Contacts of the strand formed by residues 184 - 191 (chain C) in PDB entry 2ODE


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 ILE 184 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182C  THR      4.1     0.4    +      -       -      -
    183C  GLY*     1.3    78.8    -      -       -      +
    185C  VAL*     1.3    63.9    +      -       -      +
    186C  GLU*     4.3     0.9    +      -       +      -
    199C  PHE*     4.1    28.0    -      -       +      -
    200C  ASP      3.5     8.1    -      -       -      +
    201C  VAL*     4.3    15.9    -      -       +      -
    210C  LYS*     3.3    34.8    -      -       +      +
    211C  TRP*     4.6     2.5    -      -       +      -
    213C  HIS*     4.0    10.1    -      -       +      -
    214C  CYS*     4.4    17.3    -      -       +      -
     76D  THR      4.4     2.8    -      -       -      +
     77D  GLU*     2.7    30.6    +      -       -      +
     78D  PHE*     4.0    30.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 185 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181C  THR*     4.3    13.7    -      -       +      -
    182C  THR      4.7     0.9    -      -       -      +
    184C  ILE*     1.3    79.5    -      -       -      +
    186C  GLU*     1.3    69.2    +      -       -      +
    187C  THR*     4.0     4.3    +      -       -      +
    198C  MET      3.6     1.6    -      -       -      +
    199C  PHE*     3.4     1.8    -      -       -      -
    200C  ASP*     2.8    50.8    +      -       +      +
     77D  GLU*     4.0    10.8    -      -       -      +
    161D  ARG*     3.5    55.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 186 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184C  ILE*     4.2     1.4    +      -       +      -
    185C  VAL*     1.3    79.4    -      -       -      +
    187C  THR*     1.3    71.0    +      -       -      +
    188C  HIS*     6.2     0.2    -      -       -      +
    197C  LYS*     4.3    15.6    -      -       -      +
    198C  MET      3.3     6.5    -      -       -      +
    199C  PHE*     3.5    43.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 187 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     50C  VAL*     4.5    11.8    -      -       +      +
     58C  GLU*     4.0    15.9    +      -       -      +
    185C  VAL*     5.3     4.5    -      -       -      +
    186C  GLU*     1.3    78.8    -      -       -      +
    188C  HIS*     1.3    73.6    +      -       -      +
    197C  LYS*     3.7     2.8    -      -       -      -
    198C  MET*     2.7    72.7    +      -       +      +
    200C  ASP*     6.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 188 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58C  GLU*     3.5    14.0    -      -       -      +
    187C  THR*     1.3    82.1    +      -       -      +
    189C  PHE*     1.3    69.2    +      -       -      +
    195C  TYR*     3.2    39.3    +      +       +      +
    196C  PHE      3.1    13.9    -      -       -      +
    197C  LYS*     4.7     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 189 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     36C  LEU*     4.8     0.9    -      -       +      -
     53C  MET*     3.7    20.9    -      -       +      -
     57C  HIS*     3.7    30.7    -      +       +      +
     58C  GLU*     3.4    34.5    -      -       +      -
    188C  HIS*     1.3    81.2    -      -       -      +
    190C  THR*     1.3    63.6    +      -       -      +
    191C  PHE*     4.5     0.7    -      -       +      -
    195C  TYR*     3.8     3.5    -      -       -      -
    196C  PHE*     2.8    73.1    +      +       +      +
    198C  MET*     3.7    35.2    -      -       +      -
    336C  PHE*     3.7    22.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with THR 190 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31C  ALA*     5.6     4.7    -      -       +      -
     57C  HIS*     4.1    17.0    +      -       -      +
    189C  PHE*     1.3    79.9    +      -       -      +
    191C  PHE*     1.3    69.5    +      -       -      +
    193C  ASP*     4.5     9.6    -      -       -      +
    194C  LEU      3.2    21.7    +      -       -      +
    195C  TYR*     3.6    21.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 191 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  HIS*     3.2    42.2    -      +       +      +
    189C  PHE*     4.5     1.8    -      -       +      -
    190C  THR*     1.3    79.3    -      -       -      +
    192C  LYS*     1.3    83.4    +      -       +      +
    193C  ASP      3.2     1.8    -      -       -      -
    194C  LEU*     2.8    25.0    +      -       -      +
    196C  PHE*     3.9    13.2    -      +       +      -
    336C  PHE*     3.9     7.9    -      +       -      -
    337C  ASP*     3.2    29.6    -      -       -      -
    340C  THR*     3.4    38.8    -      -       +      -
----------------------------------------------------------
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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