Contacts of the helix formed by residues 140 - 166 (chain B) in PDB entry 3BRU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 5.7 2.3 - - - +
76B LEU* 4.1 23.0 - - + +
138B PRO* 4.1 13.0 - - - +
139B ASP* 1.3 74.2 + - - +
141B PHE* 1.3 74.4 + - + +
142B ARG 3.3 0.7 + - - -
143B ALA* 3.9 5.6 + - - +
144B ALA* 3.7 18.5 + - - +
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TYR* 4.0 28.5 - + - -
72B ALA* 3.4 31.4 - - + -
75B GLY* 3.8 20.6 - - - -
76B LEU* 3.8 16.8 - - + -
79B ILE* 3.8 15.0 - - + -
130B LEU* 4.2 6.5 - - + -
134B MSE 4.2 12.6 - - - -
137B LEU* 3.8 24.5 - - + -
138B PRO* 2.9 40.9 + - + +
140B ASP* 1.3 85.0 - - + +
142B ARG* 1.3 65.4 + - - +
144B ALA* 3.8 1.4 - - - +
145B LEU* 2.9 28.7 + - + +
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Residues in contact with ARG 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 6.3 0.2 - - - +
194A LYS 3.2 16.6 + - - -
195A LEU* 2.5 47.3 + - + +
196A GLU* 5.4 1.6 - - - +
197A LEU* 3.5 33.2 - - - +
134B MSE 3.4 49.1 + - + +
135B GLY* 5.3 2.8 - - - +
139B ASP* 3.2 20.0 + - - +
141B PHE* 1.3 79.9 - - - +
143B ALA* 1.3 58.7 + - - +
145B LEU* 3.8 1.6 - - - +
146B ILE* 3.0 42.8 + - + +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASP 4.5 1.5 + - - +
140B ASP 3.9 6.5 + - - +
141B PHE 3.4 0.4 - - - -
142B ARG* 1.3 78.9 - - - +
144B ALA* 1.3 57.7 + - - +
146B ILE* 3.9 8.3 - - - +
147B GLY* 2.9 26.3 + - - -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LEU* 4.0 20.6 - - + -
79B ILE* 4.2 15.0 - - + +
140B ASP 3.7 12.9 + - - +
141B PHE 3.3 6.0 + - - +
142B ARG 3.3 0.8 - - - -
143B ALA* 1.3 77.7 - - - +
145B LEU* 1.3 62.6 + - - +
147B GLY* 3.6 1.7 + - - -
148B VAL* 3.2 28.1 + - - +
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LEU* 4.2 18.4 - - + -
79B ILE* 3.8 26.2 - - + -
127B VAL* 4.1 26.4 - - + +
130B LEU* 3.8 28.3 - - + +
131B GLY* 3.7 26.7 - - - +
134B MSE 4.3 3.4 - - - -
137B LEU* 4.2 11.0 - - + -
141B PHE* 2.9 25.1 + - + +
142B ARG 3.8 2.7 - - - +
144B ALA* 1.3 74.8 - - - +
146B ILE* 1.3 64.7 + - - +
148B VAL* 3.3 7.4 + - - +
149B LEU* 3.1 28.6 + - - +
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 6.0 0.9 - - - +
195A LEU* 4.0 20.9 - - + +
196A GLU* 3.8 34.1 - - + +
142B ARG* 3.0 35.4 + - + +
143B ALA* 4.1 7.0 - - - +
145B LEU* 1.3 77.2 - - - +
147B GLY* 1.3 56.1 + - - +
149B LEU* 3.4 8.3 + - + +
150B GLU* 3.0 54.5 + - + +
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Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ALA 2.9 18.6 + - - -
144B ALA 3.6 2.7 + - - -
145B LEU 3.3 0.4 - - - -
146B ILE* 1.3 77.0 - - - +
148B VAL* 1.3 56.2 + - - +
150B GLU* 3.9 9.7 - - - +
151B THR* 2.9 32.9 + - - -
154B ARG* 4.5 1.7 + - - -
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Residues in contact with VAL 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ILE* 4.2 15.9 - - + +
83B ASP* 4.0 33.0 - - + +
127B VAL* 3.8 17.5 - - + -
144B ALA 3.2 15.0 - - - +
145B LEU* 3.3 7.6 + - - +
146B ILE 3.2 0.4 - - - -
147B GLY* 1.3 75.2 - - - +
149B LEU* 1.3 65.2 + - - +
151B THR* 3.3 6.9 + - - -
152B TRP* 3.2 57.3 + - + +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LEU* 5.8 2.2 - - + -
192A ARG* 3.8 47.6 - - - +
195A LEU* 3.8 19.1 - - + -
127B VAL* 3.7 21.8 - - + +
131B GLY* 6.3 0.2 - - - -
145B LEU 3.1 16.7 + - - +
146B ILE* 3.4 8.7 + - + +
148B VAL* 1.3 77.5 - - - +
150B GLU* 1.3 56.2 + - + +
152B TRP* 3.4 28.9 + - + +
153B GLN* 3.1 32.3 + - - +
183B TRP* 5.0 5.9 - - + -
187B GLU* 4.3 17.0 - - + +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ARG* 5.5 3.4 - - - +
196A GLU* 5.6 1.2 - - - +
198A ARG* 5.1 8.8 + - - -
146B ILE* 3.0 39.9 + - + +
147B GLY* 3.9 7.2 - - - +
149B LEU* 1.3 73.6 - - + +
151B THR* 1.3 66.1 + - - +
153B GLN* 3.2 19.0 + - - +
154B ARG* 2.9 48.5 + - - +
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Residues in contact with THR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASP* 5.0 8.8 + - - +
147B GLY 2.9 17.9 + - - -
148B VAL* 3.3 10.2 + - - -
150B GLU* 1.3 76.4 - - - +
152B TRP* 1.3 66.8 + - + +
154B ARG* 3.3 25.2 + - - +
155B ARG* 3.3 34.7 + - + +
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Residues in contact with TRP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B TYR* 3.9 18.2 - + - -
83B ASP* 4.1 10.1 + - - -
86B PHE* 3.4 38.3 - + + +
87B ALA* 5.2 3.6 - - - +
90B LEU* 3.6 20.1 - - + +
94B PHE* 5.1 0.3 - - - -
125B CYS* 3.9 5.2 - - - -
127B VAL* 3.8 19.7 - - + -
148B VAL* 3.2 31.9 + - + +
149B LEU* 3.6 25.4 - - + +
150B GLU 3.3 0.2 - - - -
151B THR* 1.3 80.5 - - + +
153B GLN* 1.3 55.1 + - - +
155B ARG* 3.4 7.9 + - - +
156B THR* 2.7 36.9 + - - -
183B TRP* 3.4 42.1 - + + -
187B GLU* 3.6 21.8 - - - -
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Residues in contact with GLN 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG* 2.8 42.5 + - - +
149B LEU 3.1 21.3 + - - +
150B GLU* 3.2 18.0 + - - +
152B TRP* 1.3 74.0 - - - +
154B ARG* 1.3 60.1 + - + +
156B THR* 3.2 0.9 + - - -
157B ALA* 2.8 31.6 + - - +
176B ASP 5.7 0.4 - - - +
179B ALA* 3.5 17.4 - - + +
180B GLU* 3.8 28.1 + - - +
183B TRP* 3.8 24.6 - - + +
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLY 4.5 1.8 + - - -
150B GLU* 2.9 39.8 + - - +
151B THR* 3.3 36.7 + - - +
153B GLN* 1.3 75.3 - - + +
155B ARG* 1.3 58.5 + - + +
157B ALA* 3.5 6.9 + - - +
158B GLN* 3.1 27.7 + - - +
161B ARG* 4.9 1.7 + - - -
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Residues in contact with ARG 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ALA* 3.2 33.7 + - - +
90B LEU* 3.5 29.6 + - + +
91B ASP* 2.7 37.2 + - - +
94B PHE* 3.9 21.9 - - + +
95B LEU* 4.2 15.0 - - - +
151B THR* 3.3 25.7 + - + +
152B TRP* 3.6 8.7 - - - +
153B GLN 3.2 0.6 - - - -
154B ARG* 1.3 75.8 - - + +
156B THR* 1.3 59.0 + - - +
158B GLN* 3.4 17.2 + - - +
159B LEU* 3.1 24.3 + - - +
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B PHE* 3.7 19.0 - - + -
105B LEU* 4.5 9.2 - - + -
152B TRP 2.7 18.1 + - - -
153B GLN 3.2 3.3 + - - -
155B ARG* 1.3 73.2 - - - +
157B ALA* 1.3 60.8 + - - +
159B LEU* 3.2 5.7 + - + +
160B PHE* 2.9 59.5 + - + -
179B ALA* 3.9 9.6 - - + -
182B PHE* 4.4 10.3 - - + -
183B TRP* 2.8 22.2 + - - +
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B GLN 2.8 17.6 + - - +
154B ARG* 3.6 8.7 - - - +
155B ARG 3.4 0.2 - - - -
156B THR* 1.3 75.1 - - - +
158B GLN* 1.3 56.3 + - - +
160B PHE* 3.0 3.7 + - - +
161B ARG* 2.9 36.5 + - - +
175B PRO* 3.8 19.5 - - - +
176B ASP* 3.6 24.7 - - - +
179B ALA* 3.5 9.7 - - + +
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Residues in contact with GLN 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 5.9 5.0 - - - +
154B ARG 3.1 16.2 + - - +
155B ARG* 3.7 18.3 + - - +
156B THR 3.2 0.2 - - - -
157B ALA* 1.3 75.6 - - - +
159B LEU* 1.3 62.1 + - - +
160B PHE 3.3 0.3 + - - -
161B ARG* 3.3 18.9 + - + +
162B GLU* 3.2 23.0 + - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B PHE* 3.7 44.4 - - + +
101B PRO* 3.6 33.0 - - + +
104B ARG* 3.7 37.0 - - + +
105B LEU* 4.0 20.2 - - + +
155B ARG 3.1 13.4 + - - +
156B THR* 3.4 9.4 - - + +
158B GLN* 1.3 76.9 - - - +
160B PHE* 1.3 64.4 + - + +
162B GLU* 3.3 9.4 + - - +
163B ALA* 3.0 23.2 + - - +
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LEU* 3.8 31.4 - - + -
156B THR* 2.9 31.8 + - + -
157B ALA 3.0 7.4 + - - +
159B LEU* 1.3 83.8 - - + +
161B ARG* 1.3 59.9 + - - +
163B ALA* 3.3 9.9 + - + +
164B GLN* 3.1 30.0 + - - +
169B LEU* 3.9 7.4 - - + +
175B PRO* 3.6 31.4 - - + -
178B LEU* 3.6 43.5 - - + -
179B ALA* 3.6 7.9 - - - -
182B PHE* 4.4 2.7 - - + -
209B PHE* 4.4 7.0 - + - -
213B PHE* 4.1 21.3 - + - -
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Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ARG 4.9 1.0 + - - -
157B ALA* 2.9 15.7 + - - +
158B GLN* 3.7 36.3 - - + +
160B PHE* 1.3 72.9 - - - +
162B GLU* 1.3 60.8 + - - +
164B GLN* 3.3 12.9 + - - +
165B ALA* 3.0 26.0 + - - +
175B PRO* 3.6 21.7 - - + +
176B ASP* 2.6 36.8 + - - -
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PRO* 3.9 12.5 - - + +
104B ARG* 2.5 40.2 + - - -
158B GLN* 3.2 10.5 + - + +
159B LEU* 3.4 13.2 - - - +
161B ARG* 1.3 77.3 - - - +
163B ALA* 1.3 64.4 + - - +
165B ALA* 3.3 18.7 + - + +
166B CYS* 3.4 16.8 + - - -
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Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PRO* 3.9 12.9 - - + +
102B LEU* 5.0 3.6 - - + +
159B LEU 3.0 13.2 + - - +
160B PHE* 3.3 14.3 + - + +
162B GLU* 1.3 75.4 - - - +
164B GLN* 1.3 58.1 + - - +
166B CYS* 3.5 1.7 + - - -
167B GLY 3.2 2.9 + - - -
168B GLU* 2.7 53.5 + - + +
169B LEU* 3.9 13.5 - - + -
213B PHE* 5.2 7.9 - - + -
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Residues in contact with GLN 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B PHE 3.1 14.7 + - - +
161B ARG* 3.5 12.2 - - - +
162B GLU 3.2 0.2 - - - -
163B ALA* 1.3 72.0 - - - +
165B ALA* 1.3 66.8 + - - +
166B CYS 3.1 2.0 - - - -
167B GLY* 3.0 14.0 + - - -
169B LEU* 3.4 28.2 - - + +
170B SER 2.8 22.2 + - - -
171B ALA* 3.6 13.6 + - - +
173B HIS* 3.2 22.5 + - - +
175B PRO* 3.3 28.2 - - - +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ARG 3.0 13.3 + - - +
162B GLU* 3.3 15.0 + - + +
164B GLN* 1.3 75.1 - - - +
166B CYS* 1.3 58.5 + - + +
167B GLY 4.0 0.2 + - - -
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Residues in contact with CYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ALA* 5.9 0.4 - - - -
101B PRO* 4.0 25.1 - - - -
162B GLU* 3.4 16.8 - - - -
163B ALA* 3.9 6.1 - - - -
164B GLN 3.1 0.4 - - - -
165B ALA* 1.3 78.2 - - - +
167B GLY* 1.3 61.6 + - - +
168B GLU* 3.3 14.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il