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Università di Padova |
Abstract
For
many years it had been believed that steric compatibility of helix interfaces
could be the source of the observed preference for particular angles between
neighbouring helices as emerging from statistical analysis of protein databanks.
Several elegant models describing how side chains on helices can interdigitate
without steric clashes were able to account quite reasonably for the observed
distributions. However, it was later recognized (Bowie, 1997 and
Walther, 1998) that the ``bare'' measured angle distribution should be
corrected to avoid statistical bias. Disappointingly, the rescaled
distributions dramatically lost their similarity with theoretical
predictions casting many doubts on the validity of the geometrical assumptions
and models. In this report we elucidate a few points concerning the proper
choice of the random reference distribution. In particular we show
the existence of crucial corrections due to the correct implementation
of the approach used to discriminate whether two helices are in contact
or not and to measure their relative orientations. By using this
new rescaling, the ``true'' packing angle preferences are well described,
even more than with the original ``bare'' distribution, by regular packing
models.