arg_forks

Analyze arginine-RNA interactions

Dependencies

You must install LOOS (download at https://github.com/GrossfieldLab/loos) to use this script. See INSTALL.md for installation instructions and dependencies.

Usage

Basic usage is

get_arg_rna_contacts.py XXXX.pdb

To assign RNA backbone suites, you must specify the location of the suite definition file from LOOS (i.e. suitename_definitions.dat) with the -b flag.

get_arg_rna_contacts.py -b $CONDA_PREFIX/share/loos/suitename_defintions.dat \
    XXXX.pdb

The -d, -s, -a, and -w flags change the cutoffs for the hydrogen bond distance, the stacking distance, the stacking angle, and the rotamer width. For example, the following changes the rotamer width to 30 deg.

get_arg_rna_contacts.py -b $CONDA_PREFIX/share/loos/suitename_defintions.dat \
    -w 30 XXXX.pdb

By default, atoms in the proteins are any atom with residue name "ARG". Atoms in the RNA are any atom with residue name "A", "C", "G", or "U" possibly followed by exactly one of "3", "5", or "N". These defaults can be changed with the -p and -r flags, respectively.

Output

Output is tab-delimited with one row per arginine-RNA hydrogen bond. The output columns are the PDB file followed by the arginine donor chain ID, residue ID, residue name, and atom name and then the RNA acceptor chain ID, residue ID, residue name, and atom name. Next are the heavy atom hydrogen bond distance in angstroms, the angle between the normal vectors of the guanidinium group and the nucleobase in deg, the protein backbone torsions (phi and psi) in deg, and the arginine rotamer. If RNA backbone suites were requested, the assigne suited and suiteness score are given next. Finally, for each RNA nucleobase that stacks on the guanidinium group, the output will contain the RNA residue name, RNA residue ID, stacking distance in angstroms, and angle between the normal vectors in deg.

For arginine rotamers and RNA backbone suites, a string containing an exclamation mark "!" indicates that the residue was assigned as an outlier. For RNA backbone suites, "NN" indicates that there was no valid dinucleotide to which to assign a backbone conformation because of a chain termination.