pyprot/AA_contacts at master · aedawid/pyprot · GitHub

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E = Epol + Eexch + Eind + Edisp
ss - disulfide covalent bridge
r - ionic repulsion (electrostatics: point charge): pol
a - ionic attraction (electrostatics: point charge): pol
pp - pi-stacking (aromatic, II-order bond): disp
cp - cation-pi (charge, aromatic, II-order bond):
HB - hydrogen bond (polarity: polar and nucleofile (-OH)): pol
vdW - hydrophobicity (dispersion: hydrophobic and aromatic): disp

***possible interaction components due to amino acids side chains character***
nuc					+					+	+
HB/PP								D		A/D	A/D	A/D		A/D	A/D	A/D	A	A	D	D
pi				+				+				+		+	+	+	+	+		+
arom	.       .       .       +       .       .       .       +       .       +       .       +       .       +      .        .       .       .       .       .
.	I	V	L	F	C	M	A	W.......G	T	S	Y	P	H......N	Q	D	E	K	R
I	vdW	vdV	vdW	vdW	vdW	vdW	vdW	vdW
V		vdW	vdW	vdW	vdW	vdW	vdW	vdW
L			vdW	vdW	vdW	vdW	vdW	vdW	(vdW)	(vdW)		(vdW)
F				vdW/pp	vdW	vdW	vdW	vdW/pp				pp		cpi	pp	pp	pp	pp	cp	cp/pp
C					ss	vdW
M						vdW	vdW	vdW
A							.
W								vdW/pp		hb	hb	hb/pp		hb/pp	hb/pp	hb/pp	hb/pp	hb/pp	cp	cp/pp
_G									.
_T										hb	hb	hb		hb	hb	hb	hb	hb	hb	hb
_S											hb	hb		hb	hb	hb	hb	hb	hb	hb
_Y												hb/pp	(vdW)	hb/cp	hb/pp	hb/pp	hb/pp	hb/pp	hb/cp	hb/cp/pp
_P													.
_H														r/pp	hb/pp	hb/pp	a/hb/pp	a/hb/pp	r/cp	r/cp/pp
N															hb/pp	hb/pp	hb/pp	hb/pp	hb/cp	h/cp/pp
Q																hb/pp	hb/pp	hb/pp	hb/cp	h/cp/pp
D																	r/pp	r/pp	a/h/cp	a/hb/cp/pp
E																		r/pp	a/h/cp	a/hb/cp/pp
K																			r	r/cp
R																				r/cp/pp

***the most significant contribution to interaction energy due to quantuum calculations***
nuc					+					+	+
HB								D		A/D	A/D	A/D		A/D	A/D	A/D	A	A	D	D
pi				+				+				+		+	+	+	+	+		+
arom				+				+		+		+		+
.	I	V	L	F	C	M	A	W.......G	T	S	Y	P	H......N	Q	D	E	K	R
I	disp		disp
V		disp	disp
L			disp				disp	disp	disp	disp		disp
F				disp
C					ss	disp
M						disp
A							.
W								.
_G									.
_T										pol	pol
_S											.
_Y												disp	disp
_P													.
_H														.			pol
N															.	pol
Q																.
D																	.
E																		.	pol
K																			.
R																				.

***interaction energy in water [quantuum calculations for pairs of AA side chains]***
OH					+					+	+
HB								D		A/D	A/D	A/D		A/D	A/D	A/D	A	A	D	D
pi				+				+				+		+	+	+	+	+		+
arom				+				+		+		+		+
.	I	V	L	F	C	M	A	W.......G	T	S	Y	P	H......N	Q	D	E	K	R
I	-1.32		-1.62
V		-1.70	-1.28
L			-1.85				-1.27	-3.02	-0.96	-1.28		-1.72
F				-1.26				X				X								X
C					.	-0.83
M						-1.55
A							.
W								X				X								X
G									.
T										-4.10	-1.59
S											.
Y												-3.28	-2.27							X
P													.
H														.			-2.31
N															.	-2.55
Q																.
D																	.
E																		.	-7.91
K																			.
R																				.

***phase separation increases: F-Y < F-K < F-R ~ Y-K < Y-R < Y-(R-D) [pi interactions increases: F < Y < W; other pi: D/E (COO), N/Q (ONH2), R (2[NH2]), H (imidazol)]
                               p-p   p-c   p-cp  p-c   p-cp  p-cp-a
***amino acids with HB donor will have favorable electrostatic interactions with the electron rich pi-system: HB vs. polar-pi