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

Line 24:

===α-helices===

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). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alphahelix/1'>α-helix</scene> 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 they 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, 310-helices and their left handed forms (see table 1 for the helix parameters).

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). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alphahelix/1'>α-helix</scene> is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alpha_sc/1'>sidechains point outward</scene>, away from the centre of the helix, where they 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 <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alpha_hbon/1'>carbonyl group of residue i interacting with the amide group of residue i+4</scene>, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 310-helices and their left handed forms (see table 1 for the helix parameters).

Table 1:

@@ Line 24: / Line 24: @@
 ===α-helices===
 <applet load='5p21' size='350' frame='true' align='right' caption='Secondary structure - Alpha' scene='User:James_D_Watson/Structural_Templates/Secondary_structure_start/1'/>
-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). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alphahelix/1'>α-helix</scene> 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 they 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).<br>
+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). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alphahelix/1'>α-helix</scene> is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alpha_sc/1'>sidechains point outward</scene>, away from the centre of the helix, where they 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 <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_alpha_hbon/1'>carbonyl group of residue i interacting with the amide group of residue i+4</scene>, 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).<br>
 <br>
 Table 1:<br>