To separate the proton structure functions into calculable processes and parton distribution functions (PDFs), there are various schemes such as the Fixed-Flavor Number (FFN) and the General Mass Variable-Flavor Number (GM-VFN) schemes. In this Next-to-Leading Order (NLO) Quantum Chromo Dynamics (QCD) analysis we determine PDFs based on the four different HERA I and II combined, H1-ZEUS combined charm production and H1 and ZEUS beauty production cross sections data sets in FFN scheme (FFNS). This FFNS QCD analysis attempts to exactly separate the role and influence of the strong coupling $\alpha_s(M^2_Z)$ as an important phenomenological parameter from contribution of the heavy-flavor data in determination of PDFs shape, fit-quality and improvement of the uncertainty bands of PDFs. To reach this goal we use two different scenarios. At the first scenario we fix the strong coupling value and determine the PDFs based on the heavy-flavor data only. In the second scenario we determine the same PDFs based on the heavy-flavor data plus the strong coupling as an extra QCD parameter.