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The `!DSSP`! algorithm is the standard method for assigning `F33f`_`[secondary structure`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Secondary_structure]`_`f to the `F33f`_`[amino acids`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Amino_acid]`_`f of a protein, given the atomic-resolution coordinates of the protein. The abbreviation is only mentioned once in the 1983 paper describing this algorithm,`:cite-ref-kabsch1983-2-0[`F5bf`_`[2`#cite-note-kabsch1983-2]`_`f] where it is the name of the `F33f`_`[Pascal`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Pascal_(programming_language)]`_`f program that implements the algorithm `*Define Secondary Structure of Proteins`*.

>>Contents

• `F0af`_`[Algorithm`#algorithm]`_`f

• `F0af`_`[π helices`#helices]`_`f

• `F0af`_`[Variants`#variants]`_`f

• `F0af`_`[See also`#see-also]`_`f

• `F0af`_`[References`#references]`_`f

• `F0af`_`[External links`#external-links]`_`f

-─

>>Algorithm

DSSP begins by identifying the intra-backbone `F33f`_`[hydrogen bonds`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Hydrogen_bond]`_`f 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 { 1 r O N + 1 r C H − − 1 r O H − − 1 r C N } ⋅ ⋅ 332 k c a l / m o l {\\displaystyle 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 A B {\\displaystyle 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 `F33f`_`[310 helix`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=310_helix]`_`f, `F33f`_`[α helix`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Α_helix]`_`f and `F33f`_`[π helix`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Π_helix]`_`f 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 `F33f`_`[beta sheet`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Beta_sheet]`_`f structures exist; a beta bridge has symbol `!B`! while longer sets of hydrogen bonds and `F33f`_`[beta bulges`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Beta_bulge]`_`f 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 C i α α C i + 2 α α → → {\\displaystyle {\\overrightarrow {C_{i}^{\\alpha }C_{i+2}^{\\alpha }}}} and C i − − 2 α α C i α α → → {\\displaystyle {\\overrightarrow {C_{i-2}^{\\alpha }C_{i}^{\\alpha }}}} is at least 70°). As of DSSP version 4, `F33f`_`[PPII helices`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Polyproline_helix]`_`f 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.`:cite-ref-dsspmanual-3-0[`F5bf`_`[3`#cite-note-dsspmanual-3]`_`f] 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

In the original DSSP algorithm, residues were preferentially assigned to α helices, rather than `F33f`_`[π helices`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Pi_helix]`_`f. In 2011, it was shown that DSSP failed to annotate many "cryptic" π helices, which are commonly flanked by α helices.`:cite-ref-pmid20888342-4-0[`F5bf`_`[4`#cite-note-pmid20888342-4]`_`f] In 2012, DSSP was rewritten so that the assignment of π helices was given preference over α helices, resulting in better detection of π helices.`:cite-ref-dsspmanual-3-1[`F5bf`_`[3`#cite-note-dsspmanual-3]`_`f] Versions of DSSP from 2.1.0 onwards therefore produce slightly different output from older versions.

>>Variants

In 2002, a continuous DSSP assignment was developed by introducing multiple hydrogen bond thresholds, where the new assignment was found to correlate with protein motion.`:cite-ref-andersen2002-5-0[`F5bf`_`[5`#cite-note-andersen2002-5]`_`f]

>>See also

• `F33f`_`[STRIDE (algorithm)`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=STRIDE_(algorithm)]`_`f an alternative algorithm

• `F33f`_`[Chris Sander (scientist)`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Chris_Sander_(scientist)]`_`f

>>References

`:cite-note-1`!1.`! "DSSP". Archived from the original on 2022-09-20. Retrieved 2018-04-30.

`:cite-note-kabsch1983-2`!2.`! `F0af`_`[↑`#cite-ref-kabsch1983-2-0]`_`f `:citerefkabschsander1983`aKabsch W, Sander C (1983). "Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features". `*Biopolymers`*. `!22`! (12): 2577–637. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1002/bip.360221211. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 6667333. `F33f`_`[S2CID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=S2CID_(identifier)]`_`f 29185760.

`:cite-note-dsspmanual-3`!3.`! `F0af`_`[↑`#cite-ref-dsspmanual-3-0]`_`f "DSSP manual Archived 2015-05-22 at the `F33f`_`[Wayback Machine`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Wayback_Machine]`_`f"

`:cite-note-pmid20888342-4`!4.`! `F0af`_`[↑`#cite-ref-pmid20888342-4-0]`_`f `:citerefcooleyarpkarplus2010`aCooley RB, Arp DJ, Karplus PA (2010). "Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices enhancing protein functionality". `*J Mol Biol`*. `!404`! (2): 232–246. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1016/j.jmb.2010.09.034. `F33f`_`[PMC`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMC_(identifier)]`_`f 2981643. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 20888342.

`:cite-note-andersen2002-5`!5.`! `F0af`_`[↑`#cite-ref-andersen2002-5-0]`_`f `:citerefandersenpalmerbrunakrost2002`aAndersen CA, Palmer AG, Brunak S, Rost B (2002). "Continuum secondary structure captures protein flexibility". `*Structure`*. `!10`! (2): 175–184. `F33f`_`[doi`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=Doi_(identifier)]`_`f:10.1016/S0969-2126(02)00700-1. `F33f`_`[PMID`:/page/wikibook/entry.mu`zim=wikipedia_en_all_nopic_2025-08.zim|entry_path=PMID_(identifier)]`_`f 11839303.

>>External links

• DSSP Analysis tool

• Continuous DSSP tool

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