STRUCTURE BASED PROPERTIES (Features) – Inter residue interactions 1. Short range interactions Residues lying within a distance of 2 residues from the central residue contribute to short range interactions. Ref: Gromiha, M. M., & Selvaraj, S. (2004). Inter-residue interactions in protein folding and stability. Progress in biophysics and molecular biology, 86, 235.. 2. Medium range interactions Residues lying within a distance of 3 or 4 residues from the central residue contribute to short range interactions. Ref: Gromiha, M. M., & Selvaraj, S. (2004). Inter-residue interactions in protein folding and stability. Progress in biophysics and molecular biology, 86, 235.. 3. Long range interactions Those residues that are 4 residues away from the central residue contribute to long range interactions. Ref: Gromiha, M. M., & Selvaraj, S. (2004). Inter-residue interactions in protein folding and stability. Progress in biophysics and molecular biology, 86, 235.. 4. Contact order CO= ∑ ( Sij / (L * N)) L= total number of residues in the protein N=total number of contacts. Sij = sequence separation between residue i and j = j-i Ref: Gromiha, M.M. Protein bioinformatics: from sequence to function. Academic Press, 2010. 5. Long range order LRO LRO = ∑ (nij/N) ; n=1 if |i-j| > 12 =0 otherwise Where i and j are two contacting residues within dist 8A N = total number of residues in the protein Ref: Gromiha, M.M. Protein bioinformatics: from sequence to function. Academic Press, 2010. 6. Contact degree Distance between Cβ carbon atoms of two residues (Cα for glycine) <= 8Å Atomic distance criteria: The total number of residues falling within the contact distance of residue is recorded as the ‘contact degree’. 푛푟 Ncnt (i) = 푗 =1 퐴푖푗 Aij =1 if i and j are in contact; 0 otherwise nr = total number of residues in the protein Ref : Sun, W., & He, J. (2011). From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation.PLoS One, 6, e19238. 7. 8 Å contact number Distance between Cα carbon atoms of two residues ≤ 8Å Count the number of such residues for each Cα carbon atom. Ref : Nishikawa, K., & Ooi, T. (2009). Prediction of the surface‐interior diagram of globular proteins by an empirical method. International journal of peptide and protein research, 16, 19- 32. 8. 14 Å contact number Distance between Cα carbon atoms of two residues ≤ 14Å Count the number of such residues for each Cα carbon atom. Ref: Nishikawa, K., & Ooi, T. (1986). Radial locations of amino acid residues in a globular protein: correlation with the sequence. Journal of biochemistry, 100, 1043-1047. 9. Total contact distance TCD = CO * LRO Or 1 푛푐 TCD = 2 푘=1 |푖 − 푗| 푛푟 i and j are contacting residues nr = no of residues in the protein nc= no of contacts in the protein Ref: Gromiha, M.M. Protein bioinformatics: from sequence to function. Academic Press, 2010. 10. Multiple contact index for two state proteins: nci = ∑ nij ; nij =1 if rij <7.5 Å; |i-j| >12 residues; 0 otherwise MCI = ∑ nmi/N ; nmi =1 if nci ≥4 ; 0 otherwise nci = number of contacts for each residue rij = distance between the residues i and j. Ref: Gromiha, M.M. Protein bioinformatics: from sequence to function. Academic Press, 2010. 11. Multiple contact index for three state proteins: nci = ∑ nij ; nij =1 if rij < 6.5 Å; |i-j| > 3 residues; 0 otherwise MCI = ∑ nmi/N ; nmi =1 if nci ≥ 5 ; 0 otherwise nci = number of contacts for each residue rij = distance between the residues i and j. Ref: Gromiha, M.M. Protein bioinformatics: from sequence to function. Academic Press, 2010. .