Detection of close contacts by covariation maps. Covariation analysis was carried out for the MSAs of 9 protein families. For each family, in the panel on the left, each trace shows what percentage of all residue pairs separated by less than 8 Å in the reference X-ray structure is present in the top L covarying pairs identified by each method. In the panel on the right, only pairs whose residues are separated by at least 20 intervening positions in sequence space are included in the analysis. True positives (covarying pairs corresponding to structural pairs < 8 Å apart) appear as upward displacements in the traces; false positives appear as horizontal segments in the traces. L ratio is the ratio between the number of sequences and the number of positions in each MSA.