Non local environment scheme


Non-local environment of an atom. (A) Linear representation of a protein sequence. The asterisk represents the amino acid (Met80) containing the atom for which non-local interaction energies are to be evaluated (Ce). The hatched area in the sequence represents the amino acids that are considered as local for Met80 (i.e. not farther than 11 residues in the sequence) and that are not considered in the calculation. Regions I, II and III represent non-local interacting amino acids for Met80, because some of their atoms are closer than 7 to Ce of Met80. (B) Two-dimensional structural representation of part of the protein chain illustrated in A. The dashed circle represents a sphere of 7 radius centered on Ce of Met80. All the atoms inside this sphere that belong to Met80 (Cb, Cg, Sd ) and the local amino acid Ile86 (Cb, Cg1, Cg2, Cd) are shown as open circles and are not considered in the calculation. All the atoms of non-local amino acids that are located within the sphere (Val13, Cg2; Phe134, Ce1, Ce2, Cx; Ala182, N, Ca, C, Cb) are shown as filled circles. All these atoms are included in the non-local interaction energy calculation of the Met80 Ce atom. The Euclidean distances between each one of these atoms and the Met80 Ce atom are calculated, and the corresponding energy values are taken from the energy functions of the atomic mean force potential. The total energy of the Met80 Ce atom is the sum of all the pairwise non-local interaction energy values.


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