pepcoil calculates the probability of a coiled-coil structure for windows of (by default) 28 residues through a protein sequence using the method of Lupas A, van Dyke M & Stock J (1991); Science 252:1162-4. It reads one or more sequences and writes a standard EMBOSS report file including the location and score of the putative coiled-coil structures and their score for each input sequence. Optionally, coiled coil regions, non-coiled coil regions and coil frameshifts are reported.
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Coiled coils are formed by two or three alpha helices in parallel and in register that cross at an angle of approximately 20 degrees, are strongly amphipathic and display a pattern of hydrophilic and hydrophobic residues that is repeated every seven residues. The seven positions of the heptad repeat are designated a through g, a and d being generally hydrophobic, while the others are hydrophilic.
The parallel two-stranded alpha-helical coiled coil is the most frequently encountered subunit-oligomerization motif in proteins.
Original program "PEPCOIL" by Peter Rice (EGCG 1991)