A method for producing a protein having an antithrombotic activity, which comprises replacing, in a protein that has an amino acid sequence having a homology of not less than 30% to the amino acid sequence of SEQ ID NO: 1 and forms a higher order structure composed of a first β strand (β1), a first a helix (α1), a second α helix (α2), a second β strand (β2), a loop, a third β strand (β3), a fourth β strand (β4) and a fifth β strand (β5) in this order from the amino terminus, at least one amino acid residue in a region from α2 to β2 and/or a region from β3 to β4 so that electric charge of the amino acid residue is changed towards positive direction.