A method for detecting hydrophobic patches on protein surfaces

P. Lijnzaad, H. J.C. Berendsen, P. Argos

Onderzoeksoutput: Bijdrage aan tijdschriftArtikelpeer review

50 Citaten (Scopus)


A method for the detection of hydrophobic patches on the surfaces of protein tertiary structures is presented. It delineates explicit contiguous pieces of surface of arbitrary size and shape that consist solely of carbon and sulphur atoms using a dot representation of the solvent-accessible surface. The technique is also useful in detecting surface segments with other characteristics, such as polar patches. Its potential as a tool in the study of protein-protein interactions and substrate recognition is demonstrated by applying the method to myoglobin, Leu/ILe/Val-binding protein, lipase, lysozyme, azurin, triose phosphate isomerase, carbonic anhydrase, and phosphoglycerate kinase. Only the largest patches, having sizes exceeding random expectation, are deemed meaningful. In addition to well-known hydrophobic patches on these proteins, a number of other patches are found, and their significance is discussed. The method is simple, fast, and robust. The program text is obtainable by anonymous ftp.

Originele taal-2Engels
Pagina's (van-tot)192-203
Aantal pagina's12
TijdschriftProteins: Structure, Function and Genetics
Nummer van het tijdschrift2
StatusGepubliceerd - 1996
Extern gepubliceerdJa


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