ap_BackboneHBondMap

Reads a PDB file and calculates a map of backbone hydrogen bonds, providing also the geometry of each bond.

The results’ table printed on stdout looks like below:

# 42 hydrogen bonds found in backbone: TYR 3 -> THR 18 : 2.620 3.346 165.58 94.25 -1.170 -0.702 0.211 2.515 16.25 163.29 LYS 4 -> LYS 50 : 2.259 3.156 120.71 159.88 -1.310 1.445 1.249 1.205 57.75 40.83 LEU 5 -> THR 16 : 1.838 2.802 143.84 -115.27 -2.834 0.102 -1.075 1.488 35.98 -84.57 ….

and provides: - H donor residue name and id (columns 1 and 2) - H acceptor residue name and id (columns 4 and 5) - two distances: r(O..H) and r(N..O) (columns 7 and 8) - planar(C-O..H) and dihedral(C-O..H-N) (columns 9 and 10) - DSSP energy for this bond (column 11) - X,Y,Z coordinates of H atom in the local coordinates system (columns 12, 13 and 14) - theta, phi spherical coordinates of H atom (columns 15 and 16) USAGE: ap_BackboneHBondMap 5edw.pdb

Keywords:

Categories:

  • core/calc/structural/BackboneHBondMap
../_images/ap_BackboneHBondMap-2gb1.png