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. Author manuscript; available in PMC: 2017 Aug 17.
Published in final edited form as: J Phys Condens Matter. 2016 Aug 22;28(41):414019. doi: 10.1088/0953-8984/28/41/414019

Table 2.

Bonds/virtual bonds considered in the models for the three proteins.

Bonds & local virtual bonds (δ = 0.05) Non-local virtual bonds(δ = 0.10)
Trp Cα[i] − Cα[i + 1] Cα[i] − Cα[i + 10] (i = i + 2)
Cα[i] − Cα[i + 2] Cα[i] − Cα[i + 20] (i = 2, i = i + 4)
Cα[i] − Cα[i + 3] Cβ[i] − Cβ[i + 10] (i = i + 4)
Cβ[i] − Cα[i] Cβ[i] − Cβ[i + 20] (i = 2, i = i + 4)
Cβ[i] − Cα[i − 1]
Cβ[i] − Cα[i + 1]
WW The same as for Trp Cα[i] − Cα[i + 10] (i = i + 2)
Cα[i] − Cα[i + 20] (i = 2, i = i + 4)
Cα[i] − Cα[i + 40] (i = 2, i = i + 16)
Cβ[i] − Cβ[i + 10] (i = i + 4)
Cβ[i] − Cβ[i + 20] (i = 2, i = i + 4)
GB3 The same as for Trp Cα[i] − Cα[i + 10] (i = i + 2)
Cα[i] − Cα[i + 20] (i = 2, i = i + 4)
Cα[i] − Cα[i + 40] (i = 2, i = i + 16)
Cα[i] − Cα[i + 60] (i = 2, i = i + 32)
Cβ[i] − Cβ[i + 10] (i = i + 4)
Cβ[i] − Cβ[i + 20] (i = 2, i = i + 4)