Contacts of the strand formed by residues 585 - 591 (chain C) in PDB entry 4OQB


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 C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572C  LEU*     4.3     9.4    -      -       +      -
    573C  GLN      3.3    17.0    -      -       -      +
    574C  LEU*     4.3     8.1    -      -       +      -
    584C  TRP*     1.3    73.7    -      -       -      +
    586C  PHE*     1.3    60.1    +      -       -      +
    587C  ARG*     4.9     9.6    -      -       -      +
    600C  LYS      3.7     2.2    -      -       -      +
    601C  LEU*     3.9     2.4    -      -       -      +
    602C  GLU*     2.9    43.1    +      -       +      +
    604C  MET*     3.9    13.4    -      -       +      +
    610C  ALA      4.1     3.1    -      -       -      +
    613C  HIS*     3.8    32.3    -      -       +      +
    614C  PHE*     3.5    45.3    -      -       +      +
    617C  LEU*     4.2     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 586 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534C  ASP*     3.4    33.9    -      -       +      -
    536C  ASP*     3.6    15.7    -      -       +      -
    537C  SER*     3.5    41.1    -      -       -      -
    571C  LYS*     4.9     3.1    -      -       +      -
    572C  LEU*     3.5     5.9    -      -       -      +
    573C  GLN*     3.0    51.4    +      -       +      +
    574C  LEU*     5.1     0.2    -      -       -      +
    575C  LEU*     4.5    10.3    -      -       +      +
    585C  ILE*     1.3    74.3    -      -       -      +
    587C  ARG*     1.3    63.6    +      -       -      +
    588C  SER*     3.8    14.6    -      -       -      -
    599C  ASN*     3.8    26.2    -      -       +      -
    600C  LYS      3.8     0.4    -      -       -      -
    601C  LEU*     3.8    30.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 587 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    570C  TYR*     3.2    28.5    -      -       +      +
    571C  LYS      3.7     3.4    -      -       -      -
    572C  LEU*     3.6    18.6    -      -       +      -
    585C  ILE*     4.9     5.3    -      -       +      +
    586C  PHE*     1.3    74.9    -      -       -      +
    588C  SER*     1.3    59.9    +      -       -      +
    589C  TRP*     3.7    16.2    -      -       +      -
    599C  ASN*     3.3     5.7    -      -       -      +
    600C  LYS*     2.9    68.4    +      -       +      +
    602C  GLU*     3.2    25.9    +      -       -      +
    613C  HIS*     3.9     8.5    +      -       -      -
    617C  LEU*     3.5    36.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 588 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534C  ASP*     4.2     4.5    +      -       -      -
    536C  ASP*     4.1    14.9    +      -       -      -
    569C  TYR*     3.8    15.2    +      -       -      -
    570C  TYR*     3.3     7.1    -      -       -      -
    571C  LYS*     2.8    49.2    +      -       -      +
    586C  PHE*     3.8    19.0    -      -       -      -
    587C  ARG*     1.3    74.2    -      -       -      +
    589C  TRP*     1.3    65.3    +      -       -      +
    598C  SER      4.0     7.1    +      -       -      -
    599C  ASN*     4.2     4.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TRP 589 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  MET*     2.8    30.8    +      -       +      +
     44A  PHE*     3.9    16.5    -      -       +      +
    569C  TYR*     3.2    24.2    +      -       -      +
    570C  TYR*     3.6    23.3    -      +       +      -
    587C  ARG*     3.7    21.1    -      -       +      -
    588C  SER*     1.3    79.0    +      -       -      +
    590C  GLY*     1.3    59.9    +      -       -      +
    598C  SER*     2.9    59.7    +      -       -      +
    599C  ASN*     3.6    32.1    -      -       -      -
    600C  LYS*     3.6    16.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 590 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ASP*     4.0    12.6    -      -       -      -
    568C  SER*     3.3     7.0    -      -       -      -
    569C  TYR*     2.9    36.8    +      -       -      -
    589C  TRP*     1.3    81.2    -      -       -      +
    591C  ARG*     1.3    60.9    +      -       -      -
    596C  ILE      3.4    12.1    -      -       -      -
    597C  GLY*     3.5     7.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 591 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  GLN*     5.1     4.3    -      -       -      -
     45A  ASP*     3.2    35.9    +      -       +      +
    565C  GLY      2.8    30.3    +      -       -      -
    566C  THR*     3.6     1.6    -      -       -      +
    567C  ASN*     3.2    39.6    -      -       +      +
    569C  TYR*     3.7     4.3    -      -       -      -
    590C  GLY*     1.3    70.6    -      -       -      -
    592C  VAL*     1.3    64.7    +      -       -      +
    593C  GLY      3.3     1.9    +      -       -      -
    594C  THR*     2.7    36.9    +      -       -      +
    596C  ILE*     3.0    17.9    +      -       +      -
    744C  PHE*     5.3     0.6    -      -       -      +
    745C  GLY      2.8    20.3    +      -       -      +
    746C  MET*     3.6    25.3    +      -       -      +
    747C  LYS      3.0    32.1    +      -       -      +
    749C  PRO*     4.5     1.0    -      -       -      +
----------------------------------------------------------
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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