Turns in Proteins: Difference between revisions

All β-turns contain four residues and are divided into classes based on the range of their [[Psi and Phi Angles|phi and psi]]  values for the second and third residues.<ref name=beta>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?doc=TRUE&pdbcode=n/a&template=doc_p_bturns.html Characteristics of β-turn classes]</ref>  Most classes have a hydrogen bond between the backbond atoms of residues one(''i'') and four (''i + 3''), and this attraction is the major force maintaining the conformation of the bend in the chain, but in several classes a Pro in the third position ''i + 2'') has the cis configuration which produces a conformation which can not form a hydrogen bond (hbonds).   

Seven β-turns are shown as blue traces in myohemerytherin in the scene to the right (<scene name='Turns_in_Proteins/Hemery1/1'>Initial scene</scene>). There are only five blue segments because, in two cases, one β-turn follows another one. Only five of the turns contain hydrogen bonds shown in magenta. As explained on [[Calculate structure]] the '''calculate structure;''' command does not detect beta turns which have a Pro in the cis configuration and lack a hbond.  Since the command has this limitation, the initial scene was produced by manually selecting and coloring the turns and forming the hbonds.  <scene name='Turns_in_Proteins/Calculate_structure/2'>Show</scene> the results of the '''calculate structure;''' command.

<blockquote>In order to color turns blue and display hbonds for secondary structures on any Proteopedia page which does not display it, click on the Jmol frank, in the main menu click on Console, in the bottom box of the console enter the commands: <span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span> and then click Run.  

Can you locate the cis configured Pro in the two turns without hbonds? Turns shown in <scene name='Turns_in_Proteins/Hemery_wf/2'>wireframe</scene> (If you are using ver. 12, run ''calculate hbonds structure'' in the console after clicking the green link.) without the side chains so that the backbone atoms can be clearly seen.  One can see that the hydrogen bonds are positioned between the first and the fourth residues of the turn and involve backbone atoms.