Proline kink geometry calculation
The method quantifies three aspects of the helix's coordinates that are referenced to the proline kink (PK) itself: the bend angle, the wobble angle and the face-shift.
This web site contains documentation describing how to run the program, and a .tar file with the (Fortran 77) source code, executable and a complete example.
Inputs required:
1.
Protein data
2.
Center pre-proline helix
3.
Axes pre-proline helix
4.
Axes post-proline helix
5.
Atom number C-alpha proline
6.
Atom number C-alpha residue i-4 from proline
7.
Atom number C-alpha residue i-3 from proline
8.
Total number of atoms in the protein
9.
Number of cycles of the study
10. Example
The program ProKink has also been implemented as an analysis feature of the program Simulaid. This implementation includes the calculation of the helix axes the option of scanning a whole trajectory, visualization of the kinked backbone fragment with their helix axes and a dial plot of the three resulting angles (face-shift, bend-angle and wobble-angle)
It has also been observed that when the pre-proline helix does not include the proline itself then the helix is better defined. As a result, contrary to the earlier implementation, the proline is included only into the post-proline helix.
The calculation of the helix axis uses the method of Kahn (based on the observation that in a perfect helix, the bisector of the angle formed by three consecutive alpha carbons should intersect with the helix axis) as implemented by J.A. Christopher & T.O. Baldwin.