Calculate structure: Difference between revisions

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===Summary of observations obtained from using ''Calculate structure''===

~~These observations are from the use of~~ ''Calculate structure'' 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.

''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.

* 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~~. 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 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.

* 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 β-turns.

* 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.

* T: segments that have more than two residues indicate two contiguous or nested β-~~turn~~, 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 two hbonds.

=== Illustrations ===

Calculate structure: Difference between revisions

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@@ Line 26: / Line 26: @@
 ===Summary of observations obtained from using ''Calculate structure''===
-These observations are from the use of ''Calculate structure'' 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.
+''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.
-* 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. 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 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.
-* 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 β-turns.
+* 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.
-* T: segments that have more than two residues indicate two contiguous or nested β-turn, 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 two hbonds.
 === Illustrations ===