Steps for contact mapping

1. See the Setup file, this:

• We produced a human reference SH2 CSV file. We hand annotated/identified differences (as noted in the notebook)
• We produced a human reference SH2 Fasta file
• We used promals3d to align
• We produced a structure reference file for all PDB IDs for the uniprot IDs from our reference, then annotated that structure reference file with UniprotRefFile in order to get inclusive domains.
• We filtered to relevant PDBs that spanned SH2 domains within them.

2. AlphaFold
3. CIF file fetch
4. Adjacency