Capillary and van der Waals forces cause nanotubes to deform or even collapse under metal contacts. Using ab-initio bandstructure calculations, we find that these deformations reduce the bandgap by as much as 30%, while fully collapsed nanotubes become metallic. Moreover degeneracy lifting, due to the broken axial symmetry and wavefunctions mismatch between the fully collapsed and the round portions of a CNT, leads to a three times higher contact resistance. The latter we demonstrate by contact resistance calculations within the tight-binding approach.