Contacts of the strand formed by residues 227 - 232 (chain D) 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 GLY 227 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    222D  LEU*     3.6     9.2    -      -       -      +
    223D  ILE      2.9    29.3    +      -       -      +
    225D  GLY*     3.8     1.6    -      -       -      +
    226D  LYS*     1.3    76.0    -      -       -      +
    228D  ARG*     1.3    63.9    +      -       -      -
   2803D  SAH      4.0     3.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 228 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220D  ILE*     4.2    18.0    -      -       +      +
    221D  ASP      3.4     7.0    -      -       -      +
    222D  LEU*     3.8    20.0    -      -       +      -
    223D  ILE*     4.5     0.2    -      -       -      -
    227D  GLY*     1.3    74.2    -      -       -      -
    229D  GLY*     1.3    59.7    +      -       -      +
    271D  TYR*     3.8     4.6    +      -       -      -
    289D  GLU*     2.9    43.0    +      -       -      -
    290D  THR      5.7     0.6    +      -       -      -
    295D  ARG*     4.1     0.8    -      -       -      +
    296D  LEU*     3.5    36.4    -      -       +      +
    298D  ASN*     2.9    10.1    +      -       -      +
   2803D  SAH      2.8    57.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 229 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    220D  ILE*     3.4     8.8    -      -       -      +
    221D  ASP      2.8    31.3    +      -       -      -
    223D  ILE*     3.8    14.6    -      -       -      +
    228D  ARG*     1.3    74.7    -      -       -      +
    230D  VAL*     1.3    66.0    +      -       -      +
    296D  LEU*     3.5     6.5    -      -       -      +
    298D  ASN*     3.4    15.7    -      -       -      -
    331D  GLU*     3.9     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 230 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218D  MET*     3.7    31.2    -      -       +      -
    219D  LYS      3.3    12.1    -      -       -      +
    229D  GLY*     1.3    78.2    -      -       -      +
    231D  ILE*     1.3    64.1    +      -       -      +
    293D  LEU*     3.5    38.4    -      -       +      +
    296D  LEU*     3.8    15.6    +      -       +      -
    297D  ILE*     3.7    19.9    -      -       +      +
    331D  GLU*     3.5     8.6    +      -       -      +
    332D  LEU*     2.9    41.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 231 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    218D  MET*     3.3     3.8    -      -       -      -
    219D  LYS*     2.8    56.9    +      -       +      +
    221D  ASP*     4.1    25.4    -      -       +      +
    223D  ILE*     4.0    17.9    -      -       +      -
    230D  VAL*     1.3    76.8    -      -       -      +
    232D  ALA*     1.3    79.1    +      -       -      +
    233D  THR*     3.4     1.4    +      -       +      +
    329D  GLY*     3.7    19.3    -      -       -      +
    330D  GLU      3.4     6.3    -      -       -      +
    331D  GLU*     3.7    28.9    -      -       +      +
    332D  LEU*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 232 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    217D  GLY      3.6     5.8    -      -       -      -
    218D  MET*     4.6     1.3    -      -       -      +
    230D  VAL      4.2     1.0    +      -       -      -
    231D  ILE*     1.3    77.2    -      -       -      +
    233D  THR*     1.3    59.3    +      -       -      +
    234D  LYS      3.4    17.0    -      -       -      +
    236D  PHE*     4.2    10.1    -      -       +      -
    326D  ILE*     4.1    14.4    -      -       +      -
    327D  ALA      4.0    13.9    -      -       -      +
    329D  GLY      2.8    26.5    +      -       -      -
    330D  GLU      2.9    15.8    +      -       -      +
    332D  LEU*     4.3    10.7    -      -       +      +
----------------------------------------------------------
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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