Hydrophobic interaction is believed to be the most important factor for the stability of proteins upon buried mutations. In this work, we have analyzed the influence of different interactions to the stability of buried protein mutants by means of 49 various physical-chemical, energetic and conformational properties of amino acid residues. We found that the mutant stability is attributed with several factors including hydrophobicity. In lysozyme T4, the properties reflecting hydrophobicity, flexibility, turn and coil tendency, and long-range interactions show a strong correlation with stability. Entropy plays an important role and the contribution of hydrophobicity is minimal in barrase. The stability of human lysozyme is attributed with both hydrophobicity and secondary structure. The stability of buried mutants in staphylococcal nuclease is influenced by hydrophobicity and physical properties. Our results indicate that the stability of buried protein mutants are influenced not only with hydrophobicity but also other factors, such as, secondary structure, shape, flexibility, entropy and inter-residue contacts play an important role to the stability. We obtained the highest single property correlation of 0.83 between amino acid properties and thermal stability of buried protein mutants. The properties showing high correlation coefficient with thermal stability agree very well with experimental observations. Further, multiple regression technique combining three properties leads to the correlation in the range of 0.83-0.92 in the considered proteins. (C) 2003 Elsevier Science Ltd. All rights reserved.