Amino Acids in Nine Ligand-Prefer Ramachandran Regions

Table 1

Distribution of amino acids in nine ligand-prefer Ramachandran regions.

Region	Number 1^1	Number 2^2	Probability^3	Top three AA occurrences^4	Top three AA observed at ligand site^5	Secondary structure features^6	Top three frequently ligand^7
I	1,525	5,366	0.284	D(207), H(138), S(132)	H(45.8%), E(38.5%), G(36.3%)	EBS(24.7%), NBS(23%),; HC(17.2%)	NAG(4.9%), FAD(3.8%),; FMN(3.4%)
II	1,269	4,262	0.297	D(150), N(140), H(123)	H(41.8%), E(41.2%), W(39.0%)	TC(18.2%)	FAD(6.8%), NAG(4.6%),; HEM(4.2%)
III	1,895	6,779	0.279	D(329), N(218), H(153)	H(53.7%), G(42.3%), M(36.1%)	GXT(40.1%)	FAD(6.4%), HEM(4.3%),; HAG(3.3%)
IV	2,693	9,373	0.287	D(327), H(224), N(295)	H(45.6%), D(39.5%), A(37.7%)	TC(16.8%), SCH(11.9%),; BU(9.1%)	FAD(8.4%), NAG(5.8%),; HEC(3.5)
V	2,164	7,815	0.276	T(258), D(157), V(141)	C(73.2%), H(43.5%), D(39.6%)	BU(20.7%), SCH(15.1%),; TC(14.4%)	HEM(5.8%), FAD(4.1%),; NAG(3.7%)
VI	2,369	7,714	0.307	V(247), I(232), L(217)	C(63.3%), H(44.7%), W(33.1%)	αH(13.9%), πH(12.5%),; BU(7.1%)	HEM(6.4%), FAD(4.7%),; FMN(3.0%)
VII	1,690	5,208	0.325	G(837), D(207), N(113)	C(67.3%), H(51.2%), R(41.8%)	HC(24.0%), PP(12.5%),; BC(7.6%)	FAD(9.5%), NAD(4.8%),; NAG(4.6%)
VIII	5,974	20,007	0.298	G(1171), N(840), D(695)	C(67.1%), H(51.3%), R(41.8%)	SCH(31.5%), LHH(17.8%),; TC(15.9%)	NAG(7.5%), FAD(3.4%),; SAH(3.3%)
IX	1,482	4,609	0.322	G(1067), S(101), A(46)	C(72.2%), H(69.7%), S(59.4%)	LT2(51.1%)	FAD(9.2%), SAH(6.6%),; SAM(4.1%)
Other^8	171,545	901,640	0.190	L(90,807), A(72,088), V(69,604)	H(29.2%), C(27.6%), W(27.2%)	ALH(28.0%), EBS(12.9%),; HC(9.5%)	FAD(5.4%), HEM(4.9%),; NAG(3.0%)

Total number of level 2 residues in region ligand-prefer Ramachandran boxes, where ranges from I to IX.
²Total number of level 3 residues in region ligand-prefer Ramachandran boxes, where ranges from I to IX.
³The value in this column is calculated by the number in column 2 divided by the number in column 3.
⁴The top three occurrences level 2 residues in region ligand-prefer Ramachandran boxes.
⁵Probability is calculated by the number of level 2 residues in region ligand-prefer Ramachandran boxes divided by number of level 3 residues in the region ligand-prefer Ramachandran boxes.
⁶Only residues that are not assigned as “undefined” are listed; for additional information about DISISL assignment, refer to Table S2.
⁷Top three most frequent ligands (three-letter code in PDB file) contacted with level 2 residues in the region.
⁸The other is the remaining region (except the nine regions) in the Ramachandran plot.