DSSP (algorithm)

In protein structure, 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 DSSP is only mentioned once in the original paper by Kabsch and Sander 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 structure using a purely electrostatic definition. The energy is assumed to follow the form

$E=q_{1}q_{2}\left\{{\frac {1}{r_{ON}}}+{\frac {1}{r_{CH}}}-{\frac {1}{r_{OH}}}-{\frac {1}{r_{CN}}}\right\}\cdot 332\,\mathrm {kcal/mol}$

where q₁ = 0.42 and q₂ = 0.20.

This is based on assignment of partial charges of -0.42e and +0.20e to the carbonyl oxygen and amide hydrogen, and the opposite charges to the carbonyl carbon and amide nitrogen, respectively. The DSSP algorithm identifies a hydrogen bond if this energy E is less than -0.5 kcal/mol.

DSSP recognizes eight types of secondary structure (each identified by its own symbol), depending on the pattern of hydrogen bonds. The 310 helix, alpha helix and pi helix are symbolized as G, H and I, respectively, and are recognized by having a repetitive sequence of hydrogen bonds in which the donor residue is three, four, or five residues later in the backbone. DSSP recognizes two types of hydrogen-bond pairs in beta sheet structures, the parallel and antiparallel bridge; a lone bridge is symbolized by B (a beta bridge), whereas longer sets of H-bond pairs of the same type are symbolized by E for extended, which is equivalent to a beta sheet. Sheets with beta bulges are likewise symbolized by E. The remaining types are T for turn (featuring a hydrogen bond typical of a helix), S for a region 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