Contacts of the strand formed by residues 569 - 580 (chain C) in PDB entry 4YZ9


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 569 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    565C  ILE*     3.5     5.7    -      -       -      +
    566C  VAL*     2.5    47.2    +      -       +      +
    567C  GLY      3.3     0.2    -      -       -      -
    568C  LYS*     1.3    79.4    -      -       -      +
    570C  SER*     1.3    74.1    +      -       -      +
    571C  PHE*     4.8     4.5    -      -       +      -
    590C  MET      3.8     7.2    -      -       -      +
    591C  PHE*     4.2    10.3    -      -       +      -
    598C  VAL*     4.1    26.0    -      -       +      -
    630C  CYS*     4.0    15.7    -      -       -      +
    632C  GLU*     3.7    27.4    -      -       +      -
    639C  TYR*     3.8    22.7    -      -       +      +
    641C  ALA*     4.1    20.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 570 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    563C  VAL*     4.1    10.6    -      -       -      +
    564C  VAL      3.3    11.0    -      -       -      -
    565C  ILE*     4.1    17.0    -      -       -      -
    569C  ILE*     1.3    77.5    -      -       -      +
    571C  PHE*     1.3    65.9    +      -       -      +
    589C  GLY*     3.0     2.6    -      -       -      -
    590C  MET*     2.8    55.0    +      -       -      +
    598C  VAL*     3.9     4.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 571 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    563C  VAL*     3.3     6.8    -      -       -      +
    564C  VAL*     2.9    56.5    +      -       +      -
    566C  VAL*     4.7     5.8    -      -       +      -
    569C  ILE*     4.8     3.4    -      -       +      -
    570C  SER*     1.3    78.5    -      -       -      +
    572C  CYS*     1.3    74.2    +      -       -      +
    573C  PRO*     4.0    22.0    -      -       +      -
    587C  TYR*     3.9    26.7    -      +       +      -
    588C  ARG      3.2    16.6    -      -       -      +
    589C  GLY*     3.7     2.0    -      -       -      -
    598C  VAL*     3.9    28.7    -      -       +      -
    600C  ARG*     5.8     0.7    -      -       -      -
    639C  TYR*     3.4    41.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with CYS 572 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562C  SER      3.4    13.9    -      -       -      +
    563C  VAL*     4.2    13.5    -      -       -      -
    571C  PHE*     1.3    82.9    -      -       -      +
    573C  PRO*     1.3    69.7    -      -       -      +
    574C  LYS*     3.2     3.1    -      -       +      +
    575C  ASP*     3.1    37.3    +      -       +      +
    587C  TYR*     3.6     5.2    -      -       -      +
    588C  ARG*     3.1    16.2    +      -       -      +
    589C  GLY*     5.6     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with PRO 573 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562C  SER*     3.4    23.3    -      -       -      +
    564C  VAL*     3.3    34.8    -      -       +      -
    571C  PHE*     3.8    11.4    -      -       +      +
    572C  CYS*     1.3    82.7    -      -       -      +
    574C  LYS*     1.3    61.8    +      -       +      +
    575C  ASP      3.4     0.5    +      -       -      -
    576C  VAL*     3.8     6.6    -      -       -      +
    587C  TYR*     3.7    27.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 574 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    562C  SER*     4.2    32.3    -      -       -      +
    572C  CYS*     3.2     3.7    -      -       +      -
    573C  PRO*     1.3    80.7    -      -       +      +
    575C  ASP*     1.3    58.7    +      -       -      +
    576C  VAL*     3.7     5.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 575 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572C  CYS*     3.1    31.3    +      -       +      +
    574C  LYS*     1.3    76.5    -      -       +      +
    576C  VAL*     1.3    69.4    +      -       -      +
    577C  LEU*     4.0     3.5    -      -       -      +
    587C  TYR*     3.4    16.6    -      -       -      +
    588C  ARG*     3.1    47.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 576 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    573C  PRO      3.8     8.5    -      -       -      +
    574C  LYS      3.7     6.0    +      -       -      +
    575C  ASP*     1.3    80.6    +      -       -      +
    577C  LEU*     1.3    63.7    +      -       -      +
    578C  GLY*     3.7    18.2    -      -       -      +
    585C  ILE*     4.1    12.3    -      -       +      -
    586C  VAL      3.6    11.4    -      -       -      +
    587C  TYR*     3.8    23.3    -      -       +      -
    715C  CYS*     4.4    14.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 577 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    575C  ASP*     4.0     5.1    +      -       -      +
    576C  VAL*     1.3    75.0    -      -       -      +
    578C  GLY*     1.3    57.8    +      -       -      +
    586C  VAL*     2.9    14.3    +      -       +      +
    587C  TYR      3.9     4.9    -      -       -      +
    588C  ARG*     3.4    63.9    -      -       +      +
    597C  ALA*     4.0     8.5    -      -       +      -
    644C  LEU*     3.3    33.4    -      -       +      -
    714C  LEU*     3.4    22.6    -      -       +      +
    715C  CYS*     2.8    28.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 578 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    576C  VAL*     3.5    11.7    -      -       -      +
    577C  LEU*     1.3    82.2    -      -       -      +
    579C  HIS*     1.3    63.1    +      -       -      +
    585C  ILE*     3.9     1.4    -      -       -      -
    586C  VAL*     3.0    31.3    +      -       -      +
    713C  GLY      3.3    14.4    -      -       -      -
    715C  CYS*     3.8    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 579 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    578C  GLY*     1.3    77.2    -      -       -      +
    580C  GLY*     1.3    71.6    +      -       -      +
    584C  THR      3.3    13.5    -      -       -      +
    585C  ILE*     4.1    12.8    -      -       +      -
    586C  VAL*     4.4     2.2    -      -       -      +
    690C  LYS*     6.1     2.1    +      -       -      -
    693C  ASN*     4.9     0.2    -      -       -      +
    712C  PHE*     3.2     6.4    -      -       -      -
    713C  GLY*     3.0    29.7    +      -       -      -
    715C  CYS*     6.0     2.2    -      -       -      -
    734C  THR*     6.1     4.7    -      -       +      -
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Residues in contact with GLY 580 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    579C  HIS*     1.3    88.3    -      -       -      +
    581C  ALA*     1.3    68.6    +      -       -      +
    582C  GLU      3.8     0.5    +      -       -      -
    583C  GLY*     3.8     3.1    +      -       -      -
    584C  THR*     2.9    26.6    +      -       -      +
    688C  ASP*     4.9     2.0    -      -       -      -
    693C  ASN*     5.4     0.2    -      -       -      -
    711C  ASP*     3.5    17.3    -      -       -      -
    712C  PHE*     4.0     4.9    -      -       -      +
----------------------------------------------------------
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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