How does the concept of natural rights fit into the social contract theory?

The idea and theory of a social contract achieved prominence in Europe around 1600, when it became one of the leading ways of explaining and delimiting people's duty of obedience to their government, and of their right to resist and overthrow government when it becomes oppressive. It was at about this time that political philosophers adopted a new view of the central problems of political philosophy. In the Middle Ages, the central problems had been widely considered to be: What is the best form of government, and why? What should the laws require, so that the laws of a polity are good, and not bad? Questions about why and under what circumstances people have a duty to obey decent government, when they may justly exercise their right to resist oppressive government, and what distinguishes a legitimate law from an illegitimate law, were considered; but they were thought peripheral and secondary. However, with the onset of the Protestant Reformation and the European Wars of Religion (1524-1651), questions of political obligation became urgent. Catholic subjects found themselves with Protestant rulers, and Protestant subjects found themselves with Catholic rulers. But it was widely assumed that rulers had the duty to protect and defend the one true religion, and Catholicism and Protestantism were widely considered incompatible rivals for that title. So subjects found themselves governed by rulers who they thought were failing in their duty to defend true religion. Moreover, since many rulers persecuted the other confession, many subjects thought their rulers were actively persecuting the true religion. In these conditions, the burning questions for political theory were obviously the limits of the duty of obedience, the limits of the right of resistance, and the limits of a law's legitimacy. People wanted to know when they were morally obligated to obey and when they weren't; when they could justly resist and overthrow government they disliked and when they couldn't; and when a law which they disliked was legitimately imposed and when it wasn't. By the 17th century, these had come to be considered the central problems of political philosophy. Questions of the best form of government, or of when a law has good content, came to seem secondary.