*3.2. DOT Residues in Contact with RNA*

The residues in contact with RNA molecules are obtained by using distance cut-offs mentioned in literature, that is, 3.5 Å and 6 Å [43–45]. Binding residues in DOT regions are obtained by taking common residues in the DOT dataset and RNA contacting residues. We have classified protein–RNA complexes in non-ribosomal and ribosomal classes because of the difference in their interaction pattern, number of interacting amino acids, and residue bias in them [46]. Therefore, using the type of complex and distance cut-off for interacting residues, we divided protein–RNA complexes into four different datasets: (1) NR3.5: non-ribosomal complex with a contact distance of 3.5 Å; (2) RB3.5: ribosomal complex with a contact distance of 3.5 Å; (3) NR6: non-ribosomal complex with a contact distance of 6 Å; and (4) RB6: ribosomal complex with a contact distance of 6 Å.

We computed the frequency of each DOT residue involved in binding using the Equation (1).

$$\text{Frequency of binding residues in DOT region} = \frac{N\_{ib}}{N\_{id}}\tag{1}$$

where *Nib*: number of *i*th residues binding in the DOT region and *Nid*: number of *i*th residues in DOT.

Moreover, the differences in the frequency of binding residues in DOT regions and in the protein complexes are obtained.
