Calculate structure: Difference between revisions

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''Calculate structure'' was used to identify the turns in myohemerthyrin and Domain 2 of chain A Glycogen Phosphorylase. Two proteins is a small sample, but it does give some indication of the nature of the T: segments (turns) reported in the summary and of the pattern of blue colored trace segments in the displayed structure. There are additional samples, which you can analyze, following these two proteins.

* Most T: segments in the summary contain one or two residues but a few contain three or four residues.

* Most T segments in the summary contain one or two residues but a few contain three or four residues. With isolated turns DSSP reports two, three and four residues for 3-, 4-, and 5-turns, respectively. If the turn is overlapping with a structure of higher priority fewer residues will be included in the segment.

* The presence of a one-residue T: segments in the summary ~~is not necessarily an indicator~~ of a ~~n-turn~~. ~~Some of these~~ single residues ~~are found~~ in the interior of a helix ~~and are~~ not colored blue (~~found in~~ Domain 2 of chain A Glycogen Phosphorylase). Even if the single residue is colored blue in the structure, the turn in which it is located is not an isolated turn but part of a helix, and these single blue colored residues can be at the end or interior of the helix.

* 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 3-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 ~~3-turns (~~β-turns) have two to three residues colored blue in the structure, rarely four~~. This coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify isolated β-turns~~.

* 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. These nested turns are easily identified by residue ''i'' being involved in two hbonds.

* 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. These nested turns are easily identified by residue ''i'' being involved in at least two hbonds.

* This coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify isolated β-turns.

=== Illustrations ===

Calculate structure: Difference between revisions

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 ''Calculate structure'' was used to identify the turns in myohemerthyrin and Domain 2 of chain A Glycogen Phosphorylase. Two proteins is a small sample, but it does give some indication of the nature of the T: segments (turns) reported in the summary and of the pattern of blue colored trace segments in the displayed structure. There are additional samples, which you can analyze, following these two proteins.
-* Most T: segments in the summary contain one or two residues but a few contain three or four residues.
+* Most T segments in the summary contain one or two residues but a few contain three or four residues. With isolated turns DSSP reports two, three and four residues for 3-, 4-, and 5-turns, respectively. If the turn is overlapping with a structure of higher priority fewer residues will be included in the segment.
-* The presence of a one-residue T: segments in the summary is not necessarily an indicator of a n-turn. Some of these single residues are found in the interior of a helix and are not colored blue (found in Domain 2 of chain A Glycogen Phosphorylase). Even if the single residue is colored blue in the structure, the turn in which it is located is not an isolated turn but part of a helix, and these single blue colored residues can be at the end or interior of the helix.
+* 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 3-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 3-turns (β-turns) have two to three residues colored blue in the structure, rarely four. This coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify isolated β-turns.
+* 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. These nested turns are easily identified by residue ''i'' being involved in two hbonds.
+* 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. These nested turns are easily identified by residue ''i'' being involved in at least two hbonds.
+* This coloration and the hbond bond between ''i'' and ''i'' + 3 can be used to identify isolated β-turns.
 === Illustrations ===