Contacts of the strand formed by residues 218 - 223 (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 MET 218 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    215B  GLU*     3.7    34.1    -      -       +      +
    216B  GLU*     3.4    14.7    -      -       -      +
    217B  GLY*     1.3    82.9    -      -       -      +
    219B  LYS*     1.3    61.7    +      -       -      +
    230B  VAL*     3.6    11.4    -      -       +      -
    231B  ILE      3.3     5.4    -      -       -      +
    233B  THR*     3.4     7.0    +      -       -      +
    236B  PHE*     4.5     5.2    -      -       +      -
    242B  VAL*     3.5    22.7    -      -       -      +
    243B  VAL*     3.8    22.4    -      -       +      -
    293B  LEU*     3.6    24.0    -      -       +      +
    297B  ILE*     5.1     0.4    -      -       -      -
    332B  LEU*     3.8    31.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 219 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218B  MET*     1.3    75.0    -      -       -      +
    220B  ILE*     1.3    69.5    +      -       -      +
    221B  ASP*     3.8     8.5    +      -       -      -
    230B  VAL*     3.3     6.7    -      -       -      -
    231B  ILE*     2.8    59.6    +      -       +      +
    232B  ALA      5.6     0.2    -      -       -      -
    233B  THR*     3.7    20.8    -      -       +      +
    293B  LEU*     5.2     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 220 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219B  LYS*     1.3    80.3    -      -       -      +
    221B  ASP*     1.3    67.8    +      -       -      +
    228B  ARG*     4.2    27.6    -      -       +      +
    229B  GLY      3.4    11.2    -      -       -      +
    230B  VAL*     4.7     1.1    -      -       +      +
    291B  ASN*     5.8     1.6    -      -       -      +
    293B  LEU*     3.4    27.1    -      -       +      -
    296B  LEU*     3.7    22.9    -      -       +      -
     19E  ARG*     6.2     1.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 221 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    256A  LYS*     3.0    33.1    +      -       -      +
    219B  LYS*     3.8     9.8    +      -       +      -
    220B  ILE*     1.3    80.1    -      -       -      +
    222B  LEU*     1.3    72.2    +      -       -      +
    223B  ILE*     3.9     5.5    -      -       +      +
    228B  ARG*     3.4     3.5    -      -       -      +
    229B  GLY*     2.8    32.1    +      -       -      +
    231B  ILE*     3.8    28.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 222 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  ILE*     3.8    10.3    -      -       +      +
    256A  LYS*     2.7    52.0    +      -       +      -
    259A  GLU*     4.4     2.7    -      -       -      +
    274A  TYR*     3.7    36.3    -      -       +      +
    281A  THR*     5.7     2.0    -      -       +      -
    220B  ILE*     6.2     0.2    -      -       +      -
    221B  ASP*     1.3    79.7    +      -       -      +
    223B  ILE*     1.3    61.6    +      -       -      +
    227B  GLY*     3.6    13.9    -      -       -      +
    228B  ARG*     4.0    14.1    -      -       +      -
     19E  ARG*     3.4    48.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 223 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    252A  ILE*     3.8     3.1    -      -       -      -
    256A  LYS*     5.4     0.4    -      -       -      +
    281A  THR*     3.5     3.1    +      -       -      -
    221B  ASP*     4.3     9.9    -      -       +      +
    222B  LEU*     1.3    81.4    -      -       -      +
    224B  ASP*     1.3    70.2    +      -       +      +
    225B  GLY      3.1     1.0    +      -       -      -
    226B  LYS*     2.9    41.4    +      -       +      -
    227B  GLY      2.9    13.8    +      -       -      +
    229B  GLY*     3.7    20.4    -      -       -      +
    231B  ILE*     3.7    30.1    -      -       +      -
    331B  GLU*     3.4    38.1    -      -       +      +
----------------------------------------------------------
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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