PyMol

• select residues based on residue number

select nterm, resi 42+74+43+56+39

• mutate one amino acid

cmd.wizard("mutagenesis")
cmd.fetch("target.pdb")
cmd.get_wizard().set_mode("LEU")
cmd.get_wizard().do_select("chain A and resid 22")
cmd.get_wizard().apply()
cmd.save("mutated_target.pdb")