Contacts of the strand formed by residues 579 - 584 (chain A) in PDB entry 1GEN


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 LYS 579 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573A  ASN*     3.5     1.8    -      -       -      -
    574A  TRP      2.9    23.2    +      -       -      -
    577A  ASN*     2.9    39.4    +      -       +      +
    578A  LYS*     1.3    79.3    -      -       -      +
    580A  THR*     1.3    60.6    +      -       -      +
    581A  TYR*     3.5     7.2    -      -       +      -
    590A  ARG*     3.6    35.6    -      -       +      +
    591A  TYR      3.6    11.0    -      -       -      +
    592A  ASN*     3.5    26.7    +      -       -      +
    593A  GLU      5.3     1.1    -      -       -      +
    599A  ASP*     2.8    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 580 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    524A  TYR*     3.3    39.0    -      -       +      +
    572A  PHE      3.3     8.7    -      -       -      +
    573A  ASN*     2.7    21.5    +      -       -      +
    578A  LYS      4.1     0.2    +      -       -      -
    579A  LYS*     1.3    71.4    -      -       -      +
    581A  TYR*     1.3    62.1    +      -       -      +
    582A  ILE*     4.1    21.8    -      -       +      -
    589A  TRP      3.6     0.5    -      -       -      +
    590A  ARG*     3.4     4.3    -      -       -      -
    591A  TYR*     2.8    43.1    +      -       +      +
    593A  GLU*     2.7    20.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 581 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    571A  ALA*     3.2     6.2    -      -       -      +
    572A  PHE*     2.7    47.1    +      +       +      +
    574A  TRP*     3.3    41.8    -      +       +      -
    577A  ASN*     2.7    23.9    +      -       -      -
    579A  LYS*     3.5    22.0    -      -       +      -
    580A  THR*     1.3    72.4    -      -       -      +
    582A  ILE*     1.3    62.7    +      -       -      +
    583A  PHE*     3.7    23.0    -      -       +      -
    588A  PHE*     3.7    32.8    -      +       +      -
    589A  TRP      3.3     4.0    -      -       -      +
    590A  ARG*     3.4    33.6    +      -       +      -
    602A  PHE*     5.5     0.4    -      +       -      -
    610A  TRP*     4.0    12.8    -      +       -      -
----------------------------------------------------------
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Residues in contact with ILE 582 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    535A  PHE*     4.2    14.1    -      -       +      -
    559A  LEU*     3.7    29.8    -      -       +      -
    561A  LEU*     4.3    13.9    -      -       +      -
    568A  VAL*     3.7    34.3    -      -       +      -
    570A  ALA      3.8     4.0    -      -       -      +
    571A  ALA*     4.3     3.8    -      -       +      -
    580A  THR*     4.1    19.3    -      -       +      +
    581A  TYR*     1.3    80.4    -      -       -      +
    583A  PHE*     1.3    63.5    +      -       -      +
    588A  PHE*     3.1     5.1    -      -       -      +
    589A  TRP*     2.9    41.7    +      -       +      +
    591A  TYR*     4.4     8.3    -      -       +      -
    598A  MET*     4.3    17.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 583 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    568A  VAL*     3.6     4.7    -      -       -      +
    569A  ASP*     2.8    29.2    +      -       +      -
    570A  ALA*     2.8    29.1    +      -       +      +
    572A  PHE*     3.8    17.5    -      +       -      -
    581A  TYR*     3.7    29.6    -      -       +      -
    582A  ILE*     1.3    75.0    -      -       -      +
    584A  ALA*     1.3    61.5    +      -       -      +
    585A  GLY      5.6     0.2    -      -       -      +
    587A  LYS      3.6     2.5    -      -       -      +
    588A  PHE*     3.6    16.4    -      +       +      -
    606A  ILE*     3.9    15.7    -      -       +      -
    610A  TRP*     3.7    30.3    -      +       -      -
    617A  LEU*     3.8    22.2    -      -       +      +
    620A  VAL*     3.8    20.0    -      -       +      -
    631A  PHE*     3.8    17.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with ALA 584 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    565A  VAL*     4.6     8.3    -      -       +      -
    567A  ARG      3.9    21.1    -      -       -      +
    568A  VAL*     4.2     4.3    -      -       +      -
    569A  ASP*     3.7     7.0    -      -       -      -
    582A  ILE      4.2     0.6    +      -       -      -
    583A  PHE*     1.3    74.4    -      -       -      +
    585A  GLY*     1.3    59.8    +      -       -      +
    586A  ASP*     3.1     1.4    +      -       -      +
    587A  LYS*     2.9    34.7    +      -       -      +
    589A  TRP*     3.7    23.2    -      -       +      -
----------------------------------------------------------
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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