6.7 Change the secondary structure of a peptide

VEGA ZZ is able to change the secondary structure of a peptide moving the Phi, Psi and Omega torsions. To show the dialog window, you must select Edit Change Secondary struct. in main menu.


Change the secondary structure


The Structure type box allows to specify the secondary structure type: several pre-defined structure types are already defiend (Alpha helix, Left handed helix, 3.10 helix, Pi helix, Beta strand, Antiparallel beta strand and Parallel beta strand) but you can create custom structures selecting Custom and changing the Phi, Psi and Omega torsion values:


Phi, Psi and Omega torsion angles


The checkboxes at the left of each torsion name allow to enable/disable which angles are changed to the characteristic secondary structure value, eventually preserving the original torsions. Checking Fix bond angles, the bond angles distorted by the rotation of the torsions are reverted to the canonical value and checking Consider selected atoms only, the torsion modification is applied to the selected/visible atoms only, keeping the other atoms unchanged.
Add the side chains and Add the hydrogens checkboxes are intentionally disabled and are operative when you build a peptide from its primary structure (for more information, see how to build a peptide). Clicking Apply button, the secondary structure of the peptide in the current workspace is changed.


the routine changing the torsion angles is working outside the rings. In other words, it's unable to change the secondary structure of cyclic peptides, including peptides with disulfide bridges. To avoid this problem, you could temporally open the ring breaking one bond (e.g. a disulfide bridge or a backbone bond), change the secondary structure and, if it's possible, rebuild the broken bond.


The following table shows Phi, Psi and Omega values of the most common secondary structures:


Secondary structure Phi Psi Omega
Alpha helix -57.8 -47.0 180.0
Left helix 7.8 47.0 180.0
310 helix -74.0 -4.0 180.0
Pi helix -57.1 -69.7 180.0
Beta strand -135.0 135.0 180.0
Antiparallel beta strand -140.0 135.0 180.0
Parallel beta strand -120.0 115.0 180.0