Calculate structure: Difference between revisions

Line 33:

* 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 />

* 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

* There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do Open home page of PDB]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn and then if you click the one residue turn will appear in the Jmol applet.

=== Illustrations ===

Calculate structure: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 33: / Line 33: @@
 * 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 />
-* 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
+* There are two resources at RCSB Protein Data Bank<ref name="RCSB">[http://www.pdb.org/pdb/home/home.do Open home page of PDB]</ref> that can be useful when analyzing the turns or any secondary structures of a protein. After going to the PDB site and selecting your protein of interest by entering the PDB ID or name of the protein, click on the Sequence tab. First, clicking on 'Sequence & DSSP' under the Chain A heading opens in a separate window the sequence and secodary structures of chain A of the protein. Second, in the 'Sequence & Structure Relationships' box click on 'Enable Jmol to view annotations in 3D' and then 'Display Jmol'. The Jmol applet remains on top as you scroll down to the annotated sequence. Clicking on a secondary structure in the DSSP bar results in that structure being high lighted in the Jmol applet. The turns that are identified as having only one residue are not shown on the DSSP bar, but if you hoover the cursor over the DSSP bar in the area of that one residue a label will appear identifying the turn and then if you click the one residue turn will appear in the Jmol applet.
 === Illustrations ===