PLCC_Graphtypes

The graph types of PLCC

This page explains the different graph types. It is recommended that you read the more general explanation on [PLCC_Images] first. There are 6 different graph types:

1. alpha graph: consists of all alpha-helices in the protein and the contacts between them
2. alphalig graph: consists of all alpha-helices, ligands and the contacts between them
3. beta graph: consists of all beta-strands and the contacts between them
4. betalig graph: consists of all beta-strands, ligands and the contacts between them
5. albe graph: consists of all alpha-helices, beta-strands and the contacts between them
6. albelig graph: consists of all alpha-helices, beta-strands, ligands and the contacts between them

They are best explained with some images, so let's have a look at all these graphs for the sucrose-specific porin ScrY from Salmonella typhimurium (PDB 1A0S, chain P).

You already know the legend from the [PLCC_Images] page of course, but here it is again as a reminder:

The albelig graph

The albelig graph consists of all alpha-helices, beta-strands, ligands and the contacts between them. It shows a lot and may seem confusing in the beginning, but after checking out some graphs and reading the descriptions below you will surely be able to get some info from this graph within seconds. As you know, the vertices of the graph represent the SSEs of the protein and they appear in the same order as in the primary structure (from the N- to the C-terminus). The edges in the graph represent spatial contacts between SSE pairs. Note that consecutive vertices of the graph are not necessarily connected by an edge, this is because "coiled" regions separate these SSEs in the amino acid (AA) sequence.

For now, look at the footer and note that the numbers in the graph order (G) and sequence order (S) line are equal. This is always the case for the albelig graph because this graph contains all SSEs of the protein's amino acid sequence. Ligands are always listed after the real SSEs of a chain (the same way as in PDB files), so you can be sure that the SSE left of the first ligand (SSE 28 in this case) is closest to the C-terminus in the amino acid sequence.

The albe graph (a.k.a. alpha-beta graph)

The albe graph consists of all alpha-helices, beta-strands and the contacts between them. It still is pretty large for this protein chain, the only thing that's missing is the ligand. Because it is the last SSE in the sequence the G and S numbers are still equal for all SSEs in this graph.

The alphalig graph

The alphalig graph consists of all alpha-helices, ligands and the contacts between them. The only edge in this graph is a ligand contact with alpha-helix 8. Note that the numbers in the graph order (G) and sequence order (S) line of the footer differ for this graph. This is because the beta-strands in between the helices are missing in it.

The alpha graph

The alpha graph consists of all alpha-helices and the contacts between them. Note that the alpha-helices are all isolated vertices in this graph (i.e., no contacts exist between them in the protein). You can check this in the albe or albelig graphs above.

The betalig graph

The betalig graph consists of all beta-strands, ligands and the contacts between them. Note that the ligand is an isolated vertex in the beta graph because it is in contact with alpha-helices only.

The beta graph

The beta graph consists of all beta-strands and the contacts between them. Note the beta barrel in the protein, which is clearly visible as a circle of anti-parallel beta-strands in this graph. Go back to the albelig graph and find it there as well!