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Table of bonds and their energies defined here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987896/
RSA - relative accessible surface area (relative solvent accessibility) of amino acid residue.
Measure of residue solvent exposure, in other words the extent of accessibility of acid to solvent (water)
RSA = ASA/MaxASA
ASA - solvent-accessible solvent area,
MaxASA - max solvent area for acid, taken from Rose (1985) !maybe change to Tein (2013)
Bfactor - temp factor, reflects to atomic fluctuations
Anionic acids: ASP, GLU
Cationic acids: LYS, ARG, HIS (TYR, SER)
- Barlow and Thornton. Distance cutoff of 4 Å between N-O atom pairs as a definition of salt bridge formation. Greater than this distance apart do not qualify as forming a salt bridge
Kumar and Nussinov. Distance cutoff of 4 Å between functional group centroids
https://sci-hub.se/https://doi.org/10.1002/prot.22248
http://pubs.sciepub.com/ajme/3/2/3/index.html
Donor and acceptor atoms of polar sidechains are defined from the article and released in functions isDonor() and isAcceptor()
Distance criterion: b/w donor and acceptor < 3.5 A
Angles criterion: DHA angle > 90 (donor-hydrogen-acceptor)
Hydrogen bonds between polar sidechains and mainchain/sidechain atom groups:
Hydrogen bonds between polar sidechains and water:\
- HA distance < 2.52 for SC as a donor
- 2.72 < DA distance <3.25 for SC as an acceptor
- https://pubs.rsc.org/en/content/articlelanding/2016/sc/c5sc01386k#!divAbstract
- https://sci-hub.se/10.1016/0022-2836(91)90271-7#
- https://www.jbc.org/content/273/25/15458.full.pdf
Involved aromatic side chain rings of acids: HIS, TYR, TRP, PHE
Consider 2 cases of angle b/w normals to ring planes of acids (pipi_angle):
- pipi_angle < 90 and
- pipi_angle < 90
Constraints:
- distance b/w centres of rings <= 4.4 A & pipi_angle < 30
- distance b/w centres of rings <= 5.5 A & 60 < pipi_angle < 120
version2: distance < 6 A
- https://en.wikipedia.org/wiki/Cation%E2%80%93pi_interaction
- https://www.pnas.org/content/96/17/9459
- https://pubs.rsc.org/en/content/articlelanding/2018/sc/c7sc04905f#fn1
We assume Lys and Arg are always protonated.
Cationic sidechain (Lys or Arg (more likely)) and Aromatic sidechain (Phe, Tyr, or Trp)
Distance cutoff - 6 A and angle < 30 defined here and here
Other variants (anion-Pi)
CYS amino acids with S atoms, with distance cutoff < 3A (used in RING web server).
(in article 2.3 A is used)
VdW radii taken from https://sci-hub.se/https://doi.org/10.1021/j100785a001#
- https://en.wikipedia.org/wiki/Lennard-Jones_potential Distance cutoff criteria