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Database of Interacting Proteins
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Interaction types demonstrated by individual experiments
are reported according to terminology that attempts to
reflect the amount of information provided by individual
experiments; this might vary from information that a set
of proteins might form one or more complexes to detailed
information about physical contacts or covalent bonds. In
case of doubt, please, consult the table below as the terms,
when used within DIP, convey information different
then the common usage might imply.
Interaction
Type |
Description |
DIP/PSI-MI CV |
| CV ID |
Name |
| association |
Interactions defined within DIP as associations correspond to
experimentally identified groups of proteins that might form
one or more physical complexes. This term is used when
experimental evidence, even without any error, is too weak to
guarantee that all the interacting molecules are present within
the same physical complex. Most notably association term
is used to annotate lists of more than 2 proteins identified
through affinity approaches based on direct interaction of only
one of the molecules (bait) with the affinity matrix. In such
cases experiments demonstrate physical interactions within each
bait-prey pair. As affinity experiments do not demonstrate
that prey-prey pairs exist within the same complex (in fact,
all preys might be mutually exclusive when competing for the
same binding site within the bait protein) we do not
use physical interaction term.
|
MI:0914 |
association |
| physical |
Interactions defined as physical within DIP correspond to
individual physical complexes formed by all the listed
molecules.
NOTE: the use of physical interaction within DIP ensures
that, within experimental error, every pair of interacting
molecules has been observed within the same physical complex.
Physical interaction term is also used when a given experiment
does not eliminate the possiblity that additional unidentified
proteins present in the sample provide a bridge connecting two
proteins within a physical complex.
|
MI:0915 |
physical
associaton |
| direct |
Interaction is defined as direct when it is demonstrated that,
for each pair of molecules listed as participating in a given
interaction, there is at least one instance of such a pair
within the complex that is in direct (van der Waals) contact.
NOTE: according to this definition any homo-oligomer is reported as
a direct interaction although some subunits might not be in
direct contact.
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MI:0407 |
direct
interaction |
| covalent |
Interaction is defined as covalent when all participating molecules
are connected through covalent bonds. For proteins, the most common
sub-type of covalent interaction is disulfide bond (MI:0408) formed
by S-S bond between two cysteins.
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MI:0195 |
covalent
binding |
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