  We equip a knot $K$ with a set of colored bonds, that is, colored intervals
properly embedded into $\mathbb{R}^3 \setminus K$. Such a construction can be
viewed as a structure that topologically models a closed protein chain
including any type of bridges connecting the backbone residues. We introduce an
invariant of such colored bonded knots that respects the HOMFLYPT relation,
namely the HOMFLYPT skein module of colored bonded knots. We show that the
rigid version of the module is freely generated by colored $\Theta$-curves and
handcuff links, while the non-rigid version is freely generated by the
trivially embedded $\Theta$-curve. The latter module, however, does not provide
information about the knottedness of the bonds.
