In this work, we predict G-protein coupled receptors (GPCRs) using hydrophobicity of amino acid sequences and Fast Fourier Transform for feature generation. We analyze whether the GPCRs classification strategy depends on the way the feature space may be exploited. Consequently, we show that the sequence pattern based information could easily be exploited in the frequency domain using proximity rather than increasing margin of separation between the classes. We thus develop a simple proximity based approach known as nearest neighbor (NN) for classifying the 17 GPCRs subfamilies. The NN classifier has outperformed the one against all implementation of support vector machine using both Jackknife and independent dataset. The results validate the importance of the understanding and efficient exploitation of the feature space. It also shows that simple classification strategies may outperform complex ones because of the efficient exploitation of the feature space. (C) 2008 Elsevier Inc. All rights reserved.