How to calculate the profitability of the company while negotiating a contract with key account customers?

Percentage share of your expense statement can be obtained from your finance dept. 

Similarly you may obtain the landed cost of the products / services being considered for the contract.

Load the margin and know your bottom line and thereafter keep the range for negotiations.

Somtimes the situation demands to forego lucarative margins to win the deal and try making the losses from after sales service and sale of spare parts and consumables.