Analysis of the heterogeneity of packing in proteins showed that diffe
rent groups of the protein preferentially contribute to low-or high-de
nsity regions. Statistical distribution reveals the two preferable val
ues for packing density in the form of two peaks. One peak occurs in t
he range of densities 0.55-0.65, the other occurs in the range 0.75-0.
8. The high-density peak is originated primarily by high packing insid
e the hydrogen bonded backbone and to some extent by side chains. Pola
r/charged and apolar side chains both contribute to the low-density pe
ak. The average packing density values of individual atomic groups sig
nificantly vary for backbone atoms as well as for side chain atoms. Th
e carbonyl oxygen atoms of protein backbone and the end groups of side
chains show lower packing density than the rest of the protein. The s
ide-chain atomic groups of a secondary structure element when packed a
gainst the neighboring secondary structure element form stronger conta
cts with the side chains of this element than with its backbone. Analy
sis of the low-density regions around each buried peptide group was do
ne for the set of proteins with different types of packing, including
alpha-alpha, alpha-beta, and beta beta packing. It was shown that cavi
ties are regularly situated in the groove of secondary structure eleme
nt packed against neighboring elements for all types of packing. Low d
ensity in the regions surrounding the peptide groups and the end group
s of side chains can be explained by their positioning next to a cavit
y formed upon the association of secondary structure elements. The mod
el proposed can be applied to the analysis of protein internal motions
, mechanisms of cellular signal transduction, diffusion through protei
n matrix, and other events.