DIHEDRAL ANGLES

dihedral angles, phi, psi, omega, chi1, chi2, chi3, chi4, chi5, rotamers, dihedral angle, definitions, garlic, Damir Zucic.
MAIN CHAIN DIHEDRAL ANGLES
The main chain dihedral angles are defined as follows:

(1) The phi angle is the angle of right-handed rotation around N-CA bond, the value being zero if CA-C bond is cis to C-N bond. Range: from -180 to 180 degrees.

(2) The psi angle is the angle of right-handed rotation around CA-C bond, the value being zero if C-N bond is cis to N-CA bond. Range: from -180 to 180 degrees.

(3) The omega angle is the angle of right-handed rotation about C-N bond, the value being zero if CA-C bond of the preceding residue is cis to N-CA bond. Most residues in a typical protein are involved in the formation of two peptide bonds. The peptide bond formed by the residues I and I + 1 is assigned to the residue I + 1. The same applies to the omega angle. For that reason no omega angle is assigned to the first residue.

Since version 1.2, garlic uses the following procedure to calculate the main chain dihedral angles:

(1) In the first attempt, the coordinates of the main chain atoms are used to calculate the dihedral angles phi and psi. The phi angle will be missing for the first residue in each chain. The psi angle will be missing for the last residue in each chain.

(2) In the second attempt, the missing phi angles will be calculated using the coordinates of H (hydrogen) atoms, if available. The missing psi angles will be calculated using the coordinates of O (oxygen) atoms.





SIDE CHAIN DIHEDRAL ANGLES
For each side chain dihedral angle, the coordinates of four atoms are required. The table below contains the list of atoms and the range of values, for each side chain angle and for each residue. In garlic, the angle chi1 is not calculated for ALA and GLY. The angle chi2 is not calculated for ALA, CYS, GLY, SER, THR and VAL. The angle chi3 is calculated for ARG, GLN, GLU, LYS and MET, the angle chi4 is calculated for ARG and LYS and the angle CHI5 is calculated only for ARG.

CHI1
SIDE
CHAIN 		AXIS ATOMS USED TO
DEFINE ANGLE 		ZERO VALUE FORMAL RANGE
ARG CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
ASN CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
ASP CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
CYS CA-CB N-CA-CB-SG SG cis to N from -180 to +180 deg
GLN CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
GLU CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
HIS CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
ILE CA-CB N-CA-CB-CG1 CG1 cis to N from -180 to +180 deg
LEU CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
LYS CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
MET CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
PHE CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
PRO CA-CB N-CA-CB-CG CG cis to N CA-CB is part of ring
SER CA-CB N-CA-CB-OG OG cis to N from -180 to +180 deg
THR CA-CB N-CA-CB-OG1 OG1 cis to N from -180 to +180 deg
TRP CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
TYR CA-CB N-CA-CB-CG CG cis to N from -180 to +180 deg
VAL CA-CB N-CA-CB-CG1 CG1 cis to N from -180 to +180 deg
CHI2
ARG CB-CG CA-CB-CG-CD CD cis to CA from -180 to +180 deg
ASN CB-CG CA-CB-CG-OD1 OD1 cis to CA from -180 to +180 deg
ASP CB-CG CA-CB-CG-OD1 OD1 cis to CA from -180 to +180 deg
GLN CB-CG CA-CB-CG-CD CD cis to CA from -180 to +180 deg
GLU CB-CG CA-CB-CG-CD CD cis to CA from -180 to +180 deg
HIS CB-CG CA-CB-CG-ND1 ND1 cis to CA from -180 to +180 deg
ILE CB-CG1 CA-CB-CG1-CD CD cis to CA from -180 to +180 deg
LEU CB-CG CA-CB-CG-CD1 CD1 cis to CA from -180 to +180 deg
LYS CB-CG CA-CB-CG-CD CD cis to CA from -180 to +180 deg
MET CB-CG CA-CB-CG-SD SD cis to CA from -180 to +180 deg
PHE CB-CG CA-CB-CG-CD1 CD1 cis to CA from -180 to +180 deg
PRO CB-CG CA-CB-CG-CD CD cis to CA CB-CG is part of ring
TRP CB-CG CA-CB-CG-CD1 CD1 cis to CA from -180 to +180 deg
TYR CB-CG CA-CB-CG-CD1 CD1 cis to CA from -180 to +180 deg
CHI3
ARG CG-CD CB-CG-CD-NE NE cis to CB from -180 to +180 deg
GLN CG-CD CB-CG-CD-OE1 OE1 cis to CB from -180 to +180 deg
GLU CG-CD CB-CG-CD-OE1 OE1 cis to CB from -180 to +180 deg
LYS CG-CD CB-CG-CD-CE CE cis to CB from -180 to +180 deg
MET CG-SD CB-CG-SD-CE CE cis to CB from -180 to +180 deg
CHI4
ARG CD-NE CG-CD-NE-CZ CZ cis to CG from -180 to +180 deg
LYS CD-CE CG-CD-CE-NZ NZ cis to CG from -180 to +180 deg
CHI5
ARG NE-CZ CD-NE-CZ-NH1 NH1 cis to CD from -180 to +180 deg