Ridges into grooves packing

In aqueous buffer, pardaxin is comprised of four antiparallel monomers tightly packed with 2-fold symmetry of the "4-4 ridges into grooves" type the hydro-phobic amino-terminal segments of pardaxin monomers are shielded from the aqueous surface in the tetramer which most probably exposes the polar side chain to water. 

Fig. 9. Coiled-coil spirals. For the phage coat proteins and flagellin, subunits are shown enlarged next to the structures, as well as the cross sections of the coiled-coil sheets they form. The positions of the subunits in the structures are indicated in white. The core packing layers are also shown for the phage coat proteins in order to illustrate the use of knobs-into-holes and ridges-into-grooves layers.

Fig. 2.14. The projections b and c of a helix (a). The residues of an a helix are represented by white circles, i, i + 3, i + 4, etc. The helix is opened and flattened projections are represented the one face up (b), the other face down (c). These projections will allow the packing of two helices. The ridges into grooves model for helix-helix packing generates three models of interactions (d). In class I, residues forming rows are i 3n, j 3n for the first and the second helix respectively. The value for ideal helices is — 82°. In class II, residues forming rows are i + 4n and j 4n for each helix respectively the resulting angle is —60°. In class III, the residues in rows are i 4 , j 3n for the first and second helix respectively the angle Q is -H19°. The helix-helix interactions are schematically represented for the three classes (from Chothia et fl/., 1977).

The most common way of packing a helices is by fitting the ridges formed by a row of residues separated in sequence by four in one helix into the same type of grooves in the other helix. In this case the ridges and... 

One a helix may pack on another by the mutual intercalation of side chains such that a ridge of projecting side chains on one helix fits into a groove ... 

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