Aligning large language models to handle instructions with extremely long contexts has yet to be fully investigated. Previous studies have attempted to scale up the available data volume by synthesizing long instruction-following samples, as constructing such a dataset tends to be challenging for annotators. However, a lack of a well-defined strategy for ensuring data quality may introduce low-quality samples and restrict the model's performance. Thus, we propose GATEAU, a novel framework to address the unique challenge of long context alignment by identifying the influential samples enriched with long-range dependency relations. Specifically, GATEAU measures the long-range dependencies from two essential aspects: the difficulty of generating target responses due to the long-range dependencies, and the difficulty of understanding long inputs due to such dependencies. Comprehensive experiments indicate that GATEAU effectively identifies influential samples, and the model trained on these selected samples exhibits better instruction-following and long-context understanding capabilities.