How to specify to PINE peaks that are known to arise from particular residue types: for example, from residue-selective labeling


  • Pine offers the ability to specify whether peaks are known to be from a particular residue type.
  • This is accomplished by including a labeling information file along with the other files uploaded to the PINE webserver.
  • The labeling information file must include all the 15N and 1H peaks from the particular residue type along with the amino acid name in the first column. If multiple residue choices are available for some 15N and 1H peaks, the information should be repeated for all residues (see example below). All the information should be included in a single file, even if you have done selective labeling for more than one residue  (see the example below)
  • Notice that if an NH peak is labeled with a specific residue type (ARG for example), it can only be assigned to an ARG residue in the protein.
  • Please make sure that the chemical shifts of the NH peaks in the labeling file are compatible with those in your HN HSQC file.


Example of a labeling information file


  ARG    7.743    122.381
ARG    8.015    121.473             These four peaks can be assigned only to ARG residues
ARG    8.555    119.735      
ARG    7.383    117.911

HIS    7.220    116.267
HIS    6.958    122.982               These three peaks can be assigned only to HIS residues
HIS    9.263    123.305
GLY    7.373    105.609
GLY    7.954    110.980              These three peaks can be assigned only to GLY residues     
GLY    8.294    110.563

SER    7.881    114.230
SER    8.742    116.231
SER    8.365    115.314
SER    8.246    114.472           These set of peaks can be assigned to SER or TRP (Peaks have been repeated)
SER    8.303    119.001
TRP    7.881    114.230
TRP    8.742    116.231
TRP    8.365    115.314
TRP    8.246    114.472
TRP    8.303    119.001