DSSP (protein)
Encyclopedia
The DSSP algorithm is the standard method for assigning secondary structure
to the amino acid
s 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 bond
s 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:
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 bulge
s have symbol E. T
is used for turns, featuring hydrogen bonds typical of helices, S is used for regions of high curvature (where the angle between
and 
is less than 70°), and a blank (or space) is used if no other rule applies, referring to loops. These eight types are usually grouped into three larger classes: helix (G, H and I), strand (E and B) and loop (all others).
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
to the amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s 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
Pascal (programming language)
Pascal is an influential imperative and procedural programming language, designed in 1968/9 and published in 1970 by Niklaus Wirth as a small and efficient language intended to encourage good programming practices using structured programming and data structuring.A derivative known as Object Pascal...
program that implements the algorithm Define Secondary Structure of Proteins.
DSSP begins by identifying the hydrogen bond
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
s 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:
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
Beta sheet
The β sheet is the second form of regular secondary structure in proteins, only somewhat less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet...
structures exist; a beta bridge has symbol B while longer sets of hydrogen bonds and beta bulge
Beta bulge
A beta bulge is a localized disruption of the regular hydrogen bonding of a beta sheet, usually by inserting a residue with helical dihedral angles into one or both H-bonded β-strands.-Types:...
s have symbol E. T
E.T. the Extra-Terrestrial
E.T. the Extra-Terrestrial is a 1982 American science fiction film co-produced and directed by Steven Spielberg, written by Melissa Mathison and starring Henry Thomas, Dee Wallace, Robert MacNaughton, Drew Barrymore, and Peter Coyote...
is used for turns, featuring hydrogen bonds typical of helices, S is used for regions of high curvature (where the angle between
and is less than 70°), and a blank (or space) is used if no other rule applies, referring to loops. These eight types are usually grouped into three larger classes: helix (G, H and I), strand (E and B) and loop (all others).