User:James D Watson/Structural Templates: Difference between revisions

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In the Jmol viewer to the right PDB entry 5p21 has been coloured by secondary structure (α-helices are coloured magenta and β-strands are coloured yellow). A single <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta/1'>beta-strand</scene> can technically be described as a flat helix with 2 residues per turn although this may not be initially obvious. <br>

When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betasheet/1'>β-sheet</scene>. As the backbones need to come close together to interact and form a sheet, the sidechains are oriented away from the plane of the sheet. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in cartoon ~~form~~ as an arrowhead on beta ~~strands~~). β-sheets therefore occur in two varieties:<OL>

When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betasheet/1'>β-sheet</scene>. As the backbones need to come close together to interact and form a sheet, the <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta_sc/1'>sidechains are oriented away from the plane of the sheet</scene>. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in the cartoon format as an arrowhead on each beta strand). β-sheets therefore occur in two varieties:<OL>

<LI>Anti-parallel - here the beta strands aligned next to each other run in opposite directions. As the interacting carbonyls and amides align well, the hydrogen bonds appear to be straight.

<LI>Parallel - here the interacting strands run alongside each other and point in the same direction. In this conformation the carbonyl oxygen and the amides tend to be more staggered than in an anti-parallel sheet, therefore the hydrogen bonds tend to be angled.

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 <applet load='5p21' size='350' frame='true' align='right' caption='Secondary structure - Alpha' scene='User:James_D_Watson/Structural_Templates/Secondary_structure_start/2'/>
 In the Jmol viewer to the right PDB entry 5p21 has been coloured by secondary structure (α-helices are coloured magenta and β-strands are coloured yellow). A single <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta/1'>beta-strand</scene> can technically be described as a flat helix with 2 residues per turn although this may not be initially obvious. <br>
-When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betasheet/1'>β-sheet</scene>. As the backbones need to come close together to interact and form a sheet, the sidechains are oriented away from the plane of the sheet. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in cartoon form as an arrowhead on beta strands). β-sheets therefore occur in two varieties:<OL>
+When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_betasheet/1'>β-sheet</scene>. As the backbones need to come close together to interact and form a sheet, the <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_beta_sc/1'>sidechains are oriented away from the plane of the sheet</scene>. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in the cartoon format as an arrowhead on each beta strand). β-sheets therefore occur in two varieties:<OL>
 <LI>Anti-parallel - here the beta strands aligned next to each other run in opposite directions. As the interacting carbonyls and amides align well, the hydrogen bonds appear to be straight.
 <LI>Parallel - here the interacting strands run alongside each other and point in the same direction. In this conformation the carbonyl oxygen and the amides tend to be more staggered than in an anti-parallel sheet, therefore the hydrogen bonds tend to be angled.