A force field has been previously designed for a dodecasaccharide chain of chondroitin-6-sulfate (C6S) and has proved to yield valuable data going from basic conformational properties to a more detailed H-bonding network. This force field is further used here to unravel the interaction of C6S with its pathological counterpart in low density lipoprotein (LDL) particles. In particular, well-selected peptide fragment p2 (residues 3359-3377) also identified as the principal proteoglycan binding site (PPBS) of the major protein in LDL, apolipoproteinB-100 (apoB-100), was chosen. We study here the interaction between C6S and p2. The role of arginine and lysine, positively charged amino acids of p2, in the crucial interaction of C6S with LDL is highlighted. The secondary structure of p2 is shown to affect the efficiency of the interaction, as the α-helical structure of p2 allows optimal interaction with C6S also in dynamic conditions. One point mutation in p2 appeared to affect consequently p2-C6S interaction.