The V3 loop of the human immunodeficiency virus type 1 (HIV-1) envelope protein is a highly variable region that is both functionally and immunologically important. Using available amino acid sequences from the V3 region, we have used an information theoretic quantity called mutual information, a measure of covariation, to quantify dependence between mutations in the loop. Certain pairs of sites, including non-contiguous sites along the sequence, do not have independent mutations but display considerable, statistically significant, covarying mutations as measured by mutual information. For the pairs of sites with the highest mutual information, specific amino acids were identified that were highly predictive of amino acids in the linked site. The observed interdependence between variable sites may have implications for structural or functional relationships; separate experimental evidence indicates functional linkage between some of the pairs of sites with high mutual information. Further specific mutational studies of the V3 loop's role in determining viral phenotype are suggested by our analyses. Also, the implications of our results may be important to consider for V3 peptide vaccine design. The methods used here are generally applicable to the study of variable proteins.