McDonald I K, Thornton J M
Department of Biochemistry and Molecular Biology, University College London, U.K.
J Mol Biol. 1994 May 20;238(5):777-93. doi: 10.1006/jmbi.1994.1334.
We have analysed the frequency with which potential hydrogen bond donors and acceptors are satisfied in protein molecules. There are a small percentage of nitrogen or oxygen atoms that do not form hydrogen bonds with either solvent or protein atoms, when standard criteria are used. For high resolution structures 9.5% and 5.1% of buried main-chain nitrogen and oxygen atoms, respectively, fail to hydrogen bond under our standard criteria, representing 5.8% and 2.1% of all main-chain nitrogen and oxygen atoms. We find that as the resolution of the data improves, the percentages fall. If the hydrogen bond criteria are relaxed many of these unsatisfied atoms form weak hydrogen bonds. However, there remain some buried atoms (1.3% NH and 1.8% CO) that fail to hydrogen bond without any immediately obvious compensating interactions.
我们分析了蛋白质分子中潜在氢键供体和受体得到满足的频率。当使用标准标准时，有一小部分氮或氧原子不与溶剂或蛋白质原子形成氢键。对于高分辨率结构，分别有9.5%和5.1%的埋藏主链氮原子和氧原子在我们的标准标准下未能形成氢键，分别占所有主链氮原子和氧原子的5.8%和2.1%。我们发现，随着数据分辨率的提高，这些百分比会下降。如果放宽氢键标准，许多这些未满足的原子会形成弱氢键。然而，仍然有一些埋藏的原子（1.3%的NH和1.8%的CO）在没有任何立即明显的补偿相互作用的情况下未能形成氢键。
