Charge Density (Lehninger)

The Charge Density (Lehninger) track predicts regions of positive and negative charge by summing charge over a specific range of residues. DNASTAR developed this method using the pK tables of Lehninger, 2005. Since charged residues tend to lie on the surfaces of proteins, this method aids in predicting surface characteristics. A set of data is generated that can be displayed three ways: a line plot graph of average charge, a region graph of negative charge and another region graph of positive charge. The method is sensitive to small changes in parameter settings, so you may wish to set up multiple plots to compare how parameter changes affect each plot.

To apply this track to the sequence:

In the Tracks panel, check the box next to Charge Density (Lehninger). The track will now be visible in the Analysis view

To edit track options:

Select the track in the Tracks panel. Open the Track Options section, which appears as follows:

• Residues to Average – the size of the window used to average the charge on consecutive residues. Inputting a high value will smooth the curve, while a low value will make the method more sensitive to charge differences between adjacent amino acids. The default is 9.

• pH – desired pH for calculating pK values for each residue. The default is 7.0.

• Positive Region is - the threshold value for a region to be considered positive. The default is 0.1.

• Negative Region is – the threshold value for a region to be considered negative. The default is -0.1.

Click if you wish to return to the default values.