Two commercial soy protein isolates were made into fibrous meat analogs by high moisture extrusion or into gels by heating and cooling, at varying concentrations and/or temperatures. Protein-protein interactions by extrusion or gelation were investigated through protein solubility studies of raw and finished products. All samples except for extrudates exhibited similar patterns of solubility in four selected extractants. Phosphate buffer (PB) extracted the least amount of protein. Addition of dithiothreitol (DTT) to PB improved protein solubility, indicating the presence of disulfide bonds. PB + Urea and PB + Urea + DTT gave the highest and almost equal amount of extractable proteins from all samples, except for the extrudates from which protein could not be extracted effectively by PB + Urea, implying that disulfide bonding was more pronounced during extrusion than gelation. The results support our hypothesis that soy protein gels and extrudates both have the same types of chemical bonds, namely covalent disulfide bonds and non-covalent interactions. It is the relative proportion of each type of bonds in their structures that differentiates the two with respect to reversibility and structure rigidity. In forming protein gels during heat-induced gelation, non-covalent bonds play a dominant role over disulfide bonds; whereas for forming the fibrous structure of protein extrudates, non-covalent bonds and covalent disulfide bonds are both important.