Contacts of the strand formed by residues 231 - 238 (chain B) 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 THR 231 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128B  GLY*     5.7     2.3    +      -       -      -
    129B  ASN      2.8    17.5    +      -       -      -
    130B  VAL*     3.4    14.6    -      -       +      +
    131B  ASP      2.9    25.1    +      -       -      +
    229B  ASP      3.7     1.5    +      -       -      -
    230B  ALA*     1.3    71.0    -      -       -      +
    232B  LYS*     1.3    63.9    +      -       -      +
    233B  VAL*     4.3     5.6    -      -       +      -
    255B  ILE*     3.8    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 232 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    131B  ASP*     3.5     7.2    -      -       +      +
    216B  ALA      5.3     3.4    +      -       -      -
    220B  PHE*     3.7    48.2    +      -       +      +
    228B  PRO      5.5     6.3    -      -       -      -
    230B  ALA      3.4     9.8    +      -       -      +
    231B  THR*     1.3    73.6    -      -       -      +
    233B  VAL*     1.3    63.9    +      -       -      +
    253B  ASP*     4.7    20.5    +      -       -      +
    254B  ILE*     3.8    28.4    -      -       +      +
    255B  ILE*     3.0    26.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 233 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  VAL*     3.9    20.9    -      -       +      -
    131B  ASP      3.0     8.2    +      -       -      +
    132B  LEU*     3.3    31.3    -      -       +      -
    133B  VAL      2.9    24.9    +      -       -      -
    166B  TYR*     6.0     0.2    -      -       +      -
    220B  PHE*     3.7     4.9    -      -       -      -
    231B  THR*     4.2     4.5    -      -       +      +
    232B  LYS*     1.3    81.2    -      -       -      +
    234B  LEU*     1.3    63.2    +      -       -      +
    235B  ILE*     4.0    15.0    -      -       +      -
    254B  ILE*     3.8     2.5    -      -       -      -
    255B  ILE*     3.4    28.9    -      -       +      +
    257B  TYR*     4.5    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 234 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  VAL*     3.2    23.8    -      -       +      +
    135B  LEU*     3.9    18.8    -      -       +      -
    212B  ILE*     4.2    25.8    -      -       +      +
    215B  VAL*     3.9    35.2    -      -       +      -
    220B  PHE*     5.2     0.7    -      -       +      -
    233B  VAL*     1.3    75.0    -      -       -      +
    235B  ILE*     1.3    64.6    +      -       -      +
    236B  ILE*     4.0    14.6    -      -       +      -
    254B  ILE*     3.6    21.7    -      -       +      +
    255B  ILE      2.8    10.2    +      -       -      +
    256B  ARG*     3.5    15.5    -      -       +      +
    257B  TYR      2.9    28.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 235 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  LEU*     3.6    29.2    -      -       +      -
    133B  VAL      2.9     8.9    +      -       -      -
    134B  PHE*     3.4    22.4    -      -       +      -
    135B  LEU      2.8    25.4    +      -       -      +
    153B  PHE*     4.6     5.4    -      -       +      -
    233B  VAL*     4.0     9.4    -      -       +      -
    234B  LEU*     1.3    72.1    -      -       -      +
    236B  ILE*     1.3    59.7    +      -       -      +
    237B  ILE*     3.8    20.1    +      -       +      +
    257B  TYR*     3.7    37.2    -      -       +      -
    259B  ILE*     4.2    17.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 236 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135B  LEU*     3.4    29.2    -      -       +      +
    173B  PHE*     4.5     6.5    -      -       +      -
    208B  THR*     4.3    13.9    -      -       +      -
    212B  ILE*     3.8    23.1    -      -       +      -
    234B  LEU*     4.0    22.4    -      -       +      -
    235B  ILE*     1.3    73.7    -      -       -      +
    237B  ILE*     1.3    60.2    +      -       -      +
    238B  THR*     4.2     1.3    -      -       +      -
    256B  ARG*     4.4     7.2    -      -       +      -
    257B  TYR      2.9    21.4    +      -       -      +
    258B  ILE*     3.2    26.9    -      -       +      +
    259B  ILE*     2.7    34.8    +      -       -      +
    277B  PHE*     4.2    16.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 237 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  PHE*     4.7     4.0    -      -       +      -
    135B  LEU      2.9     9.6    +      -       -      +
    136B  PHE*     4.5     5.2    -      -       +      -
    137B  ASP*     2.9    28.3    +      -       -      +
    150B  ILE*     4.2    29.6    -      -       +      +
    153B  PHE*     3.9    29.4    -      -       +      -
    154B  MET*     4.1    20.0    -      -       +      -
    173B  PHE*     4.1     1.4    -      -       -      -
    235B  ILE*     4.1    12.6    -      -       +      +
    236B  ILE*     1.3    77.4    -      -       -      +
    238B  THR*     1.3    64.3    +      -       -      +
    259B  ILE*     3.6    21.3    -      -       +      -
    261B  ILE*     3.8    25.4    -      -       +      -
    295B  LEU*     4.7     5.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  ASP*     2.7    27.2    +      -       -      -
    150B  ILE*     5.9     1.6    -      -       -      -
    173B  PHE*     4.4     9.2    -      -       -      -
    206B  THR*     4.0     4.5    -      -       -      +
    208B  THR*     5.0     3.7    +      -       +      -
    236B  ILE*     4.9     2.0    -      -       +      -
    237B  ILE*     1.3    76.6    -      -       -      +
    239B  ASP*     1.3    63.7    +      -       -      +
    240B  GLY      3.1    17.2    +      -       -      +
    258B  ILE*     4.0    26.5    -      -       +      -
    259B  ILE      2.9    18.5    +      -       -      +
    260B  GLY*     3.4     1.0    -      -       -      -
    261B  ILE*     2.9    28.5    +      -       -      +
    265B  PHE*     3.8     3.3    -      -       +      -
    274B  LEU*     4.1    14.1    -      -       +      -
----------------------------------------------------------
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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