NEF Atom Names

The naming of atoms for the NMR Exchange Format (NEF) mostly follows the IUPAC convention.

Backbone

For the backbone this is:

H - amide hydrogen

N - amide nitrogen

CA - alpha carbon

HA - alpha hydrogen

C - carbonyl carbon

O - carbonyl oxygen

Side Chains

The side chains follow the usual CB/CG/CD etc. pattern. However, additional atom names have been specified to allow for non-stereospecifically assigned protons or protons with degenerate chemical shifts. Thus beta hydrogen atoms would be denoted in the following ways:

HB2 and HB3 - stereospecifically assigned beta methylene group

HBx and HBy - non-stereospecifically assigned beta methylene group

HB% - beta methylene (or methyl) group with degenerate proton chemical shifts

Note that for e.g. isopropyl groups the x and y assignments match up between the protons and carbons so that Leu HDx% are the methyl protons bound to Leu CDx.

N-terminus

By default the N-terminus is protonated. The amide protons of the N-terminus are denoted as H%.

C-terminus

By default the C-terminus carboxylate group is deprotonated. Standard atoms include:

O - carbonyl oxygen

OXT - carboxylate oxygen

Full list of possible atom names for all natural amino acids

The images below show all the possible NEF atom names for the atoms in the 20 natural amino acids. The x/y notation is for situations when the assignment is non-stereospecific and the % notation for situations where chemical shifts are degenerate. Note that for amino acids such as Val or Leu the methyl protons will usually be degenerate within a methyl group (e.g. HG1% and HG2% for Val), but that both methyl groups may also be degenerate and have the same chemical shift (in which case all Val methyl protons become HG%). Please also be aware that the x/y notation is arbitrary, i.e. HBx does not always correspond to HB2 and HBx to HB3 etc. This correspondence is simply used in the graphics for convenience and consistency. A pdf file with all atoms names is available for download.