Half sphere exposure: Difference between revisions
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Half Sphere Exposure (HSE) is a [[solvent exposure]] measure introduced in <ref>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. </ref> |
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It is found by counting the number of amino acid neighbors within two half spheres of chosen radius around the amino acid. |
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 CN sphere in two halves by the plane perpendicular to the |
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<math>C\beta-C\alpha</math> vector. HSE$_\alpha$ uses a pseudo-$C_\beta$ instead of the real $C_\beta$ atom for its |
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calculation. The position of this pseudo-$C_\beta$ atom (p$C_\beta$) is derived from the positions of preceding |
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$C_\alpha^{-1}$ and the following $C_\alpha^{+1}$. The $C_\alpha-\mbox{p}C_\beta$ vector is calculated by adding the |
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$C_\alpha^{-1}-C_\alpha^{0}$ and $C_\alpha^{+1}-C_\alpha^{0}$ vectors. This simple division of the CN sphere results in |
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two strikingly different measures, HSE-up and HSE-down. HSE-up is defined as the number of $C_\alpha$ atoms in the |
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upper half (containing the pseudo-$C_\beta$ atom) and analogously HSE-down is defined as the number of $C_\alpha$ atoms |
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in the opposite sphere. |
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This solvent exposure measure is closely related to [[contact number]] of an residue. |
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==References== |
==References== |
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Revision as of 05:08, 28 September 2006
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Half Sphere Exposure (HSE) is a solvent exposure measure introduced in [1] 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 CN sphere in two halves by the plane perpendicular to the vector. HSE$_\alpha$ uses a pseudo-$C_\beta$ instead of the real $C_\beta$ atom for its calculation. The position of this pseudo-$C_\beta$ atom (p$C_\beta$) is derived from the positions of preceding $C_\alpha^{-1}$ and the following $C_\alpha^{+1}$. The $C_\alpha-\mbox{p}C_\beta$ vector is calculated by adding the $C_\alpha^{-1}-C_\alpha^{0}$ and $C_\alpha^{+1}-C_\alpha^{0}$ vectors. 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 $C_\alpha$ atoms in the upper half (containing the pseudo-$C_\beta$ atom) and analogously HSE-down is defined as the number of $C_\alpha$ atoms in the opposite sphere.
This solvent exposure measure is closely related to contact number of an residue.
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.
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