atomdeps: Atom parameters and definitions for side chains

In compas: Conformational Manipulations of Protein Atomic Structures

Description

List of the atom dependencies and typical bond parameters in protein structures for side chains of the 20 standard amino acid types.

Usage

atomdeps

Format

A list for the 20 amino acid types, each having the attributes

• "tangle": Dihedral angle defined by atoms A-B-C-D as described below. NA's represent the free side chain dihedral angles chi for that amino acid.

• "names": The component atoms of the amino acid side chain. Represents atom D in the dihedral.

• "matx": The names of atoms A,B,C in the dihedral, with rows corresponding to the atoms in "names".

• "bangle": Planar bond angle formed between B-C-D

• "blength": Bond length between C-D

References

Engh, Richard A., and Robert Huber. "Accurate bond and angle parameters for X-ray protein structure refinement." Acta Crystallographica Section A 47.4 (1991): 392-400.

compas documentation built on Jan. 9, 2022, 1:06 a.m.