Dengue viruses (DENV) consist of 4 serotypes and each of serotype is divided in several genotypes based on the envelope gene. To find the different in protein structure of DENV-3 circulated in Surabaya, we conduct analysis of two sequences of DENV-3 genotype 1 in different clade. Information of nucleotide and amino acid were searched from the GeneBank, homology were analysed using BLAST in NCBI. The different of amino acid of 2 sequences and protein structure were analysed using software Bioedit vs 7.2.5 and PyMol respectively. We found six amino acid residu that are different in these sequences. Three of amino acids of the different sequences have significant different similarities. These amino acid residu are 140, 340 and 362. Based on physic-chemistry properties, these amino acids are more hydrophobic in sequence of clade 2. 3D prediction of protein structure show that residu 140, 340, 362 and 386 have different surface protein. Physic-chemistry properties and charge of amino acid causing different 3D structure of DENV-3 envelope protein.