Contacts of the strand formed by residues 202 - 208 (chain C) in PDB entry 3OEE


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 TYR 202 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  LEU*     3.4    37.2    -      -       +      -
    192C  ASN*     5.3     0.9    -      -       -      -
    197C  GLU*     2.6    32.1    +      -       -      -
    200C  LYS*     3.1    43.6    +      -       +      -
    201C  LEU*     1.3    73.2    -      -       -      +
    203C  CYS*     1.3    60.4    +      -       -      +
    204C  VAL*     5.2     0.9    -      -       -      -
    230C  TYR*     3.6    17.3    -      -       +      +
    259C  PHE*     3.5    41.5    -      +       +      -
    264C  LYS*     4.6    13.2    -      -       +      -
    265C  HIS      2.9    19.3    +      -       -      +
    266C  ALA*     3.0    11.5    -      -       -      +
    267C  LEU      3.0    21.7    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 203 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  LEU*     5.1     0.3    -      -       -      +
    185C  ILE*     3.7    46.0    -      -       +      -
    188C  GLN*     4.0     8.1    -      -       -      -
    201C  LEU      3.5    15.7    -      -       -      -
    202C  TYR*     1.3    73.3    -      -       -      +
    204C  VAL*     1.3    64.3    +      -       -      +
    205C  TYR      4.3     0.2    -      -       -      -
    230C  TYR*     3.0    18.4    +      -       -      +
    231C  SER*     3.0    23.4    -      -       -      +
    232C  ILE*     2.9    24.9    +      -       -      +
    267C  LEU*     3.7    15.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 204 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185C  ILE*     5.7     0.2    -      -       -      -
    202C  TYR      4.8     2.7    -      -       -      +
    203C  CYS*     1.3    80.9    -      -       -      +
    205C  TYR*     1.3    62.5    +      -       -      +
    206C  VAL*     4.4     9.2    -      -       +      -
    232C  ILE*     3.4    31.4    -      -       +      +
    234C  VAL*     4.7     8.1    -      -       +      -
    252C  ALA*     4.1    21.5    -      -       +      +
    255C  ILE*     4.5     3.4    -      -       +      -
    256C  GLY*     4.2    21.1    -      -       -      -
    259C  PHE*     4.7     6.1    -      -       +      -
    266C  ALA*     4.9     1.6    -      -       +      -
    267C  LEU      2.9    15.0    +      -       -      +
    268C  ILE*     3.4    14.7    -      -       +      -
    269C  VAL*     2.9    30.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 205 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    178C  THR*     3.4    17.0    +      -       +      +
    181C  ALA*     5.2     1.8    -      -       +      -
    182C  LEU*     5.8     1.3    -      -       +      -
    185C  ILE*     4.5    15.9    -      -       +      -
    203C  CYS      4.3     0.2    -      -       -      -
    204C  VAL*     1.3    73.9    -      -       -      +
    206C  VAL*     1.3    59.4    +      -       -      +
    207C  ALA*     4.1    13.9    -      -       +      -
    210C  GLN*     3.0    26.1    +      -       -      -
    215C  VAL*     5.4     2.7    -      -       +      -
    218C  LEU*     3.8    35.7    -      -       +      +
    222C  LEU*     5.8     1.1    -      -       +      -
    231C  SER*     5.9     1.1    -      -       -      -
    232C  ILE      3.0     8.3    +      -       -      +
    233C  ILE*     3.5    26.1    -      -       +      +
    234C  VAL      2.9    26.9    +      -       -      +
    269C  VAL*     3.6    26.9    -      -       +      -
    271C  ASP*     2.5    40.9    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 206 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204C  VAL*     4.4     2.2    -      -       +      -
    205C  TYR*     1.3    79.3    -      -       -      +
    207C  ALA*     1.3    58.3    +      -       -      +
    208C  VAL*     3.5    18.9    +      -       +      +
    234C  VAL*     3.3    10.3    -      -       +      +
    248C  ALA*     4.0    26.9    -      -       +      +
    249C  PRO*     4.1     4.9    -      -       +      -
    252C  ALA*     3.5    25.8    -      -       +      -
    268C  ILE*     4.1    10.1    -      -       +      -
    269C  VAL      2.8    20.6    +      -       -      +
    270C  TYR*     3.8    17.9    -      -       +      -
    271C  ASP*     2.8    31.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 207 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205C  TYR*     3.8    12.4    +      -       +      -
    206C  VAL*     1.3    70.6    -      -       -      +
    208C  VAL*     1.3    58.3    +      -       -      +
    209C  GLY      4.1     0.7    -      -       -      -
    210C  GLN*     3.5    25.6    -      -       +      +
    215C  VAL*     3.9    23.1    -      -       +      -
    233C  ILE*     5.3     0.6    -      -       +      +
    234C  VAL      2.8    11.9    +      -       -      +
    235C  ALA*     3.4     8.6    -      -       +      -
    236C  ALA      2.7    33.4    +      -       -      +
    237C  THR*     4.8     1.1    -      -       +      -
    271C  ASP      3.3     5.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 208 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206C  VAL*     3.9    25.4    -      -       +      +
    207C  ALA*     1.3    78.7    -      -       -      +
    209C  GLY*     1.3    64.0    +      -       -      +
    210C  GLN*     3.1     5.6    +      -       -      +
    236C  ALA      3.2     2.2    -      -       -      +
    245C  GLN*     3.5    39.3    -      -       +      +
    248C  ALA*     4.4     2.9    -      -       +      -
    249C  PRO*     4.2    17.3    -      -       +      -
    270C  TYR*     5.6     1.1    -      -       +      -
    271C  ASP      2.8    16.4    +      -       -      +
    272C  ASP      3.8    16.8    +      -       -      +
    273C  LEU*     6.2     0.7    -      -       +      -
    275C  LYS*     3.4    17.2    -      -       -      +
    276C  GLN*     3.9    21.1    -      -       +      +
----------------------------------------------------------
 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