Contacts of the strand formed by residues 585 - 592 (chain A) in PDB entry 2H3W


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 ILE 585 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    413A  THR      3.8     0.3    -      -       -      -
    414A  PHE*     2.9    50.2    +      -       +      +
    417A  PHE*     3.6    20.9    -      -       +      +
    418A  GLY*     3.7    15.9    -      -       -      +
    422A  PRO*     6.4     0.7    -      -       +      -
    433A  ILE*     3.6    29.2    -      -       +      -
    578A  TYR*     4.2     3.6    -      -       +      -
    579A  ASN      3.7    11.7    -      -       -      +
    580A  PRO*     4.1    12.8    -      -       +      -
    584A  HIS*     1.3    82.1    -      -       -      +
    586A  ASN*     1.3    70.8    +      -       -      +
    587A  PHE*     3.4    36.3    +      -       +      -
    611A  LEU*     5.0     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 586 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  ARG*     5.0     9.0    -      -       -      +
    412A  LEU      4.0     2.2    -      -       -      -
    413A  THR*     4.2    17.0    +      -       -      +
    561A  ASP*     2.8    27.3    +      -       -      +
    562A  CYS      3.1    20.0    +      -       -      +
    563A  VAL*     3.6    23.9    -      -       +      +
    578A  TYR*     3.0     8.0    -      -       -      +
    579A  ASN*     2.9    39.9    +      -       +      +
    581A  MET*     4.4     1.4    -      -       -      +
    584A  HIS*     3.4    21.4    -      -       -      -
    585A  ILE*     1.3    72.2    +      -       -      +
    587A  PHE*     1.3    60.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 587 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  ARG*     5.7     0.7    +      -       -      -
    411A  MET*     3.7     8.3    -      -       -      +
    412A  LEU*     2.8    63.3    +      -       +      +
    414A  PHE*     3.9     6.7    -      +       +      -
    433A  ILE*     4.0    19.3    -      -       +      -
    563A  VAL*     4.1     3.9    -      -       -      +
    576A  ILE*     4.5     6.1    -      -       +      -
    577A  CYS      3.5     3.8    -      -       -      -
    578A  TYR*     3.4    32.1    -      +       +      -
    585A  ILE*     3.4    37.7    -      -       +      -
    586A  ASN*     1.3    73.4    -      -       -      +
    588A  SER*     1.3    63.0    +      -       -      +
    589A  VAL*     5.1     2.9    -      -       +      -
    607A  LEU*     3.8    23.8    -      -       +      -
    611A  LEU*     3.8    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 588 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  ILE*     5.9     0.7    -      -       -      -
    410A  MET      3.8     4.3    -      -       -      -
    411A  MET*     3.7    17.5    -      -       -      -
    563A  VAL*     4.3     0.9    -      -       -      -
    564A  GLY      2.7    28.7    +      -       -      -
    565A  PHE*     3.3    21.2    -      -       -      +
    575A  GLY      3.4     2.2    +      -       -      +
    576A  ILE*     3.2     6.6    -      -       -      +
    577A  CYS*     2.8    33.5    +      -       -      +
    587A  PHE*     1.3    76.0    -      -       -      +
    589A  VAL*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 589 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    409A  ILE*     3.4     3.3    -      -       -      +
    410A  MET*     2.8    45.0    +      -       +      +
    411A  MET*     5.0     0.2    -      -       -      -
    412A  LEU*     5.7     0.4    -      -       +      -
    574A  TYR*     3.9    23.8    -      -       +      -
    575A  GLY      3.5     2.5    -      -       -      -
    576A  ILE*     4.1    24.0    -      -       +      -
    587A  PHE*     5.1     4.9    -      -       +      -
    588A  SER*     1.3    81.1    -      -       -      +
    590A  SER*     1.3    63.0    +      -       -      +
    600A  ALA*     3.5    27.0    -      -       -      +
    603A  MET*     4.1     7.6    -      -       +      -
    604A  ALA*     4.1    22.2    -      -       +      -
    607A  LEU*     5.0     7.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 590 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  LEU*     4.3     9.0    -      -       -      -
    408A  ASP      3.2     7.0    -      -       -      -
    409A  ILE*     4.5     7.4    -      -       -      +
    565A  PHE*     6.2     2.2    -      -       -      -
    566A  PHE      2.7    29.3    +      -       -      -
    567A  GLY*     4.1     2.9    -      -       -      -
    568A  PRO*     3.2    12.6    -      -       -      +
    574A  TYR*     3.2    13.2    -      -       -      -
    575A  GLY*     2.9    38.1    +      -       -      -
    589A  VAL*     1.3    75.2    -      -       -      +
    591A  ALA*     1.3    64.7    +      -       -      +
    600A  ALA*     4.6     0.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 591 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  LEU*     3.7     6.9    -      -       -      +
    408A  ASP*     2.7    50.1    +      -       +      +
    568A  PRO*     3.5    10.3    -      -       -      -
    573A  GLY      3.9     1.8    -      -       -      +
    574A  TYR*     3.9    20.0    -      -       +      -
    590A  SER*     1.3    78.3    -      -       -      +
    592A  TYR*     1.3    62.5    +      -       -      +
    598A  THR*     3.8    17.0    -      -       -      +
    599A  ASN      4.6     0.2    -      -       -      +
    600A  ALA      4.0     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 592 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116A  ILE*     4.7     1.3    -      -       +      -
    117A  TYR*     3.1    39.8    -      +       -      -
    403A  MET      5.9     1.3    -      -       -      -
    406A  ASP*     3.2    31.9    -      -       +      +
    407A  LEU*     4.3    12.3    -      -       +      -
    408A  ASP*     4.8     0.7    -      -       -      -
    567A  GLY*     3.8     3.3    -      -       -      -
    568A  PRO*     2.9    53.5    +      -       +      +
    569A  VAL      5.4     0.2    -      -       -      -
    570A  VAL      3.5    22.0    -      -       -      -
    571A  PRO*     3.6    21.7    +      -       +      +
    573A  GLY      4.6     1.6    +      -       -      -
    591A  ALA*     1.3    79.5    -      -       -      +
    593A  ASN*     1.3    63.9    +      -       -      +
    594A  SER*     3.1     9.8    +      -       -      +
    595A  CYS*     3.2    11.1    +      -       -      +
    598A  THR*     3.3    18.2    +      -       -      +
----------------------------------------------------------
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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