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

Figure 2

Workflow for selecting stable α-helical contact residues. Starting from MD simulation data we calculated the relative presence of α-helical structures using the DSSP algorithm (left path) and the relative presence of close contacts over the simulation time (right path). The resulting sets of amino acids are intersected as to yield one list of amino acids that fulfil both criteria: (i) being located within a certain distance to the TCR for more than half of the simulation time and (ii) being part of an α-helix for more than half of the simulation time. The process results in a list of amino acids that are stable α-helices and stable close contacts. The authors inspected the list in order to rule out the fact that only parts of α-helices were selected. Subjecting only parts of a helix to the fragment-fitting method would result in the calculation of a meaningless helical axis.