  ALA*     3.4     5.8    -      -       -      -
    604A  MET*     3.1    38.0    +      -       -      +
    606A  LEU*     3.5    28.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 596 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494A  LEU*     5.8     1.8    -      -       +      -
    497A  LEU*     4.1    26.5    -      -       +      -
    498A  MET*     4.7    19.5    -      -       +      -
    502A  PRO*     4.4    17.7    -      -       +      -
    505A  VAL*     3.5     7.9    -      -       -      +
    506A  THR*     3.0    34.8    +      -       -      +
    508A  VAL*     5.6     0.2    -      -       +      -
    541A  LEU*     3.8    28.7    -      -       +      -
    594A  ILE*     3.8     5.8    +      -       +      +
    595A  SER*     1.3    71.7    -      -       -      +
    597A  ASN*     1.3    60.3    +      -       -      +
    598A  PRO*     3.2    39.5    -      -       +      +
    601A  SER*     3.7    24.7    -      -       -      -
    603A  ALA*     3.9    12.1    -      -       +      -
----------------------------------------------------------
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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