Contacts of the strand formed by residues 152 - 160 (chain A) in PDB entry 1GZK


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 PHE 152 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  VAL*     4.4    12.3    -      -       +      -
    148A  THR      3.6    12.8    -      -       -      -
    149A  MET      3.3    13.9    +      -       -      +
    150A  ASN*     3.1     2.5    +      -       -      -
    151A  ASP*     1.3    95.3    -      -       +      +
    153A  ASP*     1.3    64.2    +      -       -      +
    154A  TYR      4.1     0.9    +      -       -      -
    169A  VAL*     3.8    26.2    -      -       +      -
    170A  ARG      3.3     4.5    -      -       -      +
    171A  GLU*     3.4    44.4    -      -       +      -
    172A  LYS*     3.9    10.3    +      -       -      +
    178A  TYR*     4.9     1.8    -      +       -      -
    180A  MET*     3.6    26.7    -      -       +      -
    217A  TYR*     4.2    15.7    -      +       -      -
    219A  PHE*     4.4     2.7    -      +       -      -
    228A  VAL*     3.9    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  PHE*     1.3    73.1    -      -       -      +
    154A  TYR*     1.3    63.6    +      -       -      +
    155A  LEU*     3.6     1.1    +      -       +      +
    169A  VAL*     3.2     9.0    -      -       -      +
    170A  ARG*     2.8    78.1    +      -       +      +
    172A  LYS*     3.0    38.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  PHE      4.1     1.8    +      -       -      -
    153A  ASP*     1.3    73.7    -      -       -      +
    155A  LEU*     1.3    73.5    +      -       -      +
    156A  LYS*     3.4    15.9    -      -       -      -
    157A  LEU*     3.4    18.2    +      -       -      +
    167A  ILE*     3.3    40.8    -      -       +      -
    168A  LEU      4.3     1.3    -      -       -      -
    169A  VAL*     4.6     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  ASP      3.6     1.5    +      -       -      +
    154A  TYR*     1.3    87.8    -      -       -      +
    156A  LYS*     1.3    65.2    +      -       +      +
    168A  LEU*     2.9    30.4    +      -       +      +
    169A  VAL      4.2     5.6    -      -       -      -
    170A  ARG*     3.9    35.7    -      -       +      +
    177A  TYR*     3.0    43.5    -      -       +      +
    439A  PHE*     5.6     1.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  TYR*     3.4    18.0    -      -       -      -
    155A  LEU*     1.3    84.0    -      -       +      +
    157A  LEU*     1.3    67.5    +      -       -      +
    158A  LEU*     3.8    24.9    -      -       -      +
    167A  ILE*     3.3     4.2    -      -       -      +
    168A  LEU*     2.8    47.3    +      -       +      -
    231A  TYR*     5.3     1.9    +      -       -      -
    236A  GLU*     5.5     3.4    +      -       -      -
    438A  TYR      5.4     0.2    +      -       -      -
    439A  PHE*     3.3    34.4    +      -       +      +
    440A  ASP*     4.2     9.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  TYR*     3.4    10.2    +      -       -      +
    156A  LYS*     1.3    85.1    -      -       -      +
    158A  LEU*     1.3    61.0    +      -       -      +
    159A  GLY*     3.3    22.7    -      -       -      +
    160A  LYS*     4.4    20.9    -      -       +      +
    165A  LYS*     4.3     7.4    -      -       +      -
    166A  VAL      3.1    21.8    -      -       -      +
    167A  ILE*     3.4    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  LYS*     3.6    24.4    +      -       -      +
    157A  LEU*     1.3    74.9    -      -       -      +
    159A  GLY*     1.3    58.7    +      -       -      +
    166A  VAL*     2.7    22.2    +      -       +      +
    167A  ILE      4.1     0.4    -      -       -      -
    168A  LEU*     3.7    30.1    -      -       +      +
    179A  ALA*     3.7    29.6    -      -       +      -
    231A  TYR*     3.7    35.9    -      -       +      +
    236A  GLU*     6.1     1.3    -      -       -      +
    294A  PHE*     4.6    11.5    -      -       +      -
    295A  GLY      4.1     0.9    -      -       -      +
    296A  LEU*     3.3    27.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  LEU*     3.3    12.8    -      -       -      +
    158A  LEU*     1.3    81.7    -      -       -      +
    160A  LYS*     1.3    62.3    +      -       -      -
    163A  PHE*     5.6     0.9    -      -       -      -
    165A  LYS*     3.0     3.5    -      -       -      -
    166A  VAL*     2.5    43.7    +      -       -      +
    294A  PHE*     5.9     0.9    -      -       -      -
    295A  GLY      4.1    13.2    -      -       -      -
    296A  LEU      4.5     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    157A  LEU*     4.2    17.6    -      -       +      +
    159A  GLY*     1.3    75.7    -      -       -      -
    161A  GLY*     1.3    72.8    +      -       -      +
    163A  PHE*     3.7    10.8    -      -       -      -
    164A  GLY      3.4     9.6    -      -       -      +
    165A  LYS*     4.1     9.9    -      -       +      +
    184A  ARG*     5.4     9.0    -      -       -      +
    295A  GLY      5.0     4.0    -      -       -      +
    296A  LEU      5.5     1.2    +      -       -      -
----------------------------------------------------------
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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