One of Secretary of State Condoleezza Rice's closest advisers said yesterday that he will resign at the end of the year, depriving her of a key sounding board at a time when she is still searching for a new deputy and faces difficult challenges in the Middle East.

Philip D. Zelikow, 52, holds the unassuming title of "counselor," but in many ways he is Rice's intellectual soul mate, and he plays a critical role in formulating policy at the State Department. In his resignation letter, he cited professional and personal obligations, including a need to return to an endowed chair that the University of Virginia has held vacant for four years and to pay "some truly riveting obligations to college bursars" for his children's education.As a sort of minister without portfolio, Zelikow was a one-person think tank for Rice, churning out lengthy and sometimes blunt memos calling for confronting the deteriorating situation in Iraq, overhauling the administration's detainee policies and using the North Korean nuclear crisis to build a new security structure in northeast Asia. He also played an important role in Rice's decisions to strike a nuclear energy deal with India and to offer to join European-led nuclear talks with Iran.

Zelikow proved to be a controversial figure at the State Department and in the administration for his willingness to challenge administration orthodoxy and for his sometimes abrasive approach. But Rice valued his insights and contributions, aides said, even when descriptions of some of his memos began to surface in news reports.

In an interview yesterday, Zelikow said Rice "knew I had done no wrong." At no time, he added, was he quoted reflecting on people's personalities or disclosing private discussions with Rice.

"Philip is a close friend and we will continue to enjoy this friendship in the years ahead," Rice said in a statement. "I appreciate Philip's dedicated service during this time of historical change."...

While Zelikow's name was sometimes floated for open jobs, such as deputy secretary of state, Rice aides said he was not seriously considered for anything but his current post, which did not require Senate confirmation. Zelikow had rubbed some lawmakers the wrong way when he served as executive director of the commission that investigated the attacks of Sept. 11, 2001.

Friends said that Zelikow, who was appointed in February 2005, never intended to serve a full four years at the State Department but that he feels bad about leaving Rice before she has selected a deputy. If he did not leave now, he would not be listed in University of Virginia course catalogues for the upcoming semester, which would then delay his return until September.

Once he leaves the government, Zelikow will be able to supplement his salary with consulting projects and by writing books. He said he wants to write scholarly books, not a tell-all on the Bush administration, which is"no doubt a disappointment to my wife."

Asked what his departure means, Zelikow said:"Liberated from this weight, the secretary will soar higher and higher."...