The use of Balasubramanian plots in the analysis of protein dynamics data

Morffew, A J; Todd, Stephen

doi:10.1016/0263-7855(84)80024-7

Cited by 2 publications

(2 citation statements)

References 11 publications

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“…This format has been used to illustrate the backbone conformation of crystal structures of rubredoxin (24), cytochrome c ' (25), myohemerythrin (26), cupredoxin (27) and mengovirus (28). Such plots have been computer animated to represent motion of the peptide backbone during molecular dynamics simulation (23).…”

Section: Corformational Chain Plotsmentioning

confidence: 99%

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The linked φψ chain plot for visual comparison of the backbone conformation of peptides and proteins

McClain

Erickson

1995

International Journal of Peptide and Protein Research

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A new graphic method is described for presenting in two dimensions the φ and ψ dihedral angles that describe the backbone conformation of a peptide or protein chain. For each residue in sequence, φ and ψ are plotted as dots on the y‐axis above the next two points on the x‐axis representing the residue number. Each dot is linked to the next dot by a slanting line segment (link) and each cis‐peptide bond (ω∼0°) between residues X and Y is indicated by marking dots ψx and φy with a diamond. This linked φ and ψ chain plot is more useful than an unlinked φ and ψ chain plot for visually recognizing helices, sheets and turns and for graphically comparing several protein structures. Overlaying the linked φ and ψ chain plots for 15 β‐hairpins classified as type‐I' β‐turns revealed that three were significantly different from the rest. The dihedral angles (mean f standard deviation) of the loop residues (L1, L2) for a cluster of 12 β‐hairpins with an inverse‐common, type‐I′β‐turn (φL1= 52±7°, ψL1=40±8°, φL2=80±9°, ψL2= ‐1±13°) are similar to the standard dihedral angles for the type‐1′ turn (60, 30, 90 and 0°, respectively).

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Section: Corformational Chain Plotsmentioning

confidence: 99%

“…The sequence of residues in a short chain can be indicated by labeling each point with its sequence number or by connecting the points with a series of arrows. For a longer chain, however, the points are so dense that the sequence numbers and arrows must be omitted to avoid confusion (23).…”

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confidence: 99%