Figures for Notes on Loops

This page contains all the figures used in the notes on loops. You may want to keep this page open, or print this page when going through the notes.

Figure 3.1 Example of a Type I and Type II turns

The turn comprises four residues (labelled R1 to R4) with one hydrogen bond (dotted) stabilizing the turn. The hydrogen bond is between the carbonyl oxygen of residue one (coloured blue) and the amide nitrogen of residue four (coloured red). Residues are coloured according to their position in the chain starting with blue at the N-terminal and progressing through cyan, green, and finally red which is at the C-terminal part of the chain. The difference between a Type I and Type II turn is the orientation of the peptide bond between the second and third residue (coloured cyan and green respectively). Note that the second residue of the Type II is almost always a glycine.

The Type I turn was isolated from 5cpa.pdb and comprises residues 283 to 286 (ie. Ala, Ser, Gln, and Ile). The Type II turn was designed from the Type I turn using SwissPdb Viewer and mutating the Gln residue for a Gly residue.

Type I Beta turn
Type II Beta Turn
Type I
Type II
Pdb coordinate file
Pdb coordinate file

 

Figure 3.2 Example of Type I' and Type II' turns

Type I' Beta Turn
Type II' Beta Turn

Type I Prime

Type II Prime

Pdb coordinate file
Pdb coordinate file

Figure 3.3 Ramachandran Plots of Type I and II turns

The Ramachandran Plots were generated from the beta turn pdb files using SwissPdb Viewer . The labels R2 and R3 refer to residue 2 and 3 respectively in the beta turn as shown above in Figure 3.1. The blue contours mark the outer limits of allowed conformations of the peptide chain (using minimum van der Waals distances). The yellow contours mark the 'usual' limits of allowed conformations of the peptide chain (using maximum van der Waals distances).

Note that residue 3 (R3) of the Type II turn lies in the outer limits of allowed conformations and is almost always glycine.

 Ramachandran Plots

Figure 3.4 Ramachandran Plots of Type I' and Type II' turns

The Ramachandran Plots were generated from the beta turn pdb files using SwissPdb Viewer . The labels R2 and R3 refer to residue 2 and 3 respectively in the beta turn as shown above in Figure 3.1. The blue contours mark the outer limits of allowed conformations of the peptide chain (using minimum van der Waals distances). The yellow contours mark the 'usual' limits of allowed conformations of the peptide chain (using maximum van der Waals distances)

Note that residue 3 (R3) of the Type I' and residue 2 (R2) of Type II' turn lies in the outer limits of allowed conformations and is almost always glycine.

 Type I and II

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