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

Figure 3

Helical residues and close TCR contacts. The atomic surface in green represents stable α-helical amino acids of the MHC that were identified by the method described in Section 2.3. The atomic surface in red represents amino acids in close proximity of the TCR with varying distance cut-offs: (a) 0.8 nm, (b) 1.2 nm, and (c) 1.4 nm. Some parts of the MHC α-helices G-ALPHA1 and G-ALPHA2 comprise the protein-protein interface between TCR and pMHC and, as expected, atomic surfaces in green and red overlap. However, not all parts of the α-helices belong to the close contacts even when the cut-off is set at 1.4 nm. For calculation of the helical axis we skipped the parts that are not overlapping and not directly interacting with the TCR. Visualization was done with VMD [43]. The contact map was calculated between atoms to determine which atoms are in close contacts.

(a)

(b)

(c)