Calculate structure: Difference between revisions
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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 3, 4, or 5 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<sup>α</sup> are not used by the DSSP procedure, but the generally accepted definitions of turns involve these angles. | 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 3, 4, or 5 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<sup>α</sup> are not used by the DSSP procedure, but the generally accepted definitions of turns involve these angles. | ||
All types of β-turns contain four residues | All types of β-turns contain four residues and therefore would be included with the 4-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> There is not an absolute requirement for a hbond, but there is often one between residues one and four (''i'' + 3). In three classes a Pro in the third position has the cis configuration which does not permit the formation of a hbond ([[Turns_in_Proteins|View display of structure.]]). The turns in these three classes are not detected by DSSP since they do not contain a hbond. | ||
All γ-turns contain three residues and would be included with the 3-turns found by DSSP. | |||
After Jmol completes the ''calculate structure'' computation the results of the computation is 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. It is possible for a residue or a segment of residues to be assigned more than one structural type, for this reason the key list given below 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. Below is a copy of the summary for myohemerytherin (2mhr): (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | After Jmol completes the ''calculate structure'' computation the results of the computation is 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. It is possible for a residue or a segment of residues to be assigned more than one structural type, for this reason the key list given below 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. Below is a copy of the summary for myohemerytherin (2mhr): (<scene name='Globular_Proteins/Anti_helix_erythrin2/1'>Restore initial scene</scene>) | ||
