3JYW

structure of the 60s proteins for eukaryotic ribosome based on cryo-em map of thermomyces lanuginosus ribosome at 8.9a resolution

• Total interactions analyzed: 465
• Total true interactions: 33
• Strongest Interaction:
  • Chains: D-U
  • Int. Res.: 20
  • Norm. En. per Res.: -4.0991
• Hub Node: C(5)

All Interactions

Chains	Hydro. Bond Ener. (kJ/mol)	Elec. Ener. (kJ/mol)	VDW. Ener. (kJ/mol)	Tot. Stab. Ener. (kJ/mol)	#int. res.	# Short cont.	#Hydr. int.	#VDW pairs	#salt bridges	#Pot. fav. elec. int	#Pot. unfav. elec. int
0-D	0.0	0.0	-0.0192	-0.0192	2	0	0	15	0	0	3
0-V	0.0	1.1657	-0.47	0.6957	8	0	0	113	0	0	14
1-N	0.0	0.0	-0.0807	-0.0807	2	0	0	18	0	0	1
1-T	0.0	1.3438	-23.6146	-22.2707	21	0	0	1334	0	0	12
1-Y	0.0	0.0	-30.4532	-30.4532	21	0	0	1176	0	0	9
2-9	-9.4055	-22.9044	-78.1481	-110.458	31	1	1	2682	2	2	10
2-B	0.0	0.0	-0.0331	-0.0331	3	0	0	14	0	0	0
8-K	0.0	11.9211	40.9174	52.8385	28	27	0	1959	0	6	14
9-B	-48.7503	6.1019	-348.634	-391.2824	113	9	22	12546	0	8	23
B-L	0.0	0.0	-0.4021	-0.4021	4	0	0	88	0	0	3
C-M	0.0	6.6039	-39.121	-32.5171	24	5	0	1538	0	1	5
C-N	0.0	0.886	-15.0285	-14.1425	17	0	1	932	0	1	6
C-R	-10.9209	20.2592	-90.9225	-81.5841	46	1	0	3732	2	28	32
C-S	-19.7911	-26.6143	-120.515	-166.9203	42	6	0	3230	1	9	6
C-W	0.0	0.0	-0.0255	-0.0255	2	0	0	14	0	0	1
D-O	0.0	0.0	-13.5431	-13.5431	13	0	0	685	0	4	3
D-U	-2.6419	-24.8586	-54.4821	-81.9825	20	0	0	1828	2	5	14
D-V	0.0	0.0	-4.4642	-4.4642	7	0	0	140	0	0	0
D-Y	-4.3802	4.0128	-37.448	-37.8153	18	0	0	1504	0	2	4
E-Q	-9.9247	-4.9831	-111.263	-126.1708	52	1	1	4574	1	5	18
E-Z	-3.9947	0.0	-3.2055	-7.2003	7	0	0	120	1	6	0
F-O	0.0	0.0	-0.0037	-0.0037	2	0	0	4	0	0	0
G-L	-2.1355	-4.4051	-89.0338	-95.5744	48	0	4	3970	4	18	14
H-M	0.0	2.4238	-14.0528	-11.629	15	0	1	703	0	2	14
L-V	0.0	0.0	-0.0004	-0.0004	2	0	0	1	0	0	0
L-X	0.0	0.0	-0.2972	-0.2972	3	0	0	48	0	0	0
L-Z	0.0	0.0	-1.6051	-1.6051	5	0	0	129	0	0	1
N-W	0.0	0.0	-0.0437	-0.0437	3	0	0	15	0	3	6
O-V	-11.0004	-19.2673	-29.7393	-60.007	20	2	0	1183	1	8	8
P-T	0.0	0.0	-0.0043	-0.0043	3	0	0	6	0	1	1
R-S	0.0	-7.8054	-154.422	-162.2274	50	1	7	5238	0	6	9
T-X	-9.848	-22.4259	-55.3776	-87.6515	29	1	1	2220	1	5	5
V-Z	0.0	0.0	-0.0474	-0.0474	5	0	0	17	0	1	0

Interface residues

• 0-D: LYS1030, LYS183D
• 0-V: ARG12V, GLY13V, GLY370, HIS14V, ILE22V, LYS340, LYS360, VAL15V
• 1-N: ARG461, TYR130N
• 1-T: ALA141, ALA161, ARG115T, ASN117T, GLN111, GLY118T, LEU113T, LYS101, LYS120T, LYS121, LYS151, LYS171, LYS181, LYS51, MET131, MET88T, PHE71, PRO116T, THR112T, THR119T, VAL114T
• 1-Y: ALA31, ARG11Y, ARG21Y, ARG24Y, ARG25Y, ARG81, ASN20Y, ASN501, CYS19Y, GLN41, GLY23Y, ILE91, LEU18Y, LYS121, LYS14Y, LYS481, LYS51, MET491, SER61, THR17Y, TYR39Y
• 2-9: ALA452, ALA462, ARG369, ARG522, ARG862, ASN472, ASN742, ASN752, ASP389, CYS399, CYS429, CYS599, CYS609, GLU572, GLY439, GLY732, LEU512, LYS449, LYS459, LYS532, LYS619, LYS629, PHE419, PHE852, PRO492, SER409, SER542, THR482, THR639, TYR379, VAL502
• 2-B: GLY85B, THR84B, VAL502
• 8-K: ALA498, ARG117K, ARG123K, ARG428, ARG468, ARG488, ASP118K, GLN368, GLU408, GLU448, GLU918, GLY122K, GLY478, HIS398, LEU458, LEU528, LYS119K, LYS438, MET388, PHE121K, SER120K, SER127K, THR124K, THR898, TYR188, VAL418, VAL508, VAL518
• 9-B: ALA170B, ALA182B, ALA519, ALA529, ALA56B, ALA59B, ALA659, ALA689, ALA749, ALA759, ALA769, ALA779, ALA78B, ARG174B, ARG179, ARG184B, ARG239, ARG499, ARG54B, ARG809, ASN100B, ASN132B, ASN79B, ASN97B, ASP176B, CYS579, CYS599, CYS609, GLN339, GLN47B, GLN86B, GLU109B, GLU309, GLU80B, GLY110B, GLY129, GLY131B, GLY159, GLY167B, GLY171B, GLY172B, GLY173B, GLY509, GLY539, GLY55B, GLY669, GLY679, GLY81B, GLY85B, GLY99B, HIS50B, HIS83B, ILE112B, ILE166B, ILE169B, ILE44B, ILE48B, ILE549, ILE77B, ILE88B, LEU102B, LEU179B, LEU180B, LEU229, LEU299, LEU58B, LEU96B, LYS139, LYS177B, LYS181B, LYS619, LYS629, PHE419, PHE87B, PRO108B, PRO178B, PRO57B, SER114B, SER130B, SER409, SER589, SER729, SER819, SER95B, THR111B, THR119, THR569, THR639, THR709, THR739, THR789, THR829, THR84B, TRP559, TYR133B, TYR149, TYR189, TYR699, TYR89B, VAL107B, VAL113B, VAL165B, VAL168B, VAL169, VAL175B, VAL269, VAL45B, VAL49B, VAL649, VAL719, VAL799, VAL82B, VAL98B
• B-L: GLN8B, GLY78L, LYS77L, VAL4B
• C-M: ALA155M, ALA156M, ALA158M, ALA159M, ALA162M, ALA258C, ALA63M, ARG68M, ASN65M, GLY69M, HIS256C, HIS259C, LYS5C, LYS66M, MET261C, PHE64M, PRO257C, PRO70M, PRO96C, SER263C, THR67M, TRP262C, TYR154C, VAL260C
• C-N: ALA71N, ARG56N, ARG69N, GLN72N, GLY73N, GLY77N, LYS124C, LYS126C, LYS127C, LYS74N, PHE226C, SER125C, THR70N, THR79N, TRP122C, TYR123C, VAL78N
• C-R: ALA75C, ARG12R, ARG240C, ARG300C, ARG45R, ARG48R, ARG58C, ARG70C, ARG86R, ARG87R, ARG88R, ASN47R, ASP124R, ASP299C, ASP89R, GLN7R, GLU121R, GLU71C, GLU74C, GLY8R, GLY90R, HIS11C, LEU125R, LEU238C, LEU46R, LEU60C, LYS10R, LYS120R, LYS236C, LYS237C, LYS325C, LYS357C, LYS66C, PHE11R, PHE67C, PHE92R, PRO239C, PRO9C, SER65C, THR235C, THR55C, THR9R, VAL57C, VAL72C, VAL73C, VAL91R
• C-S: ALA11S, ALA292C, ALA295C, ALA362C, ALA37S, ARG17S, ASN293C, ASN33S, ASP299C, ASP360C, GLN32S, GLU71C, GLY16S, GLY18S, GLY294C, GLY366C, ILE13S, ILE359C, LYS12S, LYS357C, LYS35S, LYS364C, PHE298C, PHE31S, PHE365C, PRO15S, SER297C, SER34S, SER363C, SER36S, SER38S, THR19S, THR296C, THR301C, THR361C, THR55C, TRP358C, TRP51S, TYR14S, VAL57C, VAL72C, VAL73C
• C-W: HIS313C, LYS18W
• D-O: ALA28D, ARG105O, ARG31D, ASN23O, ASP33D, ILE30D, ILE34D, LEU26O, PRO29D, PRO32D, TYR120D, TYR25O, VAL24O
• D-U: ALA15U, ALA189D, ARG12U, ARG13U, ARG188D, ARG195D, ARG197D, ARG198D, ASN196D, ASP11U, GLY190D, GLY192D, LEU187D, LYS14U, LYS186D, LYS193D, SER10U, SER9U, TRP199D, TYR194D
• D-V: ALA101D, ARG107D, ARG12V, ASN92D, PHE100D, THR6V, THR8V
• D-Y: ALA51Y, ALA53Y, ALA56D, ALA62D, ALA89D, GLN59D, GLN87D, GLU54D, GLU63D, GLY57D, GLY86D, GLY88D, HIS58D, LYS52Y, LYS55D, SER53D, SER61D, THR60D
• E-Q: ALA11E, ALA24Q, ARG140E, ARG15E, ARG17Q, ARG20Q, ARG33E, ARG35E, ARG50E, ASP18Q, ASP29E, GLN16Q, GLN17E, GLN32E, GLN39E, GLU94Q, GLY23Q, HIS22Q, HIS26Q, HIS40E, ILE48Q, ILE69E, LEU27Q, LEU31Q, LEU36E, LYS21Q, LYS32Q, LYS34E, LYS69Q, PHE16E, PHE19Q, PHE20E, PRO19E, SER13E, SER14E, SER28Q, SER47Q, SER70Q, SER71Q, THR18E, THR28E, THR29Q, THR38E, TYR12E, TYR13Q, TYR30E, TYR30Q, TYR31E, TYR49E, VAL25Q, VAL33Q, VAL37E
• E-Z: ALA134E, ASP137E, GLU133E, GLU136E, LYS19Z, TYR11Z, VAL135E
• F-O: ALA10F, ARG39O
• G-L: ALA141G, ALA168G, ALA39L, ALA3L, ALA40L, ARG108G, ARG24L, ARG26L, ARG41L, ARG44L, ARG49L, ASN137G, ASP158G, ASP46L, CYS170G, GLN23L, GLU107G, GLU161G, GLU8L, GLY2L, ILE160G, LEU10L, LEU136G, LEU162G, LEU166G, LEU169G, LEU19L, LEU22L, LEU7L, LYS111G, LYS171G, LYS172G, LYS183G, LYS5L, PHE165G, PHE21L, PRO159G, PRO167G, PRO42L, PRO45L, THR43L, TYR4L, TYR6L, VAL140G, VAL163G, VAL164G, VAL18L, VAL25L
• H-M: ARG128M, ARG133M, ASN59H, ASP42H, GLY132M, HIS40H, HIS64H, ILE41H, LEU129M, LYS130M, LYS39H, LYS63H, PRO131M, TYR135M, VAL43H
• L-V: GLN64V, HIS178L
• L-X: ALA95X, ALA96X, PRO154L
• L-Z: GLN53Z, LYS83L, PHE50Z, PRO84L, THR85L
• N-W: GLN55N, HIS54N, LYS41W
• O-V: ALA91O, ARG86V, ARG92O, ASP75V, ASP84V, ASP90O, GLU83V, ILE81V, ILE93O, LEU77V, LEU80V, LYS113O, LYS116O, LYS76V, PHE94O, PRO118V, PRO82V, PRO99V, THR79V, TRP78V
• P-T: ARG38P, LYS74T, SER37P
• R-S: ALA37S, ALA82R, ARG12R, ARG17S, ARG23S, ARG30S, ARG80R, ARG86R, ARG87R, ARG88R, ASP25S, ASP89R, ASP97R, GLN81R, GLU96R, GLY116R, GLY119R, GLY134R, GLY16S, GLY18S, GLY24S, GLY90R, ILE13S, ILE28S, LEU20S, LEU93R, LYS120R, LYS27S, LYS83R, PHE21S, PHE29S, PHE31S, PHE40S, PHE92R, PHE95R, PRO117R, PRO15S, SER26S, SER84R, THR115R, THR19S, TRP85R, TYR14S, TYR94R, VAL118R, VAL135R, VAL136R, VAL137R, VAL22S, VAL91R
• T-X: ALA29X, ARG138T, GLN34X, GLN65T, GLN85T, GLU30X, GLU64T, ILE139T, ILE44X, ILE63T, ILE67T, LEU102T, LEU28X, LEU31X, LEU36X, LYS32X, LYS35X, LYS61T, MET73T, PHE84T, PRO66T, SER37X, SER69T, SER87T, THR119T, THR68T, TYR103T, TYR60T, VAL33X
• V-Z: ARG42Z, GLN38Z, GLU37V, LYS54V, THR54Z