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Peptidestructure

Richard Friedman friedman at convex.hhmi.columbia.edu
Thu Mar 20 04:26:58 EST 1997


Dear Linda,
I will reproduce an e-letter that Eric Cabot of GCG sent me
when I asked the same questions. I believe that it
answers everything but the method used in the Hydrophobicity
column, which we are still vague on.
Best wishes,
Rich

Richard,


	Here is the correspondance between the terms used in the 
Chou &
Fasman papers and PEPPLOT.
==========================================

 C&F	PEPPLOT
============	============
Pa	Alpha Stat = Pa /100
<Pa>	Alpha Ave	= <Pa>/100
Pb	Beta Stat	= Pb/100
<Pb>	Beta Ave	= Pa/100
<pt>	Turn	= Pb/10,000

==========================================

 For example, here is a comparison of the dataset analyzed 
in Prevelige and
Fasman (1989) and PEPPLOT (only the first line is shown 
here):

PEPPLOT:
	Alpha	Alpha	Beta	Beta	Alpha	Beta
	Pos Res	Stat	Ave	Stat	Ave	NH2	COOH	NH2	COOH	Turn	HPhob
	
------------------------------------------------------------
------------ ..
	1	A	1.42	1.09	0.83	1.10	0.68	0.68	1.23	0.39	0.39	0.00

Prevelige and Fasman:
	Pa	<Pa>	Pb	<Pb>	<pt>
	142	109	83	109	3.9 x 10^-5


 The following are not mentioned in the Chou and Fasman 
papers but are
documented in the PEPPLOT chapter of the GCG Program Manual:

Alpha NH2	- not mentioned in C&F paper
Alpha COOH	"
Beta NH2	"
Beta COOH	"


 I hope that this clarifies matters for you somewhat.

Regards,

	Eric L. Cabot, Ph.D.



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