Calculate structure: Difference between revisions
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* 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''. (Hover the cursor over the trace to display the name and number of the residues.) 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 /> | * 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''. (Hover the cursor over the trace to display the name and number of the residues.) 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 /> | ||
* There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do URL]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and | |||
=== Illustrations === | === Illustrations === | ||
