DSSP (algorithm)

The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the paper describing this algorithm, where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins.

DSSP begins by identifying the hydrogen bonds of the protein using a purely electrostatic definition, assuming partial charges of -0.42 e and +0.20 e to the carbonyl oxygen and amide hydrogen respectively, their opposites assigned to the carbonyl carbon and amide nitrogen. A hydrogen bond is identified if E in the following equation is less than -0.5 kcal/mol:

$E=0.084\left\{{\frac {1}{r_{ON}}}+{\frac {1}{r_{CH}}}-{\frac {1}{r_{OH}}}-{\frac {1}{r_{CN}}}\right\}\cdot 332\,\mathrm {kcal/mol}$

Based on this, eight types of secondary structure are assigned. The 3₁₀ helix, α helix and π helix have symbols G, H and I and are recognized by having a repetitive sequence of hydrogen bonds in which the residues are three, four, or five residues apart respectively. Two types of beta sheet structures exist; a beta bridge has symbol B while longer sets of hydrogen bonds and beta bulges have symbol E. T is used for turns, featuring hydrogen bonds typical of helices, S is used for regions of high curvature (if the angle between the vector from C^α_i to C^α_i+2 and the vector from C^α_i-2 to C^α_i is less than 70°), and a blank if no other rule pertains. Additionally there is " " (space) as an amino acid secondary structure 'symbol' meaning "other", but can also be interpreted as "loop".

These eight types are usually grouped into three larger classes: helix (G, H and I), strand (E and B) and loop (all others).

External links

• DSSP Analysis tool