Abstract
All of the long-range atomic interactions in 21 representative proteins of known tertiary structure have been categorized by atom types, considering 15 different types of side-chain atoms and four different types of backbone atoms. The observed distribution of atomic interactions is compared to the distribution expected for random interactions in order to detect specific interaction tendencies. Nine types of interactions yield observed values that differ by more than 50% from the expected values. 1. (a) Sulfur atoms are attracted to other sulfur atoms and avoid negatively charged oxygen (O −) atoms. 2. (b) (O −) atoms tend to interact with NH 3 +, >NH, OH and polar CH 2 groups. 3. (c) Carbonyl oxygen atoms frequently associate with neutral and polar CH 2 groups. 4. (d) Carbonyl carbon atoms are often found near NH 3 + atoms. The various atom types are ranked in terms of a scale of affinities based on the types of atoms most frequently found in their environment.
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