Calculate structure: Difference between revisions

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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.
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.
* Most T: segments in the summary contain one or two residues but a few can contain three or four residues.
* 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''.
* 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 (see analysis of Domain 2 of chain A Glycogen Phosphorylase). Even if the single residue is blue in the structure, the turn in which it is located is not isolated but part of a helix. These single turns can be at the end of the turn or interior.
* 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.
* 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''.
* 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.
* 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.
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T : A:115_A:117 β-turn 114-117, 4-turn 114-118 - 114 is part of a helix, 115-117 & part of 118 are blue, 118 is partially white. <scene name='Calculate_structure/Turn_114/2'>Display turn</scene><br>
T : A:115_A:117 β-turn 114-117, 4-turn 114-118 - 114 is part of a helix, 115-117 & part of 118 are blue, 118 is partially white. <scene name='Calculate_structure/Turn_114/2'>Display turn</scene><br>
<scene name='Calculate_structure/Turns_5_88/1'>Display the two class VIb turns</scene><br>
<scene name='Calculate_structure/Turns_5_88/1'>Display the two class VIb turns</scene><br>
Key - '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 3<sub>10</sub>-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.
Key - '''H''': α-helix; '''B''': β-bridge; '''E''': β-strand; '''G''': 3<sub>10</sub>-helix; '''I''': π-helix; '''T''': 3-, 4-, 5-turn; '''S''': bend.<br>


'''Domain 2 of chain A Glycogen Phosphorylase''' (<scene name='Calculate_structure/Domain_2/2'>Load Structure</scene>) - If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br>
'''Domain 2 of chain A Glycogen Phosphorylase''' (<scene name='Calculate_structure/Domain_2/2'>Load Structure</scene>) - If the applet is not running the signed ver. 12 of Jmol, connect with it as you did above, and then click on the above green link.<br>
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