DSSP begins by identifying the intra-backbone
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} where the r_{AB} terms indicate the distance between atoms A and B, taken from the carbon (C) and oxygen (O) atoms of the C=O group and the nitrogen (N) and hydrogen (H) atoms of the N-H group. Based on this, nine 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 (where the angle between \overrightarrow{C_i^\alpha C_{i+2}^\alpha} and \overrightarrow{C_{i-2}^\alpha C_i^\alpha} is at least 70°). As of DSSP version 4,
PPII helices are also detected based on a combination of backbone torsion angles and the absence of hydrogen bonds compatible with other types. PPII helices have symbol
P. 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 (
S,
T, and
C, where
C sometimes is represented also as blank space). ==π helices==