Contacts of the helix formed by residues 588 - 598 (chain A) in PDB entry 5ID6


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 GLY 588 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  LEU      3.7     0.6    +      -       -      -
    587A  PRO*     1.3    74.8    -      -       -      +
    589A  PRO*     1.3    75.3    -      -       -      +
    590A  ASN*     3.2    13.3    +      -       -      -
    591A  LYS*     3.2     7.1    +      -       -      +
    592A  MSE      3.0    17.8    +      -       -      +
    674A  GLU*     5.0     6.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 589 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  LEU*     4.3     9.0    -      -       +      +
    587A  PRO      3.7     2.6    -      -       -      +
    588A  GLY*     1.3    87.8    -      -       -      +
    590A  ASN*     1.3    63.2    +      -       -      +
    592A  MSE      4.4     2.0    -      -       +      +
    593A  LEU*     2.7    45.1    +      -       +      +
    670A  TYR*     3.8    19.2    -      -       +      +
    673A  VAL*     3.7    24.9    -      -       +      -
    674A  GLU*     3.6    50.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 590 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588A  GLY*     3.9    12.5    -      -       -      -
    589A  PRO*     1.3    83.2    -      -       -      +
    591A  LYS*     1.3    90.5    +      -       -      +
    594A  PRO*     3.3    18.0    -      -       -      +
    670A  TYR*     3.6    40.4    +      -       +      +
    674A  GLU*     5.6     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 591 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    588A  GLY*     3.2     8.3    +      -       -      +
    589A  PRO      3.2     0.2    -      -       -      -
    590A  ASN*     1.3    97.1    -      -       -      +
    592A  MSE      1.3    61.9    +      -       +      +
    593A  LEU      3.7     0.4    -      -       -      -
    594A  PRO*     3.4    11.4    -      -       -      +
    595A  LYS*     3.3    32.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with MSE 592 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  LEU*     3.7    15.9    -      -       +      -
    587A  PRO*     3.6    26.5    -      -       +      +
    588A  GLY      3.0    15.4    +      -       -      +
    589A  PRO*     4.2     2.0    -      -       +      +
    591A  LYS*     1.3    81.1    -      -       +      +
    593A  LEU*     1.3    67.4    +      -       -      +
    594A  PRO      3.4     0.4    -      -       -      -
    595A  LYS*     3.7    23.1    -      -       -      +
    596A  VAL*     3.1    39.9    +      -       +      +
    649A  TRP*     3.5    31.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 593 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  LEU*     4.4     5.4    -      -       +      -
    589A  PRO*     2.7    33.1    +      -       +      +
    592A  MSE      1.3    73.8    -      -       -      +
    594A  PRO*     1.3    61.4    -      -       +      +
    596A  VAL*     4.0     0.2    -      -       -      +
    597A  PHE*     3.0    39.5    +      -       +      +
    639A  PHE*     4.0    22.9    -      -       +      -
    643A  ILE*     4.4     9.0    -      -       +      -
    649A  TRP*     3.5    33.0    -      -       +      -
    669A  PHE*     4.0    26.5    -      -       +      -
    670A  TYR*     4.4    10.3    -      -       +      -
    673A  VAL*     4.2    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PRO 594 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    589A  PRO      3.6     1.1    -      -       -      +
    590A  ASN      3.3    26.9    -      -       -      +
    591A  LYS*     3.4    10.5    -      -       -      +
    593A  LEU*     1.3    95.7    -      -       +      +
    595A  LYS*     1.3    59.0    +      -       -      +
    596A  VAL      3.3     0.2    -      -       -      -
    598A  PHE*     3.3    41.9    +      -       +      +
    616A  TYR*     3.6    39.9    -      -       +      +
    639A  PHE*     4.3     6.5    -      -       +      -
    670A  TYR*     4.3    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 595 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    591A  LYS*     3.3    29.2    +      -       -      +
    592A  MSE      3.4    28.3    +      -       -      +
    593A  LEU      3.2     1.0    -      -       -      -
    594A  PRO*     1.3    79.3    -      -       -      +
    596A  VAL*     1.3    61.7    +      -       -      +
    598A  PHE      4.6     0.3    -      -       -      -
    599A  SER*     3.6    17.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 596 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    592A  MSE      3.1    30.5    +      -       +      +
    593A  LEU      4.0     2.2    -      -       -      +
    595A  LYS*     1.3    79.4    -      -       +      +
    597A  PHE*     1.3    82.2    +      -       +      +
    598A  PHE      3.2     1.7    +      -       -      -
    599A  SER*     2.4    32.6    +      -       -      +
    602A  TRP*     3.5     5.3    -      -       +      +
    646A  TYR*     4.0    27.1    -      -       +      +
    649A  TRP*     3.7    22.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 597 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    593A  LEU*     3.0    24.2    +      -       +      +
    596A  VAL*     1.3    96.1    -      -       +      +
    598A  PHE*     1.3    67.2    +      -       -      +
    599A  SER      3.6     1.1    -      -       -      -
    602A  TRP*     3.1    56.1    -      +       +      +
    603A  MSE      4.0     5.0    -      -       -      +
    638A  PHE*     3.7    18.2    -      -       +      -
    639A  PHE*     3.8    17.7    -      +       +      -
    642A  SER*     3.6    29.8    -      -       -      -
    643A  ILE*     4.1    14.1    -      -       +      -
    646A  TYR*     3.9    14.8    -      +       +      -
    649A  TRP*     3.7    31.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with PHE 598 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    594A  PRO*     3.3    37.8    +      -       +      +
    595A  LYS      4.6     0.9    -      -       -      -
    596A  VAL      3.2     0.8    -      -       -      -
    597A  PHE*     1.3    83.0    -      -       -      +
    599A  SER*     1.3    58.2    -      -       -      +
    600A  LYS      3.4     3.6    +      -       -      -
    603A  MSE      3.9    31.8    -      -       +      +
    608A  PRO*     5.0     1.1    -      -       +      -
    612A  ILE*     3.6    28.0    -      -       +      -
    613A  GLN*     4.6    13.9    -      -       +      -
    616A  TYR*     3.7    45.3    -      +       +      -
    635A  LEU*     4.2     5.2    -      -       +      -
    638A  PHE*     3.7    22.0    -      +       -      -
    639A  PHE*     4.3    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