Order of Cross Link
Definition:
Cross Links are defined as contacts (any type from possible
5 classes: 1. Hydrophobic interaction, 2. Hydrogen Bonding, 3. Aromatic
Stacking, 4. Salt bridging, 5. Cystein-bridging) established among residues
that are far apart in the protein primary sequence, but are close in its
3D fold. The order of cross link is identified as a number
of such cross-links established 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 Link Order even though several could
be registered (a central amino acid can make more than one contact 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.
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 Link values.
Left mouse click: no action
Right mouse click: on any of the "Order of Cross Link" will
generate following menu and actions:
