Geometry Dynamics of α-Helices in Different Class I Major Histocompatibility Complexes

Figure 4

Visualization of the fragment-fitting process. An ideal helical fragment of four atoms (red) is superimposed on successive pieces of an α-helix (grey) in a least-squares sense. Along the axis of the fitted helical fragment we adopt points (blue) as estimates of points on the axis of the MHC α-helix. From the very first and last superimposition we adopt one extra point each (green). The sequence of blue and green points (shown at the bottom of the figure) represents an estimate of the axis of the α-helix. Subsequently, a polynomial is fitted to these points in a least-squares sense, yielding a simple model of the α-helix from which geometric quantities can be derived.