This popup allows the user to create a graph overview of the secondary structure in a selected chain and chemical shift list. The graph is based on chemical shift differences between the observed values and the random coil values (Difference = Observed - Random Coil), 3JHnHa scalar couplings and NOE intensities. All 3 properties can be used as indicators of secondary structure elements, such as strong Hn-Hn (i,i+1) NOEs that are typically observed in alpha helices in proteins.

Residue Data

The {Residue data} tab shows an overview of the NMR data that are used as secondary structure indicators: NOE intensities, chemical shift differences and 3JHnHa scalar couplings. Values are shown on a per residue basis. Using the action buttons, the user can specify the secondary structure classification based on the residue data.

The Charts: Secondary Structure Chart popup (Residue Data).

Column Options

The Column Options is a list of all the chemical shift and 3JHnHA coupling data types that are used in the secondary structure identification. All are shown as buttons that can be used to toggle these data types on or off in the Residue data columns.

Δ δ13Cα

The difference between the observed chemical shift and the random coil value of 13C-alpha.

Δ δ13Cβ

The difference between the observed chemical shift and the random coil value of 13C-beta.

Δ δ13CO

The difference between the observed chemical shift and the random coil value of 13CO (carbonyl).

Δ δ1Hα

The difference between the observed chemical shift and the random coil value of 1H-alpha.

CSI

The chemical shift index (CSI) classification of chemical shift differences into -1, 0 and 1:

• • -1 indicates alpha helix

  • 0 no indication

  • 1 indicates beta sheet

For a detailed explanation see the original reference: Wishart, D.S. and B.D. Sykes. The 13C chemical shift index. A simple method for the identification of protein secondary structure using 13C chemical shift data. J. Biomol. NMR 4:171-180 (1994).

3JHnHα

The 3JHnHa scalar coupling, which can be used to calculate the phi angle in the protein backbone and thus are indicative of secondary structure.

See also: Vuister, G. W. & Bax, A. (1993) “Quantitative J Correlation: A New Approach for Measuring Homonuclear Three-Bond J(HNHa) Coupling Constants in 15N-Enriched Proteins”, J. Am. Chem. Soc. 115, 7772-7777.

Residue Data table

This table lists all the data for the data types selected in Column Options. NOE intensity data are only shown when NOE peak lists are considered (see {Options} tab below). NOE intensities are classified into:

• • S (Strong)

  • M (Medium)

  • W (Weak)

which are based on average peak intensity in the peak list and the boundaries set for the distinction between strong, medium and weak peaks (see {Options} tab).

Chemical shift differences are defined as: Difference = Observed - Random Coil.

Residue

Shows the residue number and name.

Sec Struc

Shows the secondary structure classification given by the user. The classification can be set using the buttons (see below):

• [Set Alpha]

• [Set Beta]

• [Set Coil]

• [Set Undef]

d_αN i,i+1

Shows the NOE intensity classification for the observed H-alpha (i) to Hn (i+1) NOE.

d_NN i,i+1

Shows the NOE intensity classification for the observed Hn (i) to Hn (i+1) NOE.

d_βN i,i+1

Shows the NOE intensity classification for the observed H-beta (i) to Hn (i+1) NOE.

d_αN i,i+3

Shows the NOE intensity classification for the observed H-alpha (i) to Hn (i+3) NOE.

d_αβ i,i+3

Shows the NOE intensity classification for the observed H-alpha (i) to H-beta (i+3) NOE.

d_αN i,i+4

Shows the NOE intensity classification for the observed H-alpha (i) to Hn (i+4) NOE.

d_NN i,i+2

Shows the NOE intensity classification for the observed Hn (i) to Hn (i+2) NOE.

d_αN i,i+2

Shows the NOE intensity classification for the observed H-alpha (i) to Hn (i+2) NOE.

Δ δ13Cα

Shows the difference between the observed chemical shift and the random coil value of 13C-alpha.

Δ δ13Cβ

Shows the difference between the observed chemical shift and the random coil value of 13C-beta.

Δ δ13CO

Shows the difference between the observed chemical shift and the random coil value of 13CO (carbonyl).

Δ δ1Hα

Shows the difference between the observed chemical shift and the random coil value of 1H-alpha.

CSI

Shows the chemical shift index (CSI) classification of chemical shift differences into -1, 0 and 1:

• • -1 indicates alpha helix

  • 0 no indication

  • 1 indicates beta sheet

For a detailed explanation see the original reference: Wishart, D.S. and B.D. Sykes. The 13C chemical shift index. A simple method for the identification of protein secondary structure using 13C chemical shift data. J. Biomol. NMR 4:171-180 (1994).

3JHnHα

Shows the 3JHnHa scalar coupling, which can be used to calculate the phi angle in the protein backbone and thus are indicative of secondary structure.

See also: Vuister, G. W. & Bax, A. (1993) “Quantitative J Correlation: A New Approach for Measuring Homonuclear Three-Bond J(HNHa) Coupling Constants in 15N-Enriched Proteins”, J. Am. Chem. Soc. 115, 7772-7777.

Set Alpha

Sets the Sec Struc (secondary structure) classification of the selected residues to Alpha helix.

Set Beta

Sets the Sec Struc (secondary structure) classification of the selected residues to Beta sheet.

Set Coil

Sets the Sec Struc (secondary structure) classification of the selected residues to Coil.

Set Undef

Sets the Sec Struc (secondary structure) classification of the selected residues to undefined.

Read CSI File

Allows the user to import a file with chemical shift index (CSI) data through the Import CSI file popup.

Make Chart

Creates a chart based on the current data and navigates to the {Chart} tab of this popup.

Options

The {Options} tab allows the user to set the options for the creation of the secondary structure chart.

The Charts: Secondary Structure Chart popup (Options).

Chain

Specifies the molecular chain for which the chart is created.

ShiftList

Specifies the chemical shift list that is used for the secondary structure residue data.

Strong/Medium

Sets the intensity boundary for the Strong - Medium boundary, which is defined relative to the average peak intensity in the NOESY peak lists.

Medium/Weak

Sets the intensity boundary for the Medium - Weak boundary, which is defined relative to the average peak intensity in the NOESY peak lists.

NOE peak lists

This is the table that lists the NOESY spectra for which peak lists can be used in the secondary structure chart.

Spectrum

The spectrum name.

Peak List

The peak list serial number for the given spectrum.

Consider?

If set to 'Yes', the peak list is used for generating the residue data in the {Residue Data} tab.

Chart

The {Chart} tab shows the secondary structure chart that is generated based on the settings in the other tabs of the popup. The chart can be printed as a postcript file by using the right mouse button (R:Print to file), which opens the Print canvas to file popup.

The Charts: Secondary Structure Chart popup (Chart).