What is the first step in determining the hydropathy index for a stretch of amino acids?

The first step in determining the hydropathy index for a stretch of amino acids involves assigning hydrophobic values to each residue. This step is crucial because the hydropathy index is a measure of the hydrophobic or hydrophilic characteristics of the individual amino acids in a protein sequence. Each amino acid has an associated hydropathy value that indicates its tendency to be hydrophobic (water-repelling) or hydrophilic (water-attracting).

By assigning these values first, you create a foundation for analyzing the entire peptide sequence. This initial assignment allows you to subsequently calculate averages, perform windowing analysis, and plot the values. Having a clear understanding of each residue's hydropathy is essential before moving on to averaging values or plotting them, as the results will depend on the correct assignment of these hydrophobic characteristics.