Contacts of the strand formed by residues 567 - 573 (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 ASN 567 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ASP*     3.0    15.3    +      -       -      +
    559C  LEU      3.5     4.4    -      -       -      +
    560C  VAL*     4.1    12.1    -      -       +      +
    565C  GLY      4.0     3.1    -      -       -      +
    566C  THR*     1.3    74.8    -      -       -      +
    568C  SER*     1.3    59.9    +      -       -      +
    591C  ARG*     3.2    20.4    -      -       -      +
    592C  VAL*     3.1    45.8    +      -       -      +
    737C  TYR*     4.6    10.7    -      -       -      +
    741C  PRO*     5.7     0.3    -      -       -      +
    742C  HIS      3.5    16.2    +      -       -      +
    744C  PHE*     4.0    19.6    -      -       -      +
    745C  GLY      5.8     0.6    +      -       -      -
    749C  PRO*     4.2    16.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 568 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     45A  ASP*     2.7    27.6    +      -       -      +
    558C  GLY*     3.5     4.2    -      -       -      -
    559C  LEU*     2.8    34.0    +      -       -      +
    566C  THR*     3.0    15.6    +      -       -      -
    567C  ASN*     1.3    74.5    +      -       -      +
    569C  TYR*     1.3    65.2    +      -       -      +
    590C  GLY      3.3    14.1    -      -       -      -
    592C  VAL*     4.3     6.1    -      -       -      +
    638C  PHE*     4.6    14.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 569 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    536C  ASP*     5.8     0.2    +      -       -      -
    556C  THR*     5.5     5.4    -      -       +      -
    557C  LEU      3.5    11.0    -      -       -      +
    558C  GLY*     4.5     0.4    -      -       -      -
    568C  SER*     1.3    77.2    -      -       -      +
    570C  TYR*     1.3    68.4    +      -       -      +
    571C  LYS*     4.4     7.2    -      -       +      +
    588C  SER*     3.8    14.2    +      -       -      -
    589C  TRP*     3.2    36.0    +      -       -      +
    590C  GLY*     2.9    51.1    +      -       -      +
    591C  ARG      3.7    10.5    -      -       -      -
    592C  VAL*     3.4    22.0    -      -       +      -
    593C  GLY      5.1     1.3    -      -       -      -
    594C  THR      5.1     4.6    +      -       -      -
    596C  ILE      4.3     5.0    +      -       -      -
    597C  GLY*     4.7     1.7    -      -       -      -
    598C  SER      5.0     0.3    +      -       -      -
    638C  PHE*     4.1     6.3    -      -       -      -
    695C  LYS*     4.6    18.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 570 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    556C  THR*     4.6     0.9    -      -       -      -
    557C  LEU*     2.8    50.8    +      -       +      +
    569C  TYR*     1.3    78.1    -      -       -      +
    571C  LYS*     1.3    60.0    +      -       -      +
    572C  LEU*     3.8    25.2    +      -       +      +
    587C  ARG*     3.2    33.2    -      -       +      +
    588C  SER      3.3    17.7    -      -       -      -
    589C  TRP*     3.6    26.5    -      +       +      -
    617C  LEU*     4.2     6.3    -      -       -      +
    621C  LYS*     3.8    42.0    -      -       +      -
    638C  PHE*     3.7    23.6    -      +       +      -
----------------------------------------------------------
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Residues in contact with LYS 571 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534C  ASP*     3.4    44.9    +      -       +      +
    554C  SER*     5.5     1.8    -      -       -      +
    555C  ALA      3.5     4.9    -      -       -      +
    556C  THR*     3.6    32.7    -      -       +      +
    569C  TYR*     4.4     6.0    -      -       +      -
    570C  TYR*     1.3    73.6    -      -       -      +
    572C  LEU*     1.3    65.0    +      -       -      +
    573C  GLN*     3.9    18.5    +      -       +      +
    586C  PHE*     3.8     3.6    -      -       +      +
    587C  ARG*     3.7     2.1    -      -       -      -
    588C  SER*     2.8    46.9    +      -       -      +
    643C  ILE*     5.9     0.4    -      -       +      -
    695C  LYS*     5.4    14.4    -      -       -      +
    698C  LEU*     5.9     4.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 572 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554C  SER*     3.4     0.9    +      -       -      -
    555C  ALA*     2.8    38.8    +      -       +      +
    557C  LEU*     5.9     3.1    -      -       +      -
    570C  TYR*     3.8    16.5    +      -       +      +
    571C  LYS*     1.3    75.5    -      -       -      +
    573C  GLN*     1.3    68.7    -      -       -      +
    585C  ILE*     4.3    16.4    -      -       +      -
    586C  PHE      3.5     6.7    -      -       -      +
    587C  ARG*     3.6    29.2    -      -       +      -
    614C  PHE*     3.6    43.5    -      -       +      +
    617C  LEU*     4.4     9.9    -      -       +      -
    618C  TYR*     4.0    24.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLN 573 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    532C  ALA      3.8     9.0    +      -       -      +
    533C  VAL*     3.7     6.3    -      -       -      +
    534C  ASP*     3.4    39.2    +      -       -      +
    545C  VAL*     4.5     6.0    -      -       +      +
    553C  PHE      3.9     5.4    -      -       -      -
    554C  SER*     3.5    21.5    +      -       -      +
    571C  LYS*     3.9    19.2    +      -       +      +
    572C  LEU*     1.3    80.7    -      -       -      +
    574C  LEU*     1.3    61.6    +      -       -      +
    575C  LEU*     3.4    27.4    -      -       +      +
    585C  ILE*     3.3    11.8    -      -       -      +
    586C  PHE*     3.0    43.2    +      -       +      +
    614C  PHE*     4.1     4.2    -      -       -      -
----------------------------------------------------------
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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