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Docking of the kinesin’s neck linker (NL) to the motor domain is the key force-generation process of the kinesin.In this process,NL’s β10 portion forms four backbone hydrogen bonds (HBs) with the motor domain.These backbone hydrogen bonds show big differences in their effective strength.The origins of these strength differences are still unclear.Using molecular dynamics method,we investigate the stability of the backbone HBs in explicit water environment.We find that the strength differences of these backbone HBs mainly arise from their relationships with water molecules which are controlled by arranging the surrounding residue sidechains.The arrangement of the residues in the C-terminal part of β10 results in the existence of the water-attack channels around the backbone HBs in this region.Along these channels the water molecules can directly attack the backbone HBs and make these HBs relatively weak.In contrast,the backbone HB at the N-terminus of β 10 is protected by the surrounding hydrophobic and hydrophilic residues which cooperate positively with the central backbone HB and make this HB highly strong.The intimate relationship between the effective strength of protein backbone HB and water revealed here should be considered when performing mechanical analysis for protein conformational changes.