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| HLA structural data were downloaded from PDB. All data were filtered by programming and were managed in the Visual FoxPro (VFP). With Biopolymer module of InsigtII software, hydrogen atoms were added to filtered molecules. Then, the program was utilized to analyze distances of every two Cα atoms of peptide nonamers and amino acid residues of HLA involved within a different distance around 26 peptide nonamers respectively. There were 26 HLA-A*0201 complexes with peptide nonamers in PDB. The position 2(P2) of 21 peptides was Leu. Meanwhile, P9 was either Leu or Val mostly (25/26). The mean number of H-bond between P1 and molecule HLA-A*0201 was 1.86, while those at P2 and P9 were 1.81, 1.95 respectively. By method of moment, some distances of two Cα atoms appeared normal school. Some amino acid residues of HLA, such as Tyr7, Glu63, Lys66, His70, Thr73, Ser77, Leu81, Tyr99, Thr143, Trp147 and Tyr171, appeared above 90% within a distance of 0.25 nm around peptide nonamers. P1 maybe is anchoring residue, just like P2 and P9. Distances of two Cα atoms of peptide nonamers can be utilized to check whether the structure of peptide is reasonable after molecular docking. Some high frequency residues can be applied to adjust binding subset for docking |
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| Keywords:human leucocyte antigen; peptide nonamers; structural data; molecular docking |
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