Calculate structure: Difference between revisions

''Calculate structure'' is based on Defined Secondary Structure of Protein (DSSP), a program written in Pascal.<ref name="DSSP">W. Kabsch & C. Sanders, ''Biopolymers'', '''22''', 2577-2636, 1983.</ref> The secondary structure recognition algorithms used in DSSP are based mainly on hydrogen-bonding patterns along with some geometric structures , such as bends. There are two different hydrogen-bonding patterns which are recognized. The one determines the value of n in the expression ''i'' + ''n'' (''i'' is a residue that forms a hydrogen bond with a residue n residues removed from residue ''i''.) where n = 3, 4 or 5. These values define three types of turns. A peptide segment that has repeating turns of the same type are called 3₁₀-helix, α-helix, or Π-helix, respectively. If the turn is isolate, it is simply called an n-turn. The other recognized pattern is a hydrogen bond which is between residues which are not close together in sequence. This type of hydrogen bond is called a bridge. Kabsch & Sanders define a ladder as a "set of one or more consecutive bridges of identical type" and a sheet as a "set of one or more ladders connected by shared residues"<ref name="DSSP" />. Bends are peptide segments with high curvature, and the determination of curvature involves angles of the C^α. Bends can overlap with helices and turns.  

The results of the ''calculate structure'' computation are printed in the upper box of the console. One part of that output is a summary of the different types of secondary structure with each type having a one letter identifier. (The summary for myohemerytherin (2mhr) is given below with a key for the one letter identifiers.) It is possible for a residue or a segment of residues to be assigned more than one structural type, and for this reason the key for the identifiers is rank ordered in decreasing priority of assignment. With bend having the lowest priority in assignment a structure is identified as a bend only if it is not assigned any other structural type. The helices and sheets which are identified on the summary can easily be associated with the corresponding structures in the applet, but the turns need some additional explanation.  

The DSSP determination of helices and β-sheets is in agreement with the generally accepted view of these two structures, but the DSSP determination of turns is not as specific as the generally accepted definition of turns. As described above DSSP identifies turns that have 4, 5, or 6 residues with a backbone hbond being present between the first and the last residues. The presence of the hbond is a requirement to be classified as a turn. [[Psi and Phi Angles|Phi and psi torsional angles]] of the C^α are not used by the DSSP procedure, but the generally accepted definitions of β and γ turns involve these angles.  

[[Turns_in_Proteins#Beta Turns|β-turns]] contain four residues and therefore are 3-turns found by DSSP. The classes of β-turns are defined by the range of psi and phi values for the second and third residues.<ref name=beta>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?doc=TRUE&pdbcode=n/a&template=doc_p_bturns.html Characteristics of β-turn classes]</ref>  β-turns often have a hbond between residues one and four (''i'' + 3) of β-turns, but there is not an absolute requirement for one. In three classes (VIa1, VIa2, VIb) a Pro in the third position has the cis configuration which does not permit the formation of a hbond ([[Turns_in_Proteins#Beta Turns|View display of structure.]]). The turns in these three classes are not detected by DSSP since they do not contain a hbond. If a trace is not colored blue but has the appearance of a β-turns, check for a cis-Pro at ''i + 2''. Also, the values for phi and psi angles at ''i + 1'' and ''i + 2'' can be [[Psi and Phi Angles|determined]] and compared to the values expected for classes VIa1, VIa2, and VIb.