Order of Cross Presence
Definition:
Cross Presence is defined as presence within a probing
sphere (centered at a given residue) of any residue that is far apart
in the protein primary sequence from the central residue, but is close
in its 3D fold. The order is identified as a number of such cross-presence
encounters among independent stretches of sequence (the size of which
varies from 15, 20 to 30 Amino Acids). Only a single occurrence is counted
for the Cross Presence Order even though several could be registered (a
central amino acid can make more than one "encounter" and each
one of those can be established with a different amino acid belonging
to a same stretch of probing sequence size (15, 20 or 30)). The higher
the order, the more important that residue must be for the protein folding/stability.
Order of Cross-Presence normally is higher than the order of Cross Link
for any given amino acid, due to the simple fact the not all "Present"
residues will actually engage in one of 5 possible contact types.
This specific STING parameter is calculated by varying three input parameters:
1. the size of the sequence stretch separating the residues in contact
(15, 20 or 30),
2. the size of the radius of the probing sphere within which the contacts
are counted (3.5, 5 and 8.5 Angstroms), and
3. The center of the probing sphere (Calpha, Cbeta
or Last Heavy
Atom [LHA] in a side chain).
Placing the cursor above this element: pop-up area will show the position
(sequence number and AA three letter code) for selected amino acid and
the Order of Cross Presence values.
Left mouse click: no action
Right mouse click: on any of the "Order of Cross Presence" will
generate following menu and actions:
