Protein Loop Geometry
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Four parameters were defined to describe the protein loop geometry.
An axis for an alpha or beta secondary structure was defined based on the
shortest of the principal moments of inertia of that structure. The
geometry of each motif was defined by four internal co-ordinates. M1 and M2
are the axis vectors of the secondary structure. Loop geometry is defined
by four parameters (The angles are in greek font in the figure.
- D - distance between alpha helix or beta strand which brace the
loop.
- Theta - the packing angle, i.e, the angle between axis M1 and M2.
- Delta - the hoist angle, i.e., the angle between axis M1 and
vector of D.
- Rho - the meridian angle, i.e., the angle between axis M2 and the plane.
[ alpha-alpha
| alpha-beta
| beta-alpha
| beta-beta links
| beta-hairpins ]
Last modified: Mon, 18-August-1997