User:Tilman Schirmer/Sandbox 100

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Revision as of 20:43, 23 March 2009 (edit) Tilman Schirmer (Talk | contribs) (→Anatomy of a protein) ← Previous diff		Revision as of 20:55, 23 March 2009 (edit) (undo) Tilman Schirmer (Talk | contribs) (→Anatomy of a protein) Next diff →
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-	<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix/3'>Alpha helix</scene>	+	<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix/4'>Alpha helix</scene>
-	<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix_backbone/3'>Alpha helix C-alpha trace</scene>	+	<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix_backbone/4'>Alpha helix C-alpha trace</scene>
-	<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix_bas/1'>Alpha helix backbone</scene>	+	<scene name='User:Tilman_Schirmer/Sandbox_100/Alpha_helix_bas/2'>Alpha helix backbone</scene>
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-	<scene name='User:Tilman_Schirmer/Sandbox_100/Turn/4'>Turn</scene>	+	<scene name='User:Tilman_Schirmer/Sandbox_100/Turn/5'>Turn</scene>
-	<scene name='User:Tilman_Schirmer/Sandbox_100/Turn_backbone/5'>Turn backbone</scene>	+	<scene name='User:Tilman_Schirmer/Sandbox_100/Turn_backbone/6'>Turn backbone</scene>
		+
		+	<scene name='User:Tilman_Schirmer/Sandbox_100/Turn1/1'>Turn1</scene>
		+	<scene name='User:Tilman_Schirmer/Sandbox_100/Turn2/1'>Turn2</scene>
		+	<scene name='User:Tilman_Schirmer/Sandbox_100/Turn3/1'>Turn3</scene>
		+	<scene name='User:Tilman_Schirmer/Sandbox_100/Turn4/1'>Turn4</scene>
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Revision as of 20:55, 23 March 2009

Contents 1 Secondary structure of proteins 1.1 Repetitive torsion angles 1.2 α-Helix 1.3 parallel β-sheet 1.4 antiparallel β-sheet 2 Anatomy of a protein 3 Notes

Secondary structure of proteins

Repetitive torsion angles

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

A polypeptide chain with a repetition of identical phi-psi torsion angles yields a helical structure.

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phi-psi = (180^o, 180^o), fully extended chain: ,

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phi-psi = (-140^o, 130^o), extended chain: , ; this is the β-strand conformation found in beta-sheets

Note:

polypeptide forms a with side-chains protruding towards alternating (up, down) directions

the polypeptide main-chain is as can been seen when looking along the chain

the point towards alternate directions

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phi-psi = (70^o, 180^o): , ; note that there are clashes (where?)

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phi-psi = (-60^o, -40^o), α-helix: ,

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phi-psi = (-50^o, -26^o), 3₁₀ helix: ,

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α-Helix

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

An α-Helix is stabilized by main-chain between O_i and N_i+4. With .

parallel β-sheet

spinqualitylabelsall models PDB ID 1tmy.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

With .

antiparallel β-sheet

spinqualitylabelsall models PDB ID 1ema.pdb Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

With .

Anatomy of a protein

spinqualitylabelsall models 1tmy Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Response regulator receiver (Rec) domain. See also 1tmy.

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Notes

see also http://proteopedia.org/wiki/index.php/User:James_D_Watson/Structural_Templates