Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 1ZOO


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 VAL 130 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  GLY      4.1     1.1    -      -       -      +
    129A  ASN*     1.3    76.6    -      -       -      +
    131A  ASP*     1.3    63.9    +      -       -      +
    132A  LEU*     4.4     1.3    -      -       +      +
    165A  SER      3.1     6.7    +      -       -      -
    166A  TYR*     3.2    39.6    -      -       +      +
    167A  GLN      2.9    17.7    +      -       -      +
    227A  ARG*     2.8    19.9    +      -       -      +
    231A  THR*     3.4    12.3    -      -       +      +
    233A  VAL*     3.8    29.6    -      -       +      -
    307B  TYR*     4.0    26.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 131 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    129A  ASN      4.2     0.4    -      -       -      -
    130A  VAL*     1.3    69.4    -      -       -      +
    132A  LEU*     1.3    59.6    +      -       -      +
    167A  GLN*     3.7     9.4    +      -       -      +
    183A  PHE*     3.6    22.0    -      -       +      -
    220A  PHE*     3.4    17.7    -      -       +      -
    225A  GLY      5.3     0.2    -      -       -      -
    226A  ALA*     3.4    11.5    -      -       -      +
    227A  ARG*     2.7    72.9    +      -       -      +
    230A  ALA*     3.9     7.6    -      -       +      -
    231A  THR      2.9    12.1    +      -       -      +
    232A  LYS*     3.5     2.7    -      -       +      +
    233A  VAL      2.9    22.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 132 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130A  VAL*     3.7     6.0    +      -       +      -
    131A  ASP*     1.3    74.3    -      -       -      +
    133A  VAL*     1.3    72.7    +      -       -      +
    134A  PHE*     3.9    23.6    -      -       +      -
    157A  VAL*     5.9     2.9    -      -       +      -
    161A  LEU*     5.8     2.2    -      -       +      -
    166A  TYR*     4.4    17.9    -      -       +      -
    167A  GLN      3.0     8.4    +      -       -      +
    168A  PHE*     3.4    26.7    -      -       +      -
    169A  ALA      3.1    22.9    +      -       -      +
    183A  PHE*     3.5     1.8    -      -       -      -
    233A  VAL*     3.3    33.4    -      -       +      -
    235A  ILE*     3.5    28.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  LEU*     1.3    77.2    -      -       -      +
    134A  PHE*     1.3    66.5    +      -       -      +
    169A  ALA*     3.4     9.0    -      -       +      +
    171A  VAL*     4.4    10.1    -      -       +      -
    183A  PHE*     3.5    27.1    -      -       +      -
    215A  VAL*     3.7    19.5    -      -       +      -
    219A  VAL*     3.8    17.3    -      -       +      -
    220A  PHE*     3.7    16.8    -      -       +      -
    233A  VAL      2.8    10.7    +      -       -      +
    234A  LEU*     3.3    24.5    -      -       +      +
    235A  ILE      2.8    31.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 134 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132A  LEU*     3.9    17.5    -      -       +      -
    133A  VAL*     1.3    73.8    -      -       -      +
    135A  LEU*     1.3    60.6    +      -       -      +
    136A  PHE*     3.8     1.1    +      -       -      -
    153A  PHE*     5.0     3.4    -      +       -      -
    154A  MET*     3.4    62.6    -      -       +      -
    157A  VAL*     4.1    24.0    -      -       +      -
    158A  MET*     3.7    28.7    -      -       +      -
    168A  PHE*     3.8    17.5    -      +       +      -
    169A  ALA      2.9    16.2    +      -       -      +
    170A  ALA*     3.3     1.4    -      -       +      +
    171A  VAL      2.8    27.0    +      -       -      +
    181A  PHE*     5.5     0.2    -      +       -      -
    235A  ILE*     3.5    31.2    -      -       +      +
    237A  ILE*     4.8     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133A  VAL      3.9     0.8    +      -       -      -
    134A  PHE*     1.3    70.2    -      -       -      +
    136A  PHE*     1.3    58.4    +      -       -      +
    171A  VAL*     3.3    34.3    -      -       +      +
    173A  PHE*     3.7    20.8    -      -       +      -
    208A  THR*     5.5     0.2    -      -       +      -
    211A  ALA*     3.9    16.6    -      -       +      +
    212A  ILE*     3.8    41.1    -      -       +      +
    215A  VAL*     4.0    11.0    -      -       +      -
    234A  LEU*     3.9    17.5    -      -       +      -
    235A  ILE      2.9    10.8    +      -       -      +
    236A  ILE*     3.3    18.8    -      -       +      +
    237A  ILE*     3.0    24.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 136 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134A  PHE      4.2     3.1    -      -       -      -
    135A  LEU*     1.3    71.7    -      -       -      +
    137A  ASP*     1.3    60.3    +      -       -      +
    147A  PHE*     3.7    33.7    -      +       -      -
    150A  ILE*     3.8    23.3    -      -       +      -
    151A  LEU*     3.8    22.2    -      -       +      -
    154A  MET*     3.6    33.4    -      -       +      -
    170A  ALA*     4.2     4.9    -      -       +      -
    171A  VAL      2.9    34.1    +      -       -      -
    172A  GLN*     3.4    24.3    -      -       +      -
    173A  PHE*     2.8    35.6    +      -       -      -
    180A  GLU*     4.0    13.0    -      -       +      -
    196A  LEU*     5.0     0.7    -      -       +      -
    199A  VAL*     4.0     6.5    -      -       +      -
    237A  ILE*     3.7     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 137 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136A  PHE*     1.3    73.0    -      -       -      +
    138A  GLY*     1.3    58.0    +      -       -      +
    139A  SER*     2.7    45.9    +      -       -      -
    142A  LEU*     3.2    19.3    -      -       +      +
    147A  PHE*     3.7     9.6    -      -       -      -
    150A  ILE*     4.0     8.0    -      -       +      +
    173A  PHE*     3.4    13.4    -      -       +      -
    206A  THR*     3.8    14.1    -      -       -      +
    237A  ILE      2.9    20.5    +      -       -      +
    238A  THR*     2.7    28.4    +      -       -      +
    239A  ASP*     3.0    19.6    +      -       -      +
    240A  GLY      3.9     0.2    +      -       -      -
    350A   MG      3.8     0.5    -      -       -      -
----------------------------------------------------------
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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