Calculate structure: Difference between revisions

Line 28:

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 trace segments colored blue.

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

* ~~Segments labeled~~ with ~~T and contain~~ one residue ~~may not~~ be ~~a 3-turn, but a β-turn (4-turn) that partially overlaps a structure that has a higher priority, and only the non-overlapping residue is reported as a turn.~~ DSSP is described as only identifying a turn as a n-turn if the turn is isolated, but in practice this does not always happen. If a T segment in the Summary is only one residue long, it can be identified as a β-turn by the presence of a hbond between ''i'' and ''i + 3''.

* T: segments with one residue can be interrupted in several ways: DSSP is described as only identifying a turn as a n-turn if the turn is isolated, but in practice this does not always happen. If a T segment in the Summary is only one residue long, it can be identified as a β-turn by the presence of a hbond between ''i'' and ''i + 3''.

* A β-turn can be nested in a 5-turn, and in the Summary this turn will show as a three residue segment. A β-turn nested in a 5-turn contains two hbonds. One located between ''i'' and ''i + 3'', and the other one is between ''i'' and ''i + 4''.

* DSSP does not identify these classes of β-turns VIa1, VIa2, and VIb because of the lack of a hbond. If a segment 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.

Calculate structure: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 28: / Line 28: @@
 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 trace segments colored blue.
 * Most T: segments in the summary contain one or two residues but a few can contain three or four residues.
-* Segments labeled with T and contain one residue may not be a 3-turn, but a β-turn (4-turn) that partially overlaps a structure that has a higher priority, and only the non-overlapping residue is reported as a turn. DSSP is described as only identifying a turn as a n-turn if the turn is isolated, but in practice this does not always happen. If a T segment in the Summary is only one residue long, it can be identified as a β-turn by the presence of a hbond between ''i'' and ''i + 3''.
+* T: segments with one residue can be interrupted in several ways:   DSSP is described as only identifying a turn as a n-turn if the turn is isolated, but in practice this does not always happen. If a T segment in the Summary is only one residue long, it can be identified as a β-turn by the presence of a hbond between ''i'' and ''i + 3''.
 * A β-turn can be nested in a 5-turn, and in the Summary this turn will show as a three residue segment. A β-turn nested in a 5-turn contains two hbonds. One located between ''i'' and ''i + 3'', and the other one is between ''i'' and ''i + 4''.
 * DSSP does not identify these classes of β-turns VIa1, VIa2, and VIb because of the lack of a hbond. If a segment 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.