Residue Annotations and binding sites
From pfaat
What are residue annotations?
As the name implies, a residue annotation allows one to annotate a residue with relevant information. They are typically used to specify SNPs, post-translational modifications, and binding sites. One should specify an annotation name (e.g. V_VXdASA or snp) and an annotation value (e.g. 5.4 or “loss of pain perception arg211 to trp”). Once residue annotations are created, one can quickly select and analyze alignment columns of interest. One can also specify a number for each residue. This field is particularly useful when the user omits domains or segments of sequence that will offset the default numbering.
How do I create residue annotations?
The easiest way to create a sequence annotation is double click on a reside which launches the residue annotation dialog for a single sequence. A screen shot below shows the 3 tabs in the residue annotation dialog.
1. On the user numbering tab, specify a number if you wish.
2. On the annotation settings tab, click the edit /Add annotations box. Specify a color and symbol. It is recommended that the Name remains as Untitled. Click the show annotation box if you would like the residue to be displayed as a colored oval to indicate the presence of a residue annotation.
3. On the Add Annotations tab, specify annotation names and annotation values
4. Click Save.
How do I view residue annotations?
You can either double click on a residue or mouse over the residue for 5 seconds. If you are not sure which residues have residue annotations, use the '''Find''' feature described below.
Can I import residue annotations in batch mode?
1. Create a comma separated file in your spreadsheet. It should have the same format as the example file "1WWW_V_VX_dasa.csv" provided here. The following columns are required: sequenceName, RCOL, GCOL, BCOL, SYMBOL . You must also specify an integer for at least one of the following: columnNumber, residueNumber, number. For example, if you decide to specify a value for residueNumer (Res index), then you must specify '''-1''' for columnNumber and number.
2. On the File menu, Click on Import -> Residue Annotations...
How do I change the numbering of my favorite sequence?
You do this by specifying the start number for the 1st residue. All other residue numbers will be incremented accordingly.
Edit -> Set -> Start Number...
1. On the Edit menu, click on Set -> Start Number...
2. Select the sequence name. e.g. NGF_HUMAN
3. Type the new start number for the first residue.
How do I find and select binding site residues?
In this example, residue annotations were created by first computing the change in residue solvent accessibility using Analysis->Compute delta RSA at Binding Site... The process was performed twice for the 2 chains of TRKA (chains X and Y of PDB 1WWW) that interact with NGF (chain V of PDB 1WWW). This yielded two residue annotations called V_VYdASA and V_VXdASA.
Alternatively, one could have computed a single residue annotation called deltaRSA by specifying both chains X and Y in the Compute delta RSA at Binding Site... dialog. The former approach requires 2 search terms where as the latter approach only requires a single search term for deltaRSA.
In this example, a theshold greater than 5 is used although other values (e.g. 0-10) are also valid.
Find -> Residue Annotations… or CTRL-R
1. Select one sequence name e.g NGF_HUMAN as described here.
2. On the Find menu, click Residue Annotations… or type CTRL-R.
3. Click on selected sequences to reduce the search time.
4. For search term A, change the Any Field drop-down to V_VYdASA , change the Contains drop-down to Is greater than, and type 5 in to the text field.
5. Click the Add button to create search term B.
6. For search term B, change the Any Field drop-down to V_VXdASA , change the Contains drop-down to Is greater than, type 5 into the text field, and change the and drop-down to or.
7. Check Select found, check Extend selection to column, check Clear Prior selection , and check Clear current found.
8. Optional: Check Hide unselcted columns. This will hide residues that are not part of the binding site.
9. Click the Find button
How do I compute percent identities at the binding site?
This feature is described here.
How do I hide residues that are not part of the binding site?
View -> Hide -> Unselected columns
1. 1. Select the binding site columns as described here.
2. On the View menu, click Hide -> Unselected columns.
How do I save the binding site residues as a publication quality graphic?
This feature is described here.
