Contacts of the strand formed by residues 218 - 223 (chain A) 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 MET 218 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215A  GLU*     3.5    45.2    -      -       +      +
    216A  GLU      3.3     6.5    -      -       -      +
    217A  GLY*     1.3    83.2    +      -       -      +
    219A  LYS*     1.3    62.6    -      -       -      +
    230A  VAL*     3.7    14.8    -      -       +      -
    231A  ILE      3.3     6.7    -      -       -      +
    232A  ALA*     5.1     0.2    -      -       -      -
    233A  THR*     3.4     6.9    +      -       -      +
    236A  PHE*     4.2     7.0    -      -       +      -
    242A  VAL*     3.5    24.0    -      -       +      +
    243A  VAL*     4.2    19.1    -      -       +      -
    293A  LEU*     3.8    17.0    -      -       +      +
    297A  ILE*     5.2     0.4    -      -       -      -
    332A  LEU*     3.8    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 219 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218A  MET*     1.3    75.6    -      -       -      +
    220A  ILE*     1.3    72.0    +      -       -      +
    221A  ASP*     5.5     3.4    -      -       -      -
    230A  VAL*     3.3     6.4    -      -       -      -
    231A  ILE*     2.8    62.7    +      -       +      +
    233A  THR*     3.6    21.6    -      -       +      +
    293A  LEU*     4.9     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 220 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  LYS*     1.3    84.8    -      -       -      +
    221A  ASP*     1.3    66.9    +      -       -      +
    222A  LEU*     6.0     0.2    -      -       +      -
    228A  ARG*     4.0    31.2    -      -       +      +
    229A  GLY      3.3    11.7    -      -       -      +
    230A  VAL*     4.5     2.2    -      -       +      +
    293A  LEU*     3.6    26.0    -      -       +      -
    296A  LEU*     3.6    22.2    -      -       +      -
    340C  SER*     5.2    16.8    -      -       -      -
    341C  LYS      6.0     0.4    -      -       -      +
     19G  ARG*     5.8     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 221 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219A  LYS*     3.8     3.1    +      -       +      -
    220A  ILE*     1.3    78.5    -      -       -      +
    222A  LEU*     1.3    75.8    +      -       -      +
    223A  ILE*     3.6     6.2    +      -       +      +
    228A  ARG*     3.5     3.5    -      -       -      -
    229A  GLY*     2.8    31.5    +      -       -      +
    231A  ILE*     3.9    39.6    -      -       +      +
    256C  LYS*     3.7    19.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 222 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220A  ILE*     6.0     0.4    -      -       +      -
    221A  ASP*     1.3    78.3    +      -       -      +
    223A  ILE*     1.3    65.1    +      -       -      +
    227A  GLY*     3.6    16.4    -      -       -      +
    228A  ARG*     4.1    11.0    -      -       +      -
    252C  ILE*     3.9    15.1    -      -       +      +
    256C  LYS*     2.8    36.5    +      -       +      -
    274C  TYR*     3.7    39.5    -      -       +      -
    276C  GLN*     5.8     3.6    -      -       -      +
    281C  THR*     5.3     3.8    -      -       +      -
     19G  ARG*     3.2    47.6    -      -       -      +
     21G  VAL*     5.3     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 223 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    221A  ASP*     4.1    15.9    -      -       +      +
    222A  LEU*     1.3    79.7    -      -       -      +
    224A  ASP*     1.3    73.0    +      -       +      +
    225A  GLY      3.1     0.5    +      -       -      -
    226A  LYS*     2.9    42.5    +      -       +      +
    227A  GLY      3.0    15.5    +      -       -      +
    229A  GLY*     4.2     9.2    -      -       -      +
    231A  ILE*     4.1    22.0    -      -       +      -
    331A  GLU*     3.6    39.3    -      -       +      +
    252C  ILE*     4.2     2.5    -      -       -      -
    256C  LYS*     5.6     0.7    -      -       -      +
    281C  THR*     3.7     2.3    +      -       -      -
----------------------------------------------------------
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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