Pair-wise residue-residue contacts in proteins can be predicted from both threading templates and sequence-based machine learning. However, most structure modeling approaches only use the template-based contact predictions in guiding the simulations, this is partly because the sequence-based contact predictions are usually considered to be less accurate than that by threading. With the rapid progress in sequence databases and machine-learning techniques, it is necessary to have a detailed and comprehensive assessment of the contact-prediction methods in different template conditions.