[no subject]
HA A D
| |
HB? | HB? P- B-------C-E
\ | / | |
\ | / Q F
\ | /
\ |
| CO HB
| | |
CA HA- CA - CB - CG
| | |
/ | \ N HB
/ | \
/ | \
/ | \ i.e. a typical L-amino-acid
|
CO | N
CG
According to IUPAC nomenclature (Biochemistry Vol 9 1970 ...Rule 2.2.2).
IF A > P,Q and D > E > F ... or two branches are identical, then
they are
numbered in a clockwise direction when viewed down the B-C bond as follows
Case I D > E = E E has highest priority and the smallest nuber
Case II D = D > E E has lowest priority and is given the largest number
Case II D = D (no E) ... see some other rule
Later on in the paper under a section for amino acid side chains (section 4.4)
it states that for residues with two hydrogens "they are designated in
accordance
with Rule 2.2.2 Case I for CH2-R and Case III for NH2."
So, if i understand all this right, in the above Newman projection, the HB on
the left should be HB1 on the one on the right HB2.
Well we have compared a variety of programs that we have including Discover
XPLOR and CONGEN and there is no concensus in the numbering.
We are currently doing structure determination from NMR constraints, where
we the NMR people gave us many assignments called pro- R and Pro - S and we've
been trying to relate this to the numbering appropriate numbering schemes
above
and again there doesn't seem to be a consensus.
To make matters worse, we also have some D-amino acids in our structure. We
believe
that this should have no bearing on the numbering of H's from the B-groups on
out.
But again the programs differ in the numbering schemes ( and not in the same
way
as for L-amino acids.)
Can anyone out there give us insight to
A) what is the proper IUPAC numbering and a more recent reference if there is
one and
B) is this what most NMR people use ??
Thanks
Donna Bassolino
Stan Krystek
Bristol Myers Squibb Pharmaceutical Research Institute
Princeton, New Jersey 08854
Bassolino(-(at)-)BMS.COM
krystek(-(at)-)BMS.COM