Fibrinogen, thrombin receptor and heparin cofactor II are three major thrombin substrates recognized specifically through its exosite, a regulatory binding site. Based on the native protein sequences, four peptides were selected to study the specificity of exosite interactions on structural basis using transferred NOE methods. The binding sequences of all the peptides are identified and possible thrombin binding sites of thrombin receptor and heparin cofactor II peptides are speculated by comparing with known hirudin-thrombin complex structures. A new binding mode may exist in thrombin-fibrinogen contacts according to its exosite binding sequence and interaction patterns. In terms of the binding sequence, it suggested that the most important factor in thrombin exosite specific binding is the hydrophobic residues position rather than the analogous sequence.