User:James D Watson/Structural Templates: Difference between revisions
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===α-helices=== | ===α-helices=== | ||
<applet load=' | <applet load='User:James_D_Watson/Structural_Templates/Secondary_structure_start/1'' size='350' frame='true' align='right' caption='Secondary structure - Alpha'/> | ||
The α-helix is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The sidechains point outward, away from the centre of the helix, where athey can interact with solvent, other protein, small molecules or macromolecules. The structure is stabilised by regular hydrogen bonds that form between the backbone carbonyl oxygens and amide hydrogens. The bonding pattern for the α-helix is characterised by the carbonyl group of residue i hydrogen interacting with the amide group of residue i+4, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 3<sub>10</sub>-helices and their left handed forms (see table 1 for the helix parameters) | The α-helix is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The sidechains point outward, away from the centre of the helix, where athey can interact with solvent, other protein, small molecules or macromolecules. The structure is stabilised by regular hydrogen bonds that form between the backbone carbonyl oxygens and amide hydrogens. The bonding pattern for the α-helix is characterised by the carbonyl group of residue i hydrogen interacting with the amide group of residue i+4, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 3<sub>10</sub>-helices and their left handed forms (see table 1 for the helix parameters) | ||
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===β-sheets=== | ===β-sheets=== | ||
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<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. | <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. | ||
</OL> | </OL> | ||
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Turns and loops | ===Turns and loops=== | ||
There are a number of small hydrogen bonded motifs and patterns which are observed regularly. These are described below:<UL> | There are a number of small hydrogen bonded motifs and patterns which are observed regularly. These are described below:<UL> | ||
<LI>Beta Turns - originally defined by the one hydrogen bond common to all (an i, i+3 hydrogen bond) but some modern descriptions do not require a hydrogen bond. | <LI>Beta Turns - originally defined by the one hydrogen bond common to all (an i, i+3 hydrogen bond) but some modern descriptions do not require a hydrogen bond. | ||