BMC Structural Biology

Table 1 An example of data from a contact-type scoring matrix

From: Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys

	ALA	ARG	ASN	ASP	CYS	GLN	GLU	GLY	HIS	ILE	LEU	LYS	MET	PHE	PRO	SER	THR	TRP	TYR	VAL
ALA	0.27	-0.12	-0.19	-0.23	-0.06	-0.21	-0.39	0.11	-0.01	0.32	0.31	-0.42	0.00	0.26	-0.05	-0.05	0.05	0.12	0.19	0.35
ARG		-0.33	-0.38	-0.24	-0.30	-0.43	-0.36	-0.15	-0.22	-0.03	0.00	-0.72	-0.31	-0.01	-0.18	-0.27	-0.22	-0.10	-0.03	-0.01
ASN			-0.04	-0.30	-0.28	-0.34	-0.57	-0.09	-0.19	-0.02	-0.14	-0.47	-0.30	-0.01	-0.20	-0.13	-0.09	-0.10	0.02	-0.07
ASP				-0.44	-0.41	-0.48	-0.70	-0.18	-0.19	-0.14	-0.22	-0.43	-0.44	-0.15	-0.29	-0.28	-0.24	-0.19	-0.08	-0.15
CYS					0.67	-0.33	-0.63	-0.08	-0.02	0.15	0.12	-0.57	-0.06	0.19	-0.19	-0.13	-0.11	0.03	0.07	0.14
GLN						-0.36	-0.67	-0.26	-0.27	-0.10	-0.09	-0.64	-0.34	-0.08	-0.26	-0.28	-0.23	-0.13	-0.08	-0.11
GLU							-0.77	-0.45	-0.39	-0.23	-0.27	-0.53	-0.57	-0.27	-0.46	-0.51	-0.44	-0.38	-0.23	-0.25
GLY								0.16	0.02	0.16	0.08	-0.43	-0.10	0.15	-0.04	-0.01	0.04	0.08	0.14	0.19
HIS									0.16	0.09	0.07	-0.55	-0.11	0.16	-0.08	-0.05	-0.03	0.11	0.16	0.09
ILE										0.71	0.55	-0.13	0.24	0.55	-0.03	0.09	0.20	0.28	0.43	0.58
LEU											0.58	-0.26	0.15	0.49	-0.01	0.02	0.12	0.27	0.35	0.51
LYS												-0.63	-0.56	-0.23	-0.49	-0.47	-0.41	-0.45	-0.20	-0.22
MET													0.24	0.25	-0.23	-0.20	-0.11	0.09	0.14	0.16
PHE														0.60	0.04	0.10	0.16	0.39	0.47	0.48
PRO															-0.04	-0.15	-0.11	0.06	0.09	0.02
SER																-0.04	-0.03	0.01	0.07	0.07
THR																	0.06	0.05	0.13	0.21
TRP																		0.48	0.35	0.26
TYR																			0.42	0.37
VAL																				0.59

An example of one of the contact-type scoring matrices used in this work. The scores are defined as described in the Methods Section. In this matrix residue-residue contacts were defined using a 12 Å distance threshold between C_βatoms and using a sequence separation filter to remove short-range interactions.

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