Lovell S C, Word J M, Richardson J S, Richardson D C
Biochemistry Department, Duke University, Durham, NC 27710-3711, USA.
Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):400-5. doi: 10.1073/pnas.96.2.400.
Previous rotamer libraries showed little significant clustering for asparagine chi2 or glutamine chi3 values, but none of those studies corrected amide orientations or omitted disordered side chains. The current survey used 240 proteins at </=1.7 A resolution with <50% homology and <30 clashes per thousand atoms (atomic overlap >/=0.4 A). All H atoms were added and optimized, and amide orientation was flipped by 180 degrees if required by H bonding or atomic clashes. A side chain was included only if its amide orientation was clearly determined and if no atom had a B factor >/=40, alternate conformation, or severe clash; that selection process yielded 1,490 Asn and 863 Gln side chains. Clear clustering was observed for Asn chi2 and Gln chi3 (except when Gln chi2 is trans). For Gln, five major and four minor rotamers cover 87% of examples. For Asn, there are seven backbone-independent rotamers covering 94% of examples plus rotamers specified for strictly alpha-helical, beta, and left-handed (+phi) Asn. Although the strongest influence on chi angles is avoidance of atomic clashes (especially with the NH2 hydrogens), some Asn or Gln rotamers are influenced by favorable van der Waals contacts and others by specific local H-bond patterns.
以往的旋转异构体库显示，天冬酰胺χ2或谷氨酰胺χ3值几乎没有明显的聚类现象，但这些研究均未校正酰胺取向或忽略无序的侧链。本次调查使用了分辨率≤1.7 Å、同源性<50%且每千个原子的冲突数<30（原子重叠≥0.4 Å）的240种蛋白质。添加并优化了所有氢原子，如果氢键或原子冲突需要，酰胺取向会翻转180度。仅当侧链的酰胺取向明确确定且没有原子的B因子≥40、没有交替构象或严重冲突时，才会纳入该侧链；该选择过程产生了1490个天冬酰胺和863个谷氨酰胺侧链。观察到天冬酰胺χ2和谷氨酰胺χ3有明显的聚类现象（谷氨酰胺χ2为反式时除外）。对于谷氨酰胺，五个主要和四个次要的旋转异构体涵盖了87%的实例。对于天冬酰胺，有七个与主链无关的旋转异构体涵盖了94%的实例，外加为严格的α螺旋、β和左旋（+φ）天冬酰胺指定的旋转异构体。尽管对χ角的最强影响是避免原子冲突（特别是与NH2氢原子的冲突），但一些天冬酰胺或谷氨酰胺旋转异构体受有利的范德华接触影响，另一些则受特定的局部氢键模式影响。
