Atomic coordinate file

From Proteopedia

Atomic coordinate files are the data files that specify three-dimensional (3D) molecular structures. At a minimum, they must specify the positions of each atom in space, typically with X, Y and Z Cartesian coordinates.

Atomic coordinate files use many possible data formats. The XYZ format (file type .xyz) is specifies only the coordinates for each atom, and is useful for small molecules. This format is not adequate for macromolecules because additional information is needed for their atoms.

Macromolecular atomic coordinate files need to specify quite a bit of information in addition to the position of each atom in space. Each atom either belongs to a Standard Residue or not. If not, it is designated a hetero atom. The position of each atom within a standard residue is specified, e.g. carbon atoms in amino acids can be the carboxy carbon (C), the alpha carbon (CA), the beta carbon (CB), and so forth. Nitrogen atoms can be in the main chain (N), or on the sidechain, e.g. in the terminal epsilon position in lysine (NE).

Bonds: Connectivity

Typically, atomic coordinate files do not specify covalent bonds between atoms. Molecular modeling or visualization software determines the positions of covalent bonds using simple rules. Typically, any two non-hydrogen atoms within 1.9 Ångstroms of each other are deemed to be covalently bonded. (The distance for a bond involving a hydrogen atom is less.) The PDB format requires that covalent bonds be specified between atoms that are not members of Standard Residues in protein or nucleic acid chains. These are specified in CONECT records.