Contacts of the strand formed by residues 233 - 237 (chain C) in PDB entry 1SOZ


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 233 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191C  GLN*     3.3     9.0    -      -       -      +
    192C  THR*     3.0    40.1    +      -       -      -
    194C  ALA      5.3     1.7    +      -       -      -
    196C  ILE*     3.7    17.0    -      -       -      -
    218C  LEU      3.4     9.4    -      -       -      -
    219C  SER*     4.0     0.9    -      -       -      -
    231C  GLY      3.9     0.2    -      -       -      -
    232C  ILE*     1.3    75.1    -      -       -      +
    234C  PHE*     1.3    67.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 234 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164B  LEU*     4.3    10.5    -      -       +      -
    178C  ARG*     4.1    11.7    -      -       -      -
    180C  GLY*     3.4    37.9    -      -       -      -
    181C  LEU*     4.5    10.5    -      -       +      -
    189C  PHE*     3.8    27.1    -      +       +      -
    190C  LEU      3.2    13.2    -      -       -      -
    191C  GLN*     3.8    22.9    -      -       +      -
    192C  THR*     5.0     2.2    -      -       -      +
    196C  ILE*     4.0     4.3    -      -       -      +
    216C  ASN*     3.7     2.6    -      -       -      -
    217C  THR      2.8    20.6    +      -       -      -
    218C  LEU      2.7    25.7    +      -       -      +
    220C  PHE*     4.1    22.4    -      +       +      -
    232C  ILE*     3.9    28.0    -      -       +      -
    233C  GLY*     1.3    77.2    -      -       -      -
    235C  ALA*     1.3    62.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 235 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189C  PHE*     3.3    11.8    -      -       -      -
    190C  LEU*     2.8    35.5    +      -       +      +
    192C  THR*     5.3     2.0    -      -       +      +
    205C  LEU*     4.3    13.0    -      -       +      -
    214C  GLY*     4.2     6.1    -      -       -      -
    215C  ILE      3.2    22.2    -      -       -      +
    216C  ASN*     3.5    23.1    -      -       -      +
    217C  THR      3.9     0.7    -      -       -      +
    234C  PHE*     1.3    75.6    -      -       -      +
    236C  ILE*     1.3    61.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 236 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94C  ASN*     4.4     5.2    -      -       -      +
    125C  THR*     3.2    28.7    -      -       -      +
    127C  LEU*     3.9    18.2    -      -       +      -
    187C  GLN*     6.5     0.9    -      -       +      -
    188C  ASN      5.3     0.9    -      -       -      +
    189C  PHE*     3.8    17.3    -      -       +      -
    190C  LEU*     5.3     0.2    -      -       -      -
    214C  GLY*     3.0     3.1    -      -       -      -
    215C  ILE*     2.8    36.5    +      -       +      +
    217C  THR*     3.0    26.0    -      -       +      +
    235C  ALA*     1.3    71.7    -      -       -      +
    237C  PRO*     1.3    82.9    -      -       +      +
    238C  PHE*     3.3     0.7    +      -       -      -
    240C  LEU*     3.6    31.9    -      -       +      -
    241C  ALA*     3.9    10.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 237 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188C  ASN*     2.9    48.7    -      -       -      +
    189C  PHE      4.5     0.2    -      -       -      -
    190C  LEU*     4.4    19.7    -      -       +      +
    213C  MET      3.7     7.9    -      -       -      +
    235C  ALA      3.7     5.5    -      -       -      +
    236C  ILE*     1.3    91.5    -      -       +      +
    238C  PHE*     1.3    59.1    +      -       +      +
    239C  GLN*     2.8    18.1    +      -       +      +
    240C  LEU*     3.0    11.0    +      -       +      +
    241C  ALA      3.0    17.0    +      -       -      -
----------------------------------------------------------
 Back to top of page


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