The different structural properties of proteases and nonproteases are well investigated in this paper. The average percentage (PL) over bar of residues having a number of long-range contacts greater than or equal to N-L( greater than or equal to N-L) for the proteases is larger than that for the nonproteases. The average number of long-range contacts per residue (P-L,P-μ) over bar greater than or equal to in four secondary structure mu (mu = H, E, T, and N) for the proteases is also larger than that for the nonproteases. We calculate the average contact order (CO) per protein, the average long-range order (LRO) per protein, and the average total contact distance (TCD) per protein, and find that the average value of LRO for the nonproteases is smaller than that for the proteases. However, both proteases and nonproteases have the same average values of CO and TCD. The average number of long-range contacts per residue CL for the proteases is larger than that for the nonproteases, however, the average number of short-range contacts per residue Cs for the proteases is smaller than that for the nonproteases. It is also shown that the square of radius of gyration for the proteases is relatively smaller than for the nonproteases. This finding implies that proteases are more compact than nonproteases. In protein molecule, each residue has a different ability to form contacts, and in general the number of residues having a small number of contacts is greater than that having a large number of contacts. Here we have concluded that the probability P(n) of amino acid residues having n pairs of contacts in all residues fits a good Gaussian distribution, and there has the same form of Gaussian distribution for 20 amino acid residues. The most probable number of contacts, n(C), for the proteases is greater than that for the nonproteases for 20 amino acid residues and one has a good correlation with the Fauchere-Pliska hydrophobicity (FPH) scale. Finally we discuss the relative contribution of amino acid residues involved in cation-pi interactions. The higher fraction of cation-Tr interactions observed in the proteases is found to be reflection of the more general, more frequent occurrence of these interactions in these proteins. All these findings would be helpful for us to understand structural differences between the proteases and other proteins. (C) 2003 Elsevier Ltd. All rights reserved.