We study the effect of the extreme environment in Hickson Compact groups (HCGs) on the molecular gas mass, \mhtwo, and the star formation rate (SFR) of galaxies as a function of atomic hydrogen (HI) content and evolutionary phase of the group. We have selected a redshift limited (D$<$100 Mpc) sample of 88 galaxies in 20 HCGs with available atomic hydrogen (HI) VLA maps, covering a wide range of HI deficiencies and evolutionary phases of the groups, and containing at least one spiral galaxy. We derived the far-infrared (FIR) luminosity (\lfir) from IRAS data and used it as a tracer of the SFR. We calculated the HI mass, \lfir and \mhtwo deficiencies. The mean deficiencies of \lfir and \mhtwo of spiral galaxies in HCGs are close to 0, indicating that their average SFR and molecular gas content are similar to those of isolated galaxies. However, there are indications of an excess in \mhtwo\($\sim$ 50%) in spiral galaxies in HCGs which can be interpreted as either an enhanced molecular gas content or as a higher concentration of \mhtwo towards the center in comparison to galaxies in lower density environments. In contrast, the mean \mhi of spiral galaxies in HCGs is only 12% of the expected value. The specific star formation rate (sSFR= SFR/stellar mass) tends to be lower for galaxies with a higher \mhtwo\ or \mhi\ deficiency. This trend is not seen for the star formation efficiency (SFE=SFR/\mhtwo). We found tentative indications for an enhancement of \mhtwo\ in spiral galaxies in HCGs in an early evolutionary phase and a decrease in later phases. We suggest that this might be due to an enhancement of the conversion from atomic to molecular gas due to on-going tidal interactions in an early evolutionary phase, followed by HI stripping and a decrease of the molecular gas content because of lack of replenishment.
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