Secondary structure: Difference between revisions

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There are three common secondary structures - helices, β-pleated sheets and turns, and there are several variations of each one of them.

*'''Helices'''. Alpha helix, pi helix and 310 helix are the three types of helices with the alpha helix being the most important. The characteristics of these three helices are given at [[Helices in Proteins]]. [[Jmol]] colors them alpha helix, 310 helix and pi helix as shown in [[Helices in Proteins]].

*'''Helices'''. [[Alpha helix]], pi helix and 310 helix are the three types of helices with the alpha helix being the most important. The characteristics of these three helices are given at [[Helices in Proteins]]. [[Jmol]] colors them alpha helix, 310 helix and pi helix as shown in [[Helices in Proteins]].

*'''Strands'''. The strands making up the sheets can be parallel or antiparallel and the pleats in the sheet can be twisted as well as being parallel. These structural differences and other characteristics of β-sheets can be seen at [[Sheets in Proteins]].

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==Displaying Secondary Structure==

If you want a convenient, static view of the structurally-determined [[Secondary structure|secondary structure]], or alternatively the ''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB entry page in Proteopedia and then on the PDBsum page navigate to the chain you are interested in from the ''Contents'' listing on left side of the main PDBsum page. The '''secondary structure''' will be illustrated above the sequence in the main view with the ''secondary structure topology'' or ''wiring diagram'' accessible on the right. The '''secondary structure''' will also be illustrated ~~above~~ the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank].

If you want a convenient, static view of the structurally-determined [[Secondary structure|secondary structure]], or alternatively the ''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB entry page in Proteopedia and then on the PDBsum page navigate to the chain you are interested in from the ''Contents'' listing on left side of the main PDBsum page. The '''secondary structure''' will be illustrated above the sequence in the main view with the ''secondary structure topology'' or ''wiring diagram'' accessible on the right. The '''secondary structure''' will also be illustrated below the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank].

Many structures displayed on Proteopedia's PDB entry pages default to the cartoon view showing alpha helices and beta-sheets. If you need to see the secondary structure represented within the structure for any Proteopedia structure window, even or any [[Jmol]] view, ''click on the Jmol frank,'' and navigate the menu that comes up to first first ''Select'' --> ''All'' and then turn on the cartoons (''Style''--->''Scheme''--->''cartoon'') and then for added help color this cartoon representation by the scheme outlined in the next section below ( ''Color''--> ''Structures'''--> ''Cartoon'' ---> ''By Scheme'' -->''Secondary Structure'') . For advanced users, this is more easily accomplished by way of Jmol commands in the console, ''select all; cartoon on, color structure''.

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* [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)

* [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentación)

* [[Backbone representations]] explains backbone traces, smoothed traces, and ribbons ("cartoon" in JSmol).

* [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].

* [[Calculate structure]]

* [[Membrane proteins]]

* [[Help:Color Keys]]

* [[Basics of Protein Structure]]

==External Resources==

* [http://bioinf.cs.ucl.ac.uk/psipred/ The PSIPRED Protein Structure Prediction Server] has a highly accurate method for protein secondary structure prediction for proteins where there is no empirically-determined 3D structure.

Secondary structure: Difference between revisions

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@@ Line 4: / Line 4: @@
 There are three common secondary structures - helices, β-pleated sheets and turns, and there are several variations of each one of them.
-*'''Helices'''. Alpha helix, pi helix and 3<sub>10</sub> helix are the three types of helices with the alpha helix being the most important.  The characteristics of these three helices are given at [[Helices in Proteins]]. [[Jmol]] colors them <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helix</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helix</span> and <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> as shown in [[Helices in Proteins]].
+*'''Helices'''. [[Alpha helix]], pi helix and 3<sub>10</sub> helix are the three types of helices with the alpha helix being the most important.  The characteristics of these three helices are given at [[Helices in Proteins]]. [[Jmol]] colors them <span style="color:#FF0080;background-color:white;font-weight:bold;">alpha helix</span>, <span style="color:#A00080;background-color:white;font-weight:bold;">3<sub>10</sub> helix</span> and <span style="color:#600080;background-color:white;font-weight:bold;">pi helix</span> as shown in [[Helices in Proteins]].
 *'''Strands'''. The strands making up the sheets can be parallel or antiparallel and the pleats in the sheet can be twisted as well as being parallel.  These structural differences and other characteristics of β-sheets can be seen at [[Sheets in Proteins]].
@@ Line 39: / Line 39: @@
 ==Displaying Secondary Structure==
-If you want a convenient, static view of the structurally-determined [[Secondary structure|secondary structure]], or alternatively the ''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB entry page in Proteopedia and then on the PDBsum page navigate to the chain you are interested in from the ''Contents'' listing on left side of the main PDBsum page. The '''secondary structure'''  will be illustrated above the sequence in the main view with the ''secondary structure topology'' or ''wiring diagram'' accessible on the right.  The '''secondary structure'''  will also be illustrated above the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank].
+If you want a convenient, static view of the structurally-determined [[Secondary structure|secondary structure]], or alternatively the ''secondary structure topology'' or ''wiring diagram'', click on ''PDBsum'' below any structure on a PDB entry page in Proteopedia and then on the PDBsum page navigate to the chain you are interested in from the ''Contents'' listing on left side of the main PDBsum page. The '''secondary structure'''  will be illustrated above the sequence in the main view with the ''secondary structure topology'' or ''wiring diagram'' accessible on the right.  The '''secondary structure'''  will also be illustrated below the sequence in the main view accessible under the ''Sequence'' tab at the [http://www.pdb.org Protein Data Bank].
 Many structures displayed on Proteopedia's PDB entry pages default to the cartoon view showing alpha helices and beta-sheets. If you need to see the secondary structure represented within the structure for any Proteopedia structure window, even or any [[Jmol]] view, ''click on the Jmol frank,'' and navigate the menu that comes up to first first ''Select'' --> ''All'' and then turn on the cartoons (''Style''--->''Scheme''--->''cartoon'') and then for added help color this cartoon representation by the scheme outlined in the next section below ( ''Color''--> ''Structures'''--> ''Cartoon'' ---> ''By Scheme'' -->''Secondary Structure'') . For advanced users, this is more easily accomplished by way of Jmol commands in the console, ''select all; cartoon on, color structure''.
@@ Line 74: / Line 74: @@
 * [[Protein primary, secondary, tertiary and quaternary structure]] (slides for teaching)
 * [[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Estructuras primaria, secundaria, terciaria y cuaternaria de las proteínas]] (en formato de presentaci&oacute;n)
+* [[Backbone representations]] explains backbone traces, smoothed traces, and ribbons ("cartoon" in JSmol).
 * [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].
 * [[Calculate structure]]
 * [[Membrane proteins]]
 * [[Help:Color Keys]]
+* [[Basics of Protein Structure]]
 ==External Resources==
 * [http://bioinf.cs.ucl.ac.uk/psipred/ The PSIPRED Protein Structure Prediction Server] has a highly accurate method for protein secondary structure prediction for proteins where there is no empirically-determined 3D structure.