Calculate structure: Difference between revisions
From Proteopedia
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 21: | Line 21: | ||
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<sup>α</sup> are not used by the DSSP procedure to identify n-turns, but the generally accepted definitions of β and γ 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 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<sup>α</sup> are not used by the DSSP procedure to identify n-turns, 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), but there is not an absolute requirement for a hbond. 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. | [[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), but there is not an absolute requirement for a hbond. 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. | ||
[[Turns_in_Proteins#Gamma Turns|γ-turns]] contain three residues having a hbond between residues ''i'' and ''i'' + 2 and therefore are not included among the turns found by DSSP. The classic γ-turns have phi and psi values at residue ''i'' + 1 of +75.0 and -64, respectively, and the inverse γ-turns have phi and psi values at residue ''i'' + 1 of -79 and +69, respectively.<ref name="Miner">Miner-White, EJ, et. al. ''One type of gamma turn, rather than the other, gives rise to chain reversal in proteins''. J. Mol. Bio. '''204''', 1983, pp. 777-782.</ref> | [[Turns_in_Proteins#Gamma Turns|γ-turns]] contain three residues having a hbond between residues ''i'' and ''i'' + 2 and therefore are not included among the turns found by DSSP. The classic γ-turns have phi and psi values at residue ''i'' + 1 of +75.0 and -64, respectively, and the inverse γ-turns have phi and psi values at residue ''i'' + 1 of -79 and +69, respectively.<ref name="Miner">Miner-White, EJ, et. al. ''One type of gamma turn, rather than the other, gives rise to chain reversal in proteins''. J. Mol. Bio. '''204''', 1983, pp. 777-782.</ref> | ||
| Line 31: | Line 31: | ||
* The presence of a one-residue T segments in the summary indicates that the β-turn overlaps a structure of higher priority (most often a helix). These single blue colored residues can be at the end or interior of the helix, and some in the interior of a helix may not be colored blue (Domain 2 of chain A Glycogen Phosphorylase). | * The presence of a one-residue T segments in the summary indicates that the β-turn overlaps a structure of higher priority (most often a helix). These single blue colored residues can be at the end or interior of the helix, and some in the interior of a helix may not be colored blue (Domain 2 of chain A Glycogen Phosphorylase). | ||
* All two-residue T segments indicate β-turns. The turns are often part of an helix, as many as three of the four residues can have the color of the helix. Isolated β-turns have two to three residues colored blue in the structure, rarely four. | * All two-residue T segments indicate β-turns. The turns are often part of an helix, as many as three of the four residues can have the color of the helix. Isolated β-turns have two to three residues colored blue in the structure, rarely four. | ||
* T segments that have more than two residues indicate two contiguous or nested β-turns, β-turn nested in a 4 or 5-turn, isolated or nested 4 or 5-turns. | * T segments that have more than two residues indicate two contiguous or nested β-turns, β-turn nested in a 4- or 5-turn, isolated or nested 4 or 5-turns. | ||
* After ''calculate structure'' and ''calculate hbonds structure'' has been run the following methods can be used to identify the different types of turns. Blue coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify overlapping and isolated β-turns. The 4- or 5-turns which are nested in some way are easily identified by residue ''i'' being involved in at least two hbonds. β-turns VIa1, VIa2, and VIb can be identified by locating a trace that has the appearance of a β-turns and is not colored blue and checking 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.<ref name=beta /> | |||
=== Illustrations === | === Illustrations === | ||
