eProS - Energy Profile Suite

Table of content

1. Globular proteins

1.1 Average coarse energy according to amino acid

Dataset: 2700 non-redundant globular proteins

	avg. coarse-grained energy		avg. coarse-grained energy
Ala	-14.71	Leu	-25.33
Arg	-5.94	Lys	-0.74
Asn	-4.33	Met	-24.21
Asp	-1.83	Phe	-25.68
Cys	-26.03	Pro	-5.45
Gln	-5.30	Ser	-6.93
Glu	-0.88	Thr	-8.40
Gly	-7.62	Trp	-20.49
His	-12.60	Tyr	-19.64
Ile	-27.33	Val	-22.60

1.2 Quantitative distribution of the secondary structures within the four quantiles

Dataset: 114 non-redundant globular proteins

	1. Quantile	2. Quantile	3. Quantile	4. Quantile
Coil	2663	2404	1803	996
Strand	495	798	1398	2017
Helix	1788	1805	1764	1959

1.3 Quantitative distribution of the amino acids within the four quantiles

Dataset: 114 non-redundat globular proteins

	1. Quantile	2. Quantile	3. Quantile	4. Quantile	Sum
Ala	23	327	1018	349	1717
Arg	253	651	203	1	1108
Asn	455	452	65	1	973
Asp	851	225	6	2	1084
Cys	0	3	78	337	418
Gln	220	475	102	2	799
Glu	1026	139	3	3	1171
Gly	397	760	447	12	1616
His	5	82	321	18	426
Ile	3	12	172	864	1051
Leu	7	21	407	1143	1578
Lys	942	91	3	3	1039
Met	2	8	89	271	370
Phe	1	11	147	528	687
Pro	393	442	117	0	952
Ser	241	692	349	2	1284
Thr	122	558	521	5	1206
Trp	0	8	148	174	330
Tyr	0	29	339	367	735
Val	5	21	430	890	1346

1.4 Energetic characterization of all amino acids according to secondary structure

Dataset: 114 non-redundant globular proteins (average free energy)

	Coil	Helix	Strand
Ala	-11,40	-14,94	-17,79
Arg	-4,53	-5,78	-7,50
Asn	-3,14	-4,17	-5,67
Asp	-0,85	-1,76	-2,87
Cys	-22,32	-27,56	-28,22
Gln	-3,63	-5,20	-7,07
Glu	0,02	-0,63	-2,02
Gly	-5,06	-7,29	-10,51
His	-10,69	-12,71	-14,41
Ile	-23,16	-27,71	-31,13
Leu	-21,02	-25,66	-29,32
Lys	0,24	-0,85	-1,62
Met	-20,32	-24,91	-27,41
Phe	-21,67	-25,77	-29,61
Pro	-4,04	-4,88	-7,42
Ser	-5,30	-6,44	-9,06
Thr	-6,42	-8,04	-10,75
Trp	-18,18	-21,02	-22,28
Tyr	-16,70	-18,70	-23,53
Val	-19,47	-23,21	-25,13

1.5 Quantitative distribution of all amino acids according to secondary structures

Dataset: 114 non-redundant globular proteins

	Coil	Helix	Sheet	Sum
Ala	523	885	309	1717
Arg	396	481	231	1108
Asn	541	297	135	973
Asp	533	405	146	1084
Cys	168	127	123	418
Gln	266	388	145	799
Glu	338	617	216	1171
Gly	1015	319	282	1616
His	163	158	105	426
Ile	252	354	445	1051
Leu	454	712	412	1578
Lys	414	433	192	1039
Met	92	188	90	370
Phe	190	267	230	687
Pro	643	233	76	952
Ser	606	402	276	1284
Thr	547	323	336	1206
Trp	101	142	87	330
Tyr	263	203	269	735
Val	361	382	603	1346

1.6 Energetic characterization of 3D-motifs

Dataset: 114 non-redundant globular proteins
Coarse-grained calculated energy values are given as averages.
Determined by PDBeMotif (for further information see Golovin A, Henrick K. MSDmotif: exploring protein sites and motifs. BMC Bioinformatics 2008, 9:312.)
In case of variable number of amino acids the total amount is given in brackets (betabulgeloop, niche, ststaple)

3D-Motif	1. AA	2. AA	3. AA	4. AA	5. AA	6. AA	eValue
alphabetamotif	-16,67	-12,43	-11,52	-11,89	-16,56		-13,81
asxmotif	-2,2	-7,25	-4,40	-11,65	-13,43		-7,79
asxturn	-2,34	-8,41	-4,79				-5,18
betabulge	-14,27	-11,23					-12,75
betabulgeloop (5)	-12,66	-2,58	-0,54	-4,92	-6,27		-5,39
betabulgeloop (6)	-9,82	-4,47	-2,87	-4,49	-7,38	-11,14	-6,70
betaturn	-13,55	-9,24	-7,82	-9,90			-10,13
gammaturn	-7,22	-14,41	-8,53				-10,05
nest	-6,98	-6,37	-11,96				-8,44
niche (3)	-8,54	-6,06	-8,59				-7,73
niche (4)	-11,5	-7,27	-6,73	-14,51			-10,00
schellmannloop	-20,15	-12,16	-6,61	-9,23	-3,92	-15,10	-11,20
stmotif	-5,07	-10,81	-5,55	-6,37	-17,66		-9,09
ststaple (5)	-13,31	-13,51	-13,22	-14,65	-9,24		-12,79
ststaple (6)	-22,45	-17,89	-9,24	-4,76	-3,31	-13,20	-11,81
stturn	-6,57	-5,59	-7,30				-6,49

1.7 Quantitative distribution of 3D-motifs

Dataset: 114 non-redundant globular proteins

3D-motif	amount
alphabetamotif	146
asxmotif	35
asxturn	121
betabulge	51
betabulgeloop	49
betaturn	821
gammaturn	23
nest	547
niche	995
schellmannloop	54
stmotif	93
ststaple	88
stturn	132

1.8 Quantitative distribution of the phi-angle within the four quantiles according to secondary structures

Dataset: 114 non-redundant globular proteins

	1. Quantile		2. Quantile		3. Quantile		4. Quantile
angle	positive	negative	positive	negative	positive	negative	positive	negative
Coil	438	2003	508	1940	137	1531	15	887
Helix	51	1610	72	1819	31	1686	2	1949
Sheet	16	437	44	795	26	1354	0	2017

1.9 Quantitative distribution of the psi-angle within the four quantiles according to secondary structures

Dataset: 114 non-redundant globular proteins

	1. Quantile		2. Quantile		3. Quantile		4. Quantile
angle	positive	negative	positive	negative	positive	negative	positive	negative
Coil	1533	908	1628	820	1283	385	730	172
Helix	242	1420	327	1564	194	1523	142	1809
Sheet	412	42	760	79	1261	119	1975	42

2. Alpha-helical membrane proteins

2.1 Amino acid-specific average coarse-grained energies

Dataset: 146 non-redundant membrane proteins

	overall	inside membrane	outside membrane
Ala	7.88	2.40	13.75
Arg	24.29	16.45	26.03
Asn	17.84	10.27	21.01
Asp	18.34	9.11	19.87
Cys	8.43	7.21	9.59
Gln	20.45	11.34	23.51
Glu	21.16	11.01	22.98
Gly	6.26	-2.23	13.72
His	16.68	4.21	22.42
Ile	14.58	13.94	15.48
Leu	16.93	15.48	18.88
Lys	27.62	21.65	28.51
Met	14.51	10.27	19.15
Phe	11.97	10.64	13.85
Pro	14.83	5.05	18.97
Ser	10.02	1.21	15.73
Thr	13.33	7.05	17.79
Trp	15.17	14.56	15.81
Tyr	14.03	9.91	16.81
Val	13.11	11.73	14.73

2.2 Quantitative distribution of the secondary structures according to four energy quartiles

Dataset: 146 non-redundant membrane proteins

	inside				outside
quartile	1. Q	2. Q	3. Q	4. Q	1. Q	2. Q	3. Q	4. Q
Coil	4	67	161	650	1451	1358	1345	1630
Strand	22	134	231	404	766	645	447	307
Helix	199	1565	3306	6440	2933	2527	1928	1801

2.3 Quantitative distribution of the amino acids according to energy quartiles

Dataset: 146 non-redundant membrane proteins

	inside					outside
quartile	1. Q	2. Q	3. Q	4. Q	sum	1. Q	2. Q	3. Q	4. Q	sum
Ala	0	0	4	1479	1483	167	427	331	462	1387
Arg	25	93	64	33	215	564	168	150	88	970
Asn	0	9	116	164	289	301	159	103	128	691
Asp	0	0	39	87	126	308	179	101	173	761
Cys	0	0	20	181	201	0	14	64	133	211
Gln	0	23	84	96	203	318	122	68	97	605
Glu	1	12	79	81	173	489	173	115	187	964
Gly	0	0	0	1160	1160	233	326	305	458	1322
His	0	0	1	163	164	189	61	40	66	356
Ile	19	390	707	300	1416	92	393	328	196	1009
Leu	105	847	928	278	2158	482	540	385	193	1600
Lys	65	61	19	8	153	672	196	106	51	1025
Met	0	18	160	250	428	138	113	75	65	391
Phe	2	58	465	591	1116	43	215	300	229	787
Pro	0	0	4	382	386	355	188	144	225	912
Ser	0	0	1	693	694	246	304	234	286	1070
Thr	0	1	51	616	668	292	253	174	220	939
Trp	5	91	166	47	309	38	99	100	61	298
Tyr	0	13	148	265	426	134	206	154	138	632
Val	5	154	642	620	1421	89	394	443	282	1208

2.4 Energetic characterization of all amino acids according to secondary structures

Dataset: 146 non-redundant membrane proteins

	inside			outside
	Coil	Helix	Strand	Coil	Helix	Strand
Ala	2,06	2,43	2,31	12,17	14,22	15,13
Arg	12,92	16,81	18,79	23,00	27,47	28,95
Asn	10,08	10,17	12,08	19,68	21,72	23,12
Asp	7,43	9,34	8,65	18,43	20,36	23,27
Cys	5,41	7,37	7,63	8,85	9,60	11,10
Gln	8,00	11,62	12,31	21,33	24,22	26,07
Glu	7,82	11,45	12,43	20,81	23,85	26,01
Gly	-1,63	-2,29	-2,40	12,11	14,56	16,03
His	4,44	4,19	4,13	19,63	23,83	24,25
Ile	11,46	14,05	14,51	13,89	15,55	17,52
Leu	13,82	15,53	16,06	16,80	19,42	21,02
Lys	12,88	22,20	25,04	26,08	29,84	30,52
Met	9,42	10,27	10,91	17,70	19,75	19,64
Phe	9,00	10,78	10,13	13,00	14,01	15,07
Pro	4,03	5,16	5,65	18,15	19,03	21,87
Ser	0,26	1,31	1,15	15,04	16,01	16,88
Thr	6,01	7,16	6,81	16,81	18,29	18,42
Trp	11,44	14,72	14,80	14,02	16,36	17,25
Tyr	7,68	10,08	10,77	15,24	17,23	18,35
Val	10,46	11,77	12,13	12,59	15,00	16,53

2.5 Quantitative distribution of all amino acids according to secondary structures

Dataset: 146 non-redundant membrane proteins

	inside				outside
	Coil	Helix	Strand	Sum	Coil	Helix	Strand	Sum
Ala	88	1307	88	1483	382	863	142	1387
Arg	29	168	18	215	347	518	105	970
Asn	19	254	16	289	290	329	72	691
Asp	14	109	3	126	310	373	78	761
Cys	17	182	2	201	74	102	35	211
Gln	18	174	11	203	194	339	72	605
Glu	25	133	15	173	352	505	107	964
Gly	112	972	76	1160	532	656	134	1322
His	17	132	15	164	123	196	37	356
Ile	71	1272	73	1416	263	560	186	1009
Leu	104	1905	149	2158	455	938	207	1600
Lys	13	127	13	153	384	519	122	1025
Met	24	373	31	428	112	238	41	391
Phe	58	979	79	1116	232	449	106	787
Pro	45	325	16	386	420	382	110	912
Ser	62	596	36	694	427	519	124	1070
Thr	51	582	35	668	325	505	109	939
Trp	16	271	22	309	85	174	39	298
Tyr	35	371	20	426	189	344	99	632
Val	64	1284	73	1421	288	680	240	1208