Lac repressor morph methods: Difference between revisions
Eric Martz (talk | contribs) →Hydrogen Bonds: polishing |
Eric Martz (talk | contribs) →Hydrogen Bonds: polishing |
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===Hydrogen Bonds=== | ===Hydrogen Bonds=== | ||
There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be probable hydrogen bonds by inspection of interatomic distances. | There are five hydrogen-bonded donor-acceptor pairs of atoms spacefilled in the "Specific contacts" animation: 1 pair in the minor groove, 2 pairs in the major groove for each protein chain. Three of these five pairs were selected from among those listed by Kalodimos ''et al.''<ref name='kalodimos'>Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Kalodimos CG, Biris N, Bonvin AM, Levandoski MM, Guennuegues M, Boelens R, Kaptein R. Science 305:386-9, 2004. [http://www.ncbi.nlm.nih.gov/pubmed/15256668 PubMed 15256668]</ref> in Fig. 2C after correcting the DNA sequence numbers in Fig. 2C to agree with those in 1L1M. All of these 3 hydrogen bonds involved protein chain A. The two hydrogen bonds shown for chain B involve the same donor-acceptor pairs on the other side of 1L1M, verified to be probable hydrogen bonds by inspection of interatomic distances. | ||
===Salt Bridges=== | ===Salt Bridges=== | ||