# Dihedral angles of alanine dipeptide

I have a number of trajectories of alanine dipeptide molecule and I'm interested in computing dihedral angles of each configuration.

$$\quad\quad\quad\quad$$ Have I selected the right atoms for computing each angle in the above image? Is possible to compute both angles, $$\phi$$ and $$\psi$$, given only the coordinates of the heavy atoms (without the hydrogen in the green circle)?

Proteopedia suggests that the $$\phi$$ and $$\psi$$ angles of a Ramachandran plot only involve carbon and nitrogen atoms in their definition and specifically the carbons and nitrogens in the backbone of the protein or $$n$$-peptide. These definitions are also used in an article from BioMol Concepts, describing new ways of presenting Ramachandran plots, which suggests these definitions are standard.
$$\phi$$ should be the dihedral from a carbonyl carbon $$\ce{C}_{i-1}$$, to the following nitrogen $$\ce{N}_i$$, to the alpha carbon $$\ce{C(\alpha)}_{i}$$, to the next carbonyl carbon $$\ce{C}_{i}$$.
$$\psi$$ should be the dihedral from nitrogen (the same from the definition of $$\phi$$) $$\ce{N}_{i}$$, to the alpha carbon $$\ce{C(\alpha)}_{i}$$, to the carbonyl carbon $$\ce{C}_{i}$$, to the next nitrogen $$\ce{N}_{i+1}$$.
So to answer your questions, your drawing depicts two different dihedral angles and the actual $$\phi$$ and $$\psi$$ angles only involve heavy, backbone atoms. In your image, $$\phi$$ is given by the (2,4,5,7) angle while $$\psi$$ is the (4,5,7,9) angle.