Contacts of the strand formed by residues 280 - 285 (chain B) in PDB entry 1ZKK


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 LYS 280 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251B  GLU*     5.7     8.1    -      -       -      +
    276B  GLN*     3.5     6.6    +      -       -      +
    277B  TYR      2.9    28.3    +      -       -      +
    278B  LEU      3.4     0.7    -      -       -      +
    279B  SER*     1.3    87.3    +      -       -      +
    281B  THR*     1.3    64.9    +      -       -      +
    282B  TYR*     3.7    32.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 281 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    251B  GLU*     4.1     1.0    -      -       -      +
    252B  ILE*     3.2    58.4    +      -       +      +
    274B  TYR*     4.6     7.6    -      -       +      -
    275B  PHE      3.4    18.4    -      -       -      +
    276B  GLN*     4.4    12.3    +      -       +      +
    280B  LYS*     1.3    76.9    +      -       -      +
    282B  TYR*     1.3    80.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 282 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    249B  LEU*     4.0    12.6    -      -       +      -
    250B  ILE      3.4    10.8    -      -       -      +
    251B  GLU*     3.5    38.5    +      -       +      -
    252B  ILE      4.3     3.1    -      -       -      +
    274B  TYR*     3.3     5.7    -      -       -      +
    275B  PHE*     2.8    50.1    +      +       +      -
    277B  TYR*     3.6    51.3    +      +       +      -
    280B  LYS*     3.7    34.6    -      -       +      +
    281B  THR*     1.3    79.6    -      -       -      +
    283B  CYS*     1.3    62.8    +      -       -      +
    316B  PRO*     5.0     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 283 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248B  ASP      3.3     2.8    -      -       -      +
    249B  LEU*     3.5     2.4    -      -       -      +
    250B  ILE*     2.9    36.6    +      -       +      +
    255B  ALA*     3.6    21.5    -      -       +      -
    272B  MET*     3.8    32.5    -      -       -      -
    273B  TYR      3.3    28.3    -      -       -      -
    274B  TYR*     4.0    12.8    -      -       +      -
    275B  PHE*     4.1     2.5    -      -       -      -
    282B  TYR*     1.3    78.6    -      -       -      +
    284B  VAL*     1.3    69.3    +      -       -      +
    285B  ASP*     4.1     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 284 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245B  TYR*     3.5    35.6    -      -       +      +
    246B  HIS      3.9     0.2    -      -       -      -
    247B  GLY*     3.4    36.3    -      -       -      +
    248B  ASP      3.5     2.9    -      -       -      +
    249B  LEU*     4.4    11.0    -      -       +      +
    271B  TYR      3.5     2.1    -      -       -      +
    272B  MET*     3.5     0.2    -      -       -      -
    273B  TYR      2.8    35.6    +      -       -      +
    275B  PHE*     3.8    20.6    -      -       +      -
    283B  CYS*     1.3    74.1    -      -       -      +
    285B  ASP*     1.3    58.9    +      -       -      +
    286B  ALA      3.4     5.4    +      -       -      -
    316B  PRO      6.0     1.3    -      -       -      +
    317B  HIS*     6.2     0.2    -      -       -      -
    318B  LEU*     4.1    15.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 285 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    247B  GLY*     3.9     0.2    -      -       -      -
    248B  ASP*     2.8    42.6    +      -       -      +
    250B  ILE*     3.9    12.3    -      -       +      -
    258B  ARG*     3.0    31.1    +      -       -      +
    262B  TYR*     2.6    26.1    +      -       -      -
    271B  TYR      4.3     1.1    -      -       -      -
    272B  MET*     3.6    20.1    -      -       +      +
    283B  CYS*     3.7     1.2    +      -       -      -
    284B  VAL*     1.3    71.1    -      -       -      +
    286B  ALA*     1.3    58.2    +      -       -      +
    287B  THR*     2.7    30.0    +      -       -      -
    288B  ARG*     5.1     1.6    +      -       -      +
----------------------------------------------------------
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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