TCR Shift Calculation

The binding mode of the TCR to the pMHC can be described in Cartesian coordinates. The TCR center is determined by projecting the positions of the TCR variable domains and averaging positions of SG atoms of conserved cysteine residues, or if absent, CA atoms, onto the pMHC plane. This allows the calculation of the mean positions of TCR. The output is represented by TCR X position and TCR Y position, where:

• A more negative TCR X position indicates that the TCR will be positioned positioned closer to the N terminus of the pMHC, while a more positive TCR X position indicates the TCR will be positioned closer to the C terminus.
• A more negative TCR Y position indicates that the TCR will be positioned closer towards the α1 helix of the MHC, while a more positive TCR Y position, indicates the TCR will closer to the α2 helix of the MHC.