IUBio

Protein surface interpretation - help

D.K. no.email at thanks.to.spam.net
Wed Oct 6 14:57:50 EST 2004


In article <ck16qo$msu$1 at korweta.task.gda.pl>, "Stefek Borkowski" <stefek at killspam.edu> wrote:
>D.K. wrote:

>> Numbers seem reasonable. CryCo gives SAS for 1flo as 6426 A^2
>> http://atlantis.weizmann.ac.il/~eyale/cryco/cryst2.cgi?id=1lfo
>>
>> I always thought of your #2 and #3 definitions as equivalent. That
>> is, molecular surface = SAS (kinda makes sense, doesn't it?)
>> IMHO, only it makes real physical sense in general and for what
>> you want it for in particular.  I always use CNS to calculate it - it
>> gives numbers very close to GRASP which is used by many/most.
>>
>> I suspect that your number for #2 is in reality total area of
>> _crystal contacts_ of a single protein molecule with other molecules
>> in the crystal lattice. 1749 A^2 in your case, accordidng to CryCo.
>>
>> To answer your question, definitely SAS - what is not accesible
>> for water (those 1.4A), would equally not be accessible by protein
>> atoms.
>>
>> DK
>
>Thank you so much DK. Your answer is very convincing. Now I am much more
>confident that my calculations make sense. The SAS area seems the most
>rationale to be used in my analysis. I am not going to bother about the
>contact area as it looks useless for my considerations. Thanks for the link
>to CryCo - it really gives in no time an on-line and moreover free
>calculation of SAS, confirming my results obtained by offline software. You
>have done a real perfect job for me. Lots of thanks again!!! May you have a
>nice day and every success in the future! :)
>Warm greetings from still sunny Poland (quite unusual for this time of
>year!).

You are very welcome! Good luck.

DK



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