Contacts of the helix formed by residues 258 - 263 (chain Z) in PDB entry 1O1F


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 PRO 258 (chain Z).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185Z  LEU*     5.1     0.9    -      -       +      -
    217Z  CYS*     4.1     2.9    -      -       +      -
    218Z  TYR      3.2    22.2    -      -       -      +
    219Z  VAL*     3.3    26.5    -      -       +      -
    223Z  PHE*     4.1     2.7    -      -       -      -
    254Z  ARG      3.7     7.9    -      -       -      +
    255Z  PHE      3.6     3.6    -      -       -      +
    257Z  CYS*     1.3    89.0    -      -       +      +
    259Z  GLU*     1.4    59.3    +      -       -      +
    260Z  THR      2.9     5.4    -      -       -      -
    261Z  LEU*     2.9    25.9    +      -       +      +
    262Z  PHE*     3.8     7.1    -      -       -      -
    306Z  TYR*     3.6    44.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 259 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    223Z  PHE*     3.1    59.0    -      -       +      +
    224Z  GLU*     4.5     0.5    +      -       -      -
    227Z  MET*     3.9    23.0    -      -       -      +
    255Z  PHE*     3.1    24.5    +      -       -      +
    256Z  ARG*     3.9     2.2    -      -       -      +
    257Z  CYS      3.3     0.4    -      -       -      -
    258Z  PRO*     1.4    73.4    -      -       -      +
    260Z  THR*     1.4    59.8    +      -       -      +
    262Z  PHE*     3.2     2.2    +      -       -      -
    263Z  GLN*     2.7    59.7    +      -       -      +
    266Z  PHE*     3.6    27.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 260 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180Z  LEU*     4.4     3.5    -      -       +      +
    185Z  LEU*     4.3    16.2    -      -       +      -
    188Z  TYR*     3.2    25.0    -      -       +      -
    256Z  ARG      3.4     2.1    +      -       -      -
    257Z  CYS      2.6    21.0    +      -       -      -
    258Z  PRO      2.9     0.8    -      -       -      -
    259Z  GLU*     1.4    77.0    -      -       -      +
    261Z  LEU*     1.3    62.5    +      -       -      +
    263Z  GLN      2.7    28.4    -      -       -      +
    264Z  PRO*     3.4     5.4    -      -       -      +
    266Z  PHE*     3.9     5.4    -      -       +      -
    267Z  ILE*     3.6    47.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 261 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155Z  SER*     4.8     4.3    -      -       -      +
    178Z  LEU*     5.1     0.7    -      -       -      +
    180Z  LEU*     3.5    31.6    -      -       +      +
    185Z  LEU*     4.0    16.2    -      -       +      -
    219Z  VAL*     5.6     0.7    -      -       +      -
    258Z  PRO*     2.9    14.6    +      -       +      +
    260Z  THR*     1.3    78.8    -      -       -      +
    262Z  PHE*     1.4    63.2    +      -       +      +
    263Z  GLN      4.9     0.2    -      -       -      -
    264Z  PRO*     4.7     1.6    -      -       -      +
    273Z  GLY*     3.8     2.8    -      -       -      -
    274Z  ILE*     3.2    52.1    +      -       +      +
    303Z  THR*     4.1    17.0    -      -       +      +
    304Z  THR*     6.5     0.2    -      -       +      -
    306Z  TYR*     4.0    30.3    -      -       +      -
    309Z  ILE*     4.3    13.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 262 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    219Z  VAL*     3.5    29.2    -      -       +      -
    223Z  PHE*     3.9     3.8    -      +       -      -
    258Z  PRO      3.8    14.4    -      -       -      -
    259Z  GLU*     3.2     2.4    +      -       -      -
    261Z  LEU*     1.4    78.8    -      -       +      +
    263Z  GLN*     1.3    72.7    +      -       -      +
    264Z  PRO*     3.6     8.3    -      -       -      +
    273Z  GLY*     4.0     4.0    +      -       -      -
    274Z  ILE*     3.6    26.9    -      -       +      -
    275Z  HIS*     3.4    41.1    -      -       +      +
    309Z  ILE*     4.6    10.8    -      -       +      -
    312Z  ARG*     3.3    50.9    -      -       +      +
    313Z  MET*     4.2    17.7    -      -       +      -
    316Z  GLU*     4.0     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 263 (chain Z). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    259Z  GLU*     2.7    63.8    +      -       -      +
    260Z  THR*     2.7    24.0    -      -       -      +
    262Z  PHE*     1.3    93.4    -      -       -      +
    264Z  PRO*     1.3    59.7    -      -       -      +
    265Z  SER*     3.1    20.1    +      -       -      +
    266Z  PHE*     3.5    25.7    +      -       +      +
    312Z  ARG*     3.4    10.7    +      -       -      +
----------------------------------------------------------
 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