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Background Prediction of the protein localization is among the most important issues in the bioinformatics that is used for the prediction of the proteins in the cells and organelles such as mitochondria. In this study, several machine learning algorithms are applied for the prediction of the intracellular protein locations. These algorithms use the features extracted from protein sequences. In contrast, protein interactions have been less investigated. Objectives As protein interactions usually occur in the same or adjacent places, using this feature to find the location would be efficient and impressive. This study did not aim at increasing the total accuracy of the conducted research. The study has focused on the features of the proteins’ interaction and their employment which lead to a higher accuracy. Materials and Methods In this study, we have examined the protein interaction network as one of the features for prediction of the protein localization and its effects on the prediction results. In this regards, we have gathered some of the most common features including Amino Acid Composition, Dipeptide Compositions, Pseudo Amino Acid Compositions (PseAAC), Position Specific Scoring Matrix (PSSM), Functional Domain, Gene Ontology information, and the Pair-wise sequence alignment. The results of the classification are compared to the ones using protein interactions. For achieving this goal different machine learning algorithms were tested. Results The best-obtained results of using single feature set obtained using SVM classifier for PseAAC feature. The accuracy of combining all features with PPI data, using the Decision Tree and Random Forest classifiers, was 82.49% and 83.35%, respectively. In another experiment, using just protein interaction data with the different cutting points resulted in obtaining an accuracy of 93.035% for the protein location prediction. Conclusion In total, it was shown that protein(s) interaction has a significant impact on the prediction of the mitochondrial proteins’ location. This feature can separately distinguish the locations well. Using this feature the accuracy of the results is raised up to 5%.