The purpose of this work is to evaluate the influence of the chromatin density in the number of clustered damages created by protons in different types of cell nuclei. For this, two detailed geometrical target models representing a fibroblast and an endothelium cell nucleus in the G0/G1 phase were implemented as the target of proton irradiations in a Monte Carlo simulation code based on the GEANT4 toolkit. The DBSCAN clustering algorithm was then used in order to determine clustered damages that could be potential simple or double strand breaks on the DNA. The influence of the DNA density has been studied by comparing the results on the relative quantification of these clustered damages. Our results show that the quantity and the complexity of clustered damages increase with increasing DNA density and thus they can depend on the cell line.