Continuous epitopes are composed of a contiguous sequence of amino acids in a protein. Anti-peptide antibodies will bind to these types of epitopes in the native protein provided the sequence is not buried in the interior of the protein. Discontinuous epitopes consist of a group of amino acids that are not contiguous but are brought together by folding of the peptide chain or by the juxtaposition of two separate polypeptide chains. When examining a protein sequence for potential antigenic epitopes, it is important to choose sequences which are hydrophilic, surface-oriented, and flexible 3 . Most naturally occurring proteins in aqueous solutions have their hydrophilic residues on the surface and their hydrophobic residues buried in the interior.
Antibodies bind to epitopes on the surface of proteins.
Additionally, it has been shown that epitopes have a high degree of mobility 4 . If the protein is an integral membrane protein and the C-terminus is part of the transmembrane segment, this sequence will be too hydrophobic and not a good choice. If a protein sequence is derived from the cDNA sequence, the leader sequence should not be included in the sequence selected for antibody generation. Hydrophilicity plots as described by Hopp and Woods 5 assign an average hydrophilicity value for each residue in the sequence. The highest point of average hydrophilicity for a series of contiguous residues is usually at or near an antigenic determinant.