Protein similarity via hydropathy plots?

Michael Coyne mjcoyne at
Thu Apr 7 12:39:37 EST 1994

Hi all...

Can anyone out there help me to understand how similarity between
hydropathy plots is assessed?  I fear I'm missing something quite obivous
here, but...  They all look like a bunch of squiggly lines tracing peaks
and valleys.

I have not been looking at these types of plots for long, and fear there
may be something very obvious to the experienced eye that escapes me.  As
an example, see R. Morona, 1994. J. Bacteriol. 176(3):733-747,
specifically Figure 6 on page 743.  I need to use an approach similar to
that outlined in this paper and others to tentatively identify an amino
acid sequence as similar (or not) to others.  My hydropathy plot looks
"just like" all the others I've seen, essentially like those in the paper
referenced above.

On what basis are these tracings, grossly similar to one another, assummed
to show similarity at a level from which a conclusion can be drawn?

Thanks for any help or comments, a suggestion as to a book that might help
me understand would also be welcome...

mjcoyne at

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