Half sphere exposure
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Half Sphere Exposure (HSE) is a protein solvent exposure measure that was first introduced in [1]. Like all solvent exposure measures it measures how buried amino acid residues are in a protein. It is found by counting the number of amino acid neighbors within two half spheres of chosen radius around the amino acid. The calculation of HSE is found by dividing a contact number (CN) sphere in two halves by the plane perpendicular to the Cβ-Cα vector. This simple division of the CN sphere results in two strikingly different measures, HSE-up and HSE-down. HSE-up is defined as the number of Cα atoms in the upper half (containing the pseudo-Cβ atom) and analogously HSE-down is defined as the number of Cα atoms in the opposite sphere.
If only Cα atoms are available (as is the case for many simplified representations of protein structure), a related measure, called HSEα, can be used. HSEα uses a pseudo-Cβ instead of the real Cβ atom for its calculation. The position of this pseudo-Cβ atom (pCβ) is derived from the positions of preceding Cα-1 and the following Cα+1. The Cα-pCβ vector is calculated by adding the Cα-1-Cα0 and Cα+1-Cα0 vectors.
HSE is used in predicting discontinuous B-cell epitopes [2] and can be predicted online from sequence [3].
[edit] References
- ^ Hamelryck T. (2005) An amino acid has two sides: A new 2D measure provides a different view of solvent exposure. Proteins Struct. Func. Bioinf. 59:38-48.
- ^ PEPITO: Improved discontinuous B-cell epitope prediction using multiple distance thresholds and Half Sphere Exposure. Michael J. Sweredoski and Pierre Baldi, Bioinformatics, 2008
- ^ http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/hse/help.html (accessed May 13, 2008)
