Specific sequence combinations at parallel and antiparallel helix–helix interfaces

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Orientation of helices at parallel and antiparallel helix–helix interfaces in proteins depends on interacting amino acids from both helices. Particularly important are amino acids at positions analogous to a and d in GCN4 leucine zipper nomenclature, which form hydrophobic core. In this work repeating sequence combinations at a and d positions characteristic for both parallel and antiparallel packing are shown. Layer packing of hydrophobic groups is compared for possible combinations of aliphatic amino acids at all four positions. Correlation between specific position of methyl groups and interhelical angle is found for parallel and antiparallel types of packing.