Hi 
What modification can I make in arginine and how to make
peptidomimetic in the above ARPF sequence?

I think you'll have to provide a little more info than you have in
order to answer this question. You could make any modification to the
arginine R group so long as it didn't mess up the amino acid backbone,
and the molecule would still be peptidomimetic, because it would still
be a peptide. Are you looking for a specific receptor/cell signaling
pathway/etc. that it could still mimic?

So you have two questions here. 

The first one is ambiguous.  How do you want to modify arginine?  Do
you want an isostere of arginine? eg, something not so polar and
basic, but will still recognize some arginine complimentarity, or, are
you asking something more nebulous, like can you make a prodrug, or
what are all the modifications to arginine to fit in your unknown
binding pocket?

The next question, you won't get an answer for 15 bucks that is even
worth 15 cents.  At the least, you would need to try a ligand based
approach, that is, model your  peptide in a water box to guess what
the secondary structure is before attempting some type of
peptidomimetic.  Better yet, do a homology search and see if you can
find this motif in other proteins or ligands(that is if you're trying
some Beta Turn mimetic).  Better even still, if you have binding site
structure from NMR, or crystallograpy then you've got something to go
on.

Then figure out what to build.

Chugs,
Bob

ARPF is a sequence at the N terminus of an endogenous peptide inhibitor to IAP.
What substitution on side chain of Arginine will make it less basic
and more hydrophobic?

Any of these would make the appropriate substitute: VAILMWYF

Or do you mean keeping arginine intact and adding on moieties to that?
Also, do you want to keep intact its signaling ability?

Try a google search "Arginine isostere"

There are probably hundreds. Acetylate it would be the easiest. But
you still gotta fill up a pocket and have it do its job.  Without
something to work from, everything said is virtually of no value. Go
to the library, look on pubmed.  Otherwise make a library of peptides
with substitutions and see what you get.  Maybe you find out you don't
need arginine.  If you want someone to design you an isostere, it's
not going to happen for 15 bucks, let alone teach you medicinal
chemistry.

IAP=integrin associated protein?  No crystal structure.  Is there a
sequence?  Homologus to what other protein?  I don't think theres a
google genius with that set of skills, and this kind of work, I don't
do for free.  Maybe someone else will get you a simplistic answer to
get you going.

Just be forewarned, any answer you get to this question without doing
your own leg work is going to be a huge waste of time in my opinion,
because you don't have any structure information to go on.

my best guesses:  4 amino phenylalanine, 4-cyano phenylalanine,
phenylalanine-4-carboxamidine, 4 guanidino-phenylalanine, Lysine.

have fun!

For those who do not know IAP is Inhibitor of apoptosis protein that
targets caspase.