Frequently Asked Questions
1. What is the ligand (substrate) nomenclature?
AFAL ligand nomenclature follows the Protein Data Bank convention: capitalized 3-letter codes.
2. The ligand that I need is not in the pre-established list. What should I do?
You may search the ligand of interest in Ligand Expo (http://ligand-expo.rcsb.org/ld-search.html) and then type the 3 letter code in the corresponding box. Remember to put the option OTHER in the pull-down menu.
3. The organism or protein family name I need is not in the pre-established list. What should I do?
You may type the name of the organisms in the corresponding box, following standard taxonomic criteria. Don´t forget put the option OTHER in the pull-down menu.
4. How long do I have to wait to receive the results?
Most results produced by AFAL are sent to the users email address in a couple of minutes. In some cases this may take significantly longer depending on the number of calculations required. Please, contact the authors directly if you encounter any problems and/or waiting times are longer than desired.
5. What happens if the e-mail does not arrive to my e-mail account?
Please check the Spam folder, submit again or contact the authors directly (marenas@utalca.cl).
6. What is the format of AFAL results?
AFAL results are sent to the users email account and a html link where tables, graphs and interactive menus are displayed.
7. What should I do if I want to analyze PDBs obtained from NMR?
Simply type <0> in the 'resolution' field.
8. What does the filter "Remove protein homologs" do?
This filter removes all proteins (PDB files) that have sequence identity to other proteins in the database greater than 30%, so as to remove redundancy. This filter was built using the software Pisces (G. Wang and R. L. Dunbrack, Jr. Bioinformatics, 19:1589-1591, 2003.)
9. Is this service only for academic use?
Yes. For other purposes please contact the author (marenas@utalca.cl)
10. Please cite the following in any work that uses AFAL
Mauricio Arenas-Salinas, Samuel Ortega-Salazar, Fernando Gonzales-Nilo, Ehmke Pohl, David S. Holmes, Raquel Quatrini. AFAL: a web service for profiling amino acids surrounding ligands in proteins. Journal of Computer-Aided Molecular Design. DOI: 10.1007/s10822-014-9783-6.
11. Results interpretation example:
If the AFAL graph shows that Alanine has a relative frequency of occurrence of 100%, this means that in all PDB files analyzed having the ligand of interest (eg. ATP), the amino acid Alanine occurs within 3.5 A around the ligand. For additional examples, see the Example section.
12. Why do I have to open one new windows of result at each consultation?
To avoid results overwriting and loss information of interest, AFAL generates a new window for each consultation.
Supporting information
13. Frequency of occurrence of each amino acid in proteins in general (ALL) and in particular protein families for all proteins available in the PDB data base (percentual). [see Arenas et al., submitted. Table S1].
14. Probable contact profiles derived from all protein family motifs stored in the Prosite database. [see Arenas et al., submitted. Table S2].
15.Types of interactions suggested on base of the R(AA)-ligand distance. [see Arenas et al., submitted. Table S3].
16. Overall frequency of occurrence of each amino acid in proteins in general (ALL) and in the protein family in particular, for protein available in PDB data base.
amino acid |
Oxidoreductases (%) |
Transferases (%) |
Hydrolases (%) |
Lyases (%) |
Isomerases (%) |
Ligases (%) |
ALL (%) |
| ALA | 8.78 | 7.87 | 7.74 | 9.36 | 9.11 | 8.09 | 8.21 |
| CYS | 1.86 | 2.05 | 2.27 | 1.88 | 1.86 | 2.08 | 2.06 |
| ASP | 5.99 | 6.01 | 6.18 | 6.15 | 6.20 | 6.12 | 6.08 |
| GLU | 7.06 | 7.65 | 6.84 | 7.22 | 7.64 | 8.19 | 7.25 |
| PHE | 4.02 | 3.70 | 3.64 | 3.61 | 3.77 | 3.87 | 3.75 |
| GLY | 7.61 | 6.75 | 7.47 | 7.60 | 7.85 | 7.28 | 7.31 |
| HIS | 3.08 | 2.96 | 2.75 | 3.09 | 3.09 | 2.84 | 2.93 |
| ILE | 5.80 | 6.21 | 6.04 | 6.08 | 6.17 | 6.04 | 6.05 |
| LYS | 5.15 | 5.70 | 5.29 | 5.20 | 5.39 | 5.52 | 5.39 |
| LEU | 8.34 | 9.00 | 8.09 | 8.73 | 8.13 | 8.72 | 8.49 |
| MET | 2.34 | 2.42 | 2.05 | 2.35 | 2.31 | 2.29 | 2.27 |
| ASN | 4.45 | 4.31 | 4.97 | 4.29 | 4.31 | 4.12 | 4.55 |
| PRO | 5.17 | 4.76 | 4.75 | 4.80 | 4.66 | 5.06 | 4.86 |
| GLN | 3.57 | 3.77 | 3.96 | 3.68 | 3.57 | 3.62 | 3,77 |
| ARG | 4.72 | 5.12 | 4.55 | 4.82 | 4.95 | 5.36 | 4.83 |
| SER | 5.57 | 5.84 | 6.41 | 5.54 | 5.31 | 5.28 | 5.89 |
| THR | 5.14 | 4.92 | 5.44 | 4.86 | 4.88 | 4.67 | 5.12 |
| VAL | 6.86 | 6.59 | 6.41 | 6.53 | 6.71 | 6.57 | 6.59 |
| TRP | 1.40 | 1.14 | 1.54 | 1.18 | 1.23 | 1.10 | 1.33 |
| TYR | 3.08 | 3.24 | 3.61 | 3.03 | 2.86 | 3.19 | 3.29 |
Additional references:
- Villar, H. O., & Kauvar, L. M. (1994). Amino acid preferences at protein binding sites. FEBS letters, 349(1), 125–30.
- Bartlett, G. J., Porter, C. T., Borkakoti, N., & Thornton, J. M. (2002). Analysis of Catalytic Residues in Enzyme Active Sites. Journal of Molecular Biology, 324(1), 105–121.
