Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis.
We developed dictionaries of two-, three-, and five-residue patterns in proteins and computed the average solvent accessibility of the central residues in their native proteins. These dictionaries serve as a look-up table for making subsequent predictions of solvent accessibility of amino acid residues. We find that predictions made in this way are very close to those made using more sophisticated methods of solvent accessibility prediction. We also analyzed the effect of immediate neighbors on the solvent accessibility of residues. This helps us in understanding how the same residue type may have different accessible surface areas in different proteins and in different positions of the same protein. We observe that certain residues have a tendency to increase or decrease the solvent accessibility of their neighboring residues in C- or N-terminal positions. Interestingly, the C-terminal and N-terminal neighbor residues are found to have asymmetric roles in modifying solvent accessibility of residues. As expected, similar neighbors enhance the hydrophobic or hydrophilic character of residues. Detailed look-up tables are provided on the web at www.netasa.org/look-up/.
Wang
Jung-Ying
JY
Department of Multimedia and Game Science, Lunghwa University of Science and Technology, Taoyuan, Taiwan.
Ahmad
Shandar
S
Gromiha
M Michael
MM
Sarai
Akinori
A
D000595:Amino Acid Sequence; D016208:Databases, Factual; D016571:Neural Networks, Computer; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D013223:Statistics as Topic
D011506:Proteins; D012997:Solvents