The study explores the role of proteins in cellular networks, moving beyond their individual functions to consider their positions within complex, hierarchical protein-protein interaction networks. Using data from the yeast *S. cerevisiae*, the research demonstrates that the phenotypic effects of gene deletions are strongly influenced by the topological position of the protein within the network. The protein-protein interaction network of *S. cerevisiae* consists of 1870 proteins and 2240 interactions, showing a scale-free topology with a power-law distribution of connections, cut off at around 20 interactions. This topology is also observed in the *H. pylori* network, indicating a common large-scale structure in biological networks. The network's structure provides both tolerance to random errors and vulnerability to the removal of highly connected proteins. Random deletions of proteins do not significantly alter the network, but the removal of highly connected proteins increases the network diameter. This suggests that yeast's robustness against mutations is partly due to the topological organization of interactions. The study also finds a strong correlation between the number of interactions a protein has and its essentiality. Proteins with fewer interactions are less likely to be essential, while highly connected proteins are more likely to be essential. This implies that proteins with central roles in the network are more critical for cellular function. The findings suggest that the inhomogeneous structure of both metabolic and protein interaction networks reflects evolutionary selection for a common large-scale structure in biological networks. This supports the idea that future studies in other organisms will reveal similar network topologies, emphasizing the importance of both individual and contextual properties in understanding cellular dynamics and robustness.The study explores the role of proteins in cellular networks, moving beyond their individual functions to consider their positions within complex, hierarchical protein-protein interaction networks. Using data from the yeast *S. cerevisiae*, the research demonstrates that the phenotypic effects of gene deletions are strongly influenced by the topological position of the protein within the network. The protein-protein interaction network of *S. cerevisiae* consists of 1870 proteins and 2240 interactions, showing a scale-free topology with a power-law distribution of connections, cut off at around 20 interactions. This topology is also observed in the *H. pylori* network, indicating a common large-scale structure in biological networks. The network's structure provides both tolerance to random errors and vulnerability to the removal of highly connected proteins. Random deletions of proteins do not significantly alter the network, but the removal of highly connected proteins increases the network diameter. This suggests that yeast's robustness against mutations is partly due to the topological organization of interactions. The study also finds a strong correlation between the number of interactions a protein has and its essentiality. Proteins with fewer interactions are less likely to be essential, while highly connected proteins are more likely to be essential. This implies that proteins with central roles in the network are more critical for cellular function. The findings suggest that the inhomogeneous structure of both metabolic and protein interaction networks reflects evolutionary selection for a common large-scale structure in biological networks. This supports the idea that future studies in other organisms will reveal similar network topologies, emphasizing the importance of both individual and contextual properties in understanding cellular dynamics and robustness.