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. Author manuscript; available in PMC: 2012 Nov 4.
Published in final edited form as: J Mol Biol. 2011 Sep 16;413(4):773–789. doi: 10.1016/j.jmb.2011.09.011

Table 1.

Summary of hot spots on the surface of the GTP-bound form of Ras

Cluster Solvent molecules Protein contacts Allosteric state Location Binding partner
MSCSa and FTMapb
1 MSCS
HEX, DMF, ETF, HEZ
FTMap
Off state: 52 probes
On state 1: 75 probes		 R68, Q95, Y96, Q99, D92
E62, R68, D92, Q95, Y96, Q99, R102		 MSCS:
Off state
FTMap:
Off state
On state 1		 Interlobal region, between switch II and helix 3 Importin-β binds Ran at this site
2 MSCS
HEX, DMF, GOL, ETF
FTMap
Off state: 61 probes
On state 1: 58 probes
On state 2: 31 probes		 H94, L133, S136, Y137+symm (see Table 3)
F90, E91, I93, H94, L133, Y137		 MSCS:
Off state
FTMap:
Off state
On state 1
On state 2		 Allosteric lobe, between helix 3 and helix 4 Near membrane
MSCS
3 GOL, DMF, RSF, GOL (second molecule) S17, I21, Q25, H27, V29, D33, T35, D38, Y40+symm (see Table 3) Off state Effector lobe, opposite switch I relative to GppNHp Raf-RBD
4 RSF, RSG F28, D30, K147 Off state Interlobal region
5 RSF, GOL A11, G12, N86, K88, S89, D92 Off state Interlobal region, between P-loop and N-terminus of helix 3 RasGAP
6 RSF, YEG D30, E31, Tyr32, GppNHp Off state Effector lobe near N-terminus of switch I RasGAP
7 RSF, GOL L23, N26, K42, Val44, V45, R149, E153, Y157 Off state Interlobal region C-terminus of helix 1 Raf-CRD
8 RSF, RSG G13, Y32, N86, K117, GppNHp Off state Interlobal region between P-loop and switch I RasGAP
FTMap
R128 Off state: 64 probes
On state 1: 58 probes
On state 2: 40 probes		 R123, S127, Q131, Y141, I142, Q143 Off state
On state 1
On state 2		 Allosteric lobe between helix 4 and helix 5 Membrane
R135 Off state: 35 probes
On state 2: 42 probes		 Q131, R135, G138, I139, P140, Y141 Off state
On state 2		 Allosteric lobe between helix 4 and helix 5 Membrane
Y71 Off state: 40 probes
On state 2: 81 probes		 K5, V7, E37, S39, D54, L56, Y71, T74 Off state
On state 2		 Effector lobe near switch II
Allosteric Off state: 83 probes
On state 1: 55 probes
On state 2: 45 probes		 R97, K101, V109, E108, P110, M111, I139, E162, I163, Q165, H166 Off state
On state 1
On state 2		 Allosteric lobe near helix 3 and loop 7 Near membrane
Loop 7 On state 2: 65 probes E76, K104, V109, P110, I163, H166 On state 2 Allosteric lobe near loop 7 opposite side from allosteric site Near membrane
a

The abbreviations for the organic solvent names are the respective residue names used in the coordinate files submitted to the PDB.

b

The number of probes reported for FTMap is the sum of probes at that site in the four structures in each set for the off state, “on” state 1 and “on” state 2.