Visualization of molecules in Jmol.

Visualization of molecules in JMol Script

Parameters of H-bonds between backbone atoms in secondary structure

	Atoms' names	Bond length (angstrom)	Angle N-O-C (degrees)
Alpha helix
1.	O(PRO88:D) - N(THR91:D)	3.06	124.3
2.	O(LYS87:D) - N(ASP90:D)	2.88	132.7
3.	O(THR28:D) - N(ASN31:D)	2.99	134.9
4.	O(PHE29:D) - N(TYR32:D)	3.12	124.8
5.	O(PRO139:A) - N(LEU142:A)	3.08	107.6
6.	O(ARG138:A) - N(TYR141:A)	2.94	121.8
Average		3.01	124.35
Beta strands
1.	O(ASP73:D) - N(THR78:D)	3.15	147.6
2.	O(THR78:D) - N(ASP73:D)	2.83	163.5
3.	O(SER71:D) - N(TYR80:D)	2.87	146.5
4.	O(TYR80:D) - N(SER71:D)	3.15	136.2
5.	O(GLN82:D) - N(THR69:D)	2.88	155.1
6.	O(LEU18:D) - N(MET83:D)	2.83	177.6
7.	O(MET83:D) - N(LEU18:D)	3.06	149.8
8.	O(SER7:D) - N(SER21:D)	2.93	141.8
9.	O(SER21:D) - N(SER7:D)	2.99	151.3
10.	O(LEU79:D) - N(CYS22:D)	2.82	159.9
11.	O(CYS22:D) - N(LEU79:D)	2.93	147.2
12.	O(VAL5:D) - N(ALA23:D)	2.99	143.2
13.	O(ALA23:D) - N(VAL5:D)	2.97	147.9
14.	O(GLN3:D) - N(SER25:D)	3.03	158.9
15.	O(SER25:D) - N(GLN3:D)	3.01	143.6
Average		2.96	151.34

The average values for h-bond length in alpha-helixes (3.01 angstrom) and for beta strands (2.96 angstrom) are quite close to those in literature sources (2.99 and 2.91 angstrom respectively). It is interesting that, for alpha-helix, residues with h-bonds are at a distance of 3 amino acids from each other, which corresponds to a 4:13 structure of a helix. For beta-strands, such a pattern is not observed, the distance between amino acids who form a bond varies greatly. But in beta-strand a pair of amino acids form two bonds, in which each amino acid is either a donor (-NH) or an acceptor (= O).

Literature sources:

1. PDB page for the protein.
2. Source about h-bonds.