Contacts of the strand formed by residues 600 - 606 (chain A) in PDB entry 6PAI


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 HIS 600 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    546A  LEU*     3.8    19.8    -      -       +      +
    547A  GLY*     4.2    14.6    -      -       -      -
    594A  THR      3.4     3.8    -      -       -      -
    595A  THR*     3.0    34.8    +      -       +      -
    598A  SER*     4.4    10.1    +      -       -      -
    599A  SER*     1.3    80.1    +      -       -      +
    601A  TYR*     1.3    64.2    +      -       -      +
    615A  GLY*     3.6     4.7    -      -       -      -
    616A  LEU*     2.9    41.9    +      -       +      +
    617A  ASN*     5.6     0.2    -      -       -      -
    618A  ILE*     3.5    38.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 601 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    592A  LEU      4.0     0.3    -      -       -      +
    593A  MET*     3.4     6.1    -      -       -      +
    594A  THR*     2.8    34.8    +      -       -      +
    596A  PHE*     3.7    24.4    -      +       +      +
    599A  SER*     3.5    41.4    +      -       -      -
    600A  HIS*     1.3    75.1    -      -       -      +
    602A  LEU*     1.3    60.9    +      -       -      +
    603A  LEU*     3.7    18.3    -      -       +      +
    613A  TYR*     4.4    11.0    -      +       -      -
    614A  PHE      3.0    23.3    -      -       -      +
    615A  GLY*     4.8     4.9    -      -       -      -
    616A  LEU*     4.0     7.5    -      -       -      +
    661A  SER*     5.3     1.0    +      -       -      -
    664A  HIS*     3.9    20.1    +      -       -      -
    665A  LYS*     4.7     1.0    -      -       -      -
    666A  LEU*     3.1    39.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 602 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    557A  ALA*     3.9    18.6    -      -       +      -
    566A  ALA*     4.5    11.2    -      -       +      -
    567A  ARG      5.5     0.2    -      -       -      +
    568A  ILE*     4.0     9.0    -      -       +      -
    591A  ILE*     3.6    34.1    -      -       +      -
    592A  LEU      3.3    17.7    -      -       -      +
    593A  MET*     4.0     4.5    -      -       +      +
    601A  TYR*     1.3    72.6    -      -       -      +
    603A  LEU*     1.3    65.1    +      -       -      +
    604A  CYS*     5.1     1.1    -      -       +      -
    613A  TYR*     3.3     4.5    -      -       -      -
    614A  PHE*     2.9    42.6    +      -       +      -
    616A  LEU*     4.0     7.3    -      -       +      +
    623A  LEU*     3.5    44.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 603 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    591A  ILE*     3.4     7.6    -      -       -      +
    592A  LEU*     2.8    41.4    +      -       +      +
    594A  THR*     4.8     4.0    -      -       -      +
    596A  PHE*     4.4    10.5    -      -       +      -
    601A  TYR*     3.7    20.6    -      -       +      +
    602A  LEU*     1.3    81.1    -      -       -      +
    604A  CYS*     1.3    61.6    +      -       -      +
    611A  LEU*     4.7     7.2    -      -       +      -
    612A  PHE      3.5     3.1    -      -       -      +
    613A  TYR*     3.6    20.6    -      -       +      -
    638A  LEU*     3.9    15.0    -      -       +      +
    649A  VAL*     4.0    31.0    -      -       +      -
    659A  ILE*     4.1    21.5    -      -       +      -
    666A  LEU*     4.3     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 604 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    566A  ALA*     4.6     5.6    -      -       +      -
    582A  LEU*     3.8    23.1    -      -       +      -
    588A  PRO*     3.8    28.7    -      -       -      -
    590A  SER      3.6     7.9    -      -       -      -
    591A  ILE*     4.0    20.4    -      -       +      -
    602A  LEU*     5.1     2.2    -      -       +      -
    603A  LEU*     1.3    76.2    -      -       -      +
    605A  ALA*     1.3    61.8    +      -       -      +
    606A  LEU*     4.3     1.2    +      -       -      -
    610A  ALA      4.2     0.3    -      -       -      +
    611A  LEU*     3.5     5.2    -      -       -      +
    612A  PHE*     2.8    53.7    +      -       +      +
    614A  PHE*     5.0     4.7    -      -       +      -
    638A  LEU*     4.6     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 605 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588A  PRO*     3.5     2.8    -      -       -      +
    589A  ARG*     2.7    32.6    +      -       -      -
    590A  SER*     3.0    13.3    +      -       -      +
    604A  CYS*     1.3    73.4    -      -       -      +
    606A  LEU*     1.3    56.2    +      -       -      +
    610A  ALA      3.6     6.7    -      -       -      +
    611A  LEU*     3.9    13.7    -      -       +      -
    636A  THR*     3.7    39.3    -      -       -      +
    638A  LEU*     4.1     8.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 606 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    564A  ILE*     4.5     0.4    -      -       +      -
    582A  LEU*     3.7    30.3    -      -       +      -
    583A  GLY      4.4    16.4    -      -       -      +
    586A  ILE*     4.0    14.8    -      -       +      +
    587A  ILE      3.8     2.0    -      -       -      +
    588A  PRO*     3.8    18.4    -      -       +      -
    589A  ARG*     4.5     2.0    -      -       -      -
    604A  CYS*     4.9     1.1    -      -       -      -
    605A  ALA*     1.3    76.8    -      -       -      +
    607A  GLY*     1.3    58.4    +      -       -      +
    608A  ASP*     3.1    32.5    +      -       -      +
    609A  GLY*     3.2    13.2    +      -       -      -
    610A  ALA*     2.9    17.8    +      -       +      +
    612A  PHE*     3.6    29.8    -      -       +      -
    628A  LYS*     5.7     1.8    -      -       -      +
    635A  PRO*     3.8     8.5    -      -       -      +
    636A  THR      4.0     3.5    +      -       -      -
----------------------------------------------------------
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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