Contacts of the helix formed by residues 140 - 164 (chain B) in PDB entry 1BMO
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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138B CYS 3.4 2.0 + - - -
139B LEU* 1.3 72.9 - - - +
141B SER* 1.3 63.1 + - - +
143B LEU* 3.6 10.1 + - - +
144B THR* 3.7 16.8 + - - +
251B ARG* 2.5 37.3 + - - +
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Residues in contact with SER 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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139B LEU* 3.0 15.6 - - - +
140B ASP* 1.3 78.3 - - - +
142B GLU* 1.3 67.2 + - - +
143B LEU 3.1 0.3 + - - -
144B THR* 2.9 23.5 + - - -
145B GLU* 3.5 11.5 + - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 2.7 52.0 + - + +
141B SER* 1.3 77.3 + - - +
143B LEU* 1.3 57.0 + - - +
145B GLU* 3.3 3.2 + - - -
146B PHE* 2.8 30.0 + - - +
245B MET* 3.5 36.9 - - + +
247B HIS* 2.8 35.2 + - - -
248B CYS* 3.6 9.0 - - - -
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS* 3.7 13.2 - - - -
139B LEU 3.1 11.9 + - - +
140B ASP* 3.7 11.4 - - - +
141B SER 3.1 0.2 + - - -
142B GLU* 1.3 76.9 - - - +
144B THR* 1.3 66.1 + - + +
146B PHE* 3.2 13.5 + - - +
147B PRO* 3.2 12.1 - - - +
248B CYS* 4.5 1.1 - - + +
251B ARG* 3.4 45.5 - - + +
252B PHE* 3.6 39.4 - - + +
255B THR* 4.6 11.4 - - - +
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP 3.7 10.0 + - - +
141B SER* 2.9 16.7 + - - -
143B LEU* 1.3 81.7 - - + +
145B GLU* 1.3 58.9 + - - +
147B PRO* 3.5 11.8 - - - +
148B LEU* 3.6 13.0 - - - +
196B VAL* 5.5 0.2 - - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER* 3.5 12.2 + - - +
142B GLU* 3.3 9.8 + - - +
143B LEU 3.2 0.4 - - - -
144B THR* 1.3 78.4 + - - +
146B PHE* 1.3 64.4 + - - +
147B PRO 3.6 0.2 - - - -
148B LEU* 3.6 9.6 + - - +
149B ARG* 2.8 66.9 + - + +
196B VAL* 3.7 30.0 - - + +
245B MET* 3.2 24.4 - - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU 2.8 11.4 + - - +
143B LEU* 3.3 13.0 - - - +
145B GLU* 1.3 74.0 - - - +
147B PRO* 1.3 75.6 - - + +
149B ARG* 2.9 6.8 + - - +
150B MET* 2.9 58.6 + - + -
243B ILE* 4.3 2.7 - - + -
244B PRO 3.3 26.9 - - - -
245B MET* 3.6 23.3 - - + -
248B CYS* 3.7 9.9 - - + -
249B THR* 3.5 26.2 - - - -
252B PHE* 3.3 45.8 - + + -
253B PHE* 4.6 0.2 - + - -
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Residues in contact with PRO 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU 3.2 14.6 - - - +
144B THR* 3.5 11.9 - - - +
145B GLU 3.7 0.2 - - - -
146B PHE* 1.3 95.8 - - + +
148B LEU* 1.3 61.4 + - + +
150B MET 3.9 0.2 - - - -
151B ARG* 2.9 42.4 + - - +
252B PHE* 3.3 27.1 - - + -
272B CYS 4.5 11.4 - - - +
273B PHE* 4.1 14.1 - - + -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR 3.6 23.8 - - - +
145B GLU 4.0 4.5 - - - +
146B PHE 3.2 0.2 - - - -
147B PRO* 1.3 83.6 - - + +
149B ARG* 1.3 64.1 + - - +
151B ARG* 3.6 23.7 + - - +
152B ASP* 3.3 24.4 + - - +
196B VAL* 3.5 31.6 - - + +
199B LEU* 3.8 15.0 - - + +
200B ALA* 3.4 39.5 - - + +
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLU* 2.8 60.9 + - - +
146B PHE* 2.9 11.8 + - - +
148B LEU* 1.3 78.5 - - - +
150B MET* 1.3 60.0 + - - +
152B ASP* 3.8 4.5 + - - +
153B TRP* 3.4 18.0 + - - +
193B ASP* 4.4 20.2 + - - -
194B HIS 3.7 19.8 + - - +
195B PRO* 4.9 1.8 - - - +
196B VAL* 3.9 16.0 - - - +
199B LEU* 4.0 15.0 - - - +
244B PRO* 3.8 32.1 - - + +
245B MET* 4.4 11.7 - - + +
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B PHE* 2.9 51.4 + - + +
147B PRO 4.2 1.3 - - - +
149B ARG* 1.3 70.9 - - - +
151B ARG* 1.3 67.5 + - - +
152B ASP 3.2 1.6 - - - -
153B TRP* 3.1 30.2 + - + +
154B LEU* 3.0 31.2 + - - +
238B LEU* 3.8 30.3 - - + -
243B ILE* 4.3 16.4 - - + -
244B PRO* 4.6 3.1 - - + +
253B PHE* 4.0 9.2 - - + -
269B TRP* 5.1 1.6 - - - -
273B PHE* 3.4 28.0 - - + -
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PRO* 2.9 20.3 + - - +
148B LEU* 3.6 38.3 + - - +
149B ARG 3.5 0.2 - - - -
150B MET* 1.3 79.5 - - - +
152B ASP* 1.3 62.7 + - - +
154B LEU* 3.2 24.1 + - - +
155B LYS 3.4 4.7 + - - -
199B LEU 4.6 2.4 + - - -
200B ALA* 5.2 0.2 - - - +
203B PHE* 3.3 56.4 - - - +
210B TYR* 3.9 22.9 - - + -
214B VAL* 4.2 15.3 - - + -
273B PHE* 2.6 53.4 + - + +
274B GLY* 4.1 1.8 - - - -
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU 3.3 14.1 + - - +
149B ARG 3.9 4.7 - - - +
151B ARG* 1.3 77.1 - - - +
153B TRP* 1.3 68.0 + - - +
154B LEU 3.0 1.2 + - - -
155B LYS* 3.1 29.9 + - - +
156B ASN* 3.1 38.4 + - - -
189B LEU* 4.7 6.1 - - - +
190B GLU 5.1 0.3 - - - +
192B GLY 4.5 10.6 + - - +
194B HIS* 4.7 2.8 - - - -
199B LEU* 4.0 28.9 - - + +
210B TYR* 4.3 14.4 + - - +
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Residues in contact with TRP 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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149B ARG 3.4 12.8 + - - +
150B MET* 3.1 25.3 + - + +
152B ASP* 1.3 81.0 - - - +
154B LEU* 1.3 76.3 + - + +
156B ASN* 3.5 6.4 + - + +
157B VAL* 3.0 53.8 + - + +
217B GLN* 3.2 31.9 - - - -
237B PRO 5.9 0.2 - - - -
238B LEU* 3.6 15.5 - - + -
242B LEU* 4.4 18.7 + - + +
243B ILE* 3.6 33.2 - - + -
244B PRO* 3.8 25.6 - - + -
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Residues in contact with LEU 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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150B MET* 3.0 24.8 + - - +
151B ARG* 3.3 13.9 - - + +
152B ASP 3.1 0.2 - - - -
153B TRP* 1.3 85.8 - - + +
155B LYS* 1.3 68.4 + - - +
157B VAL* 2.9 17.9 + - + +
158B LEU* 2.9 14.4 + - - +
213B PRO* 4.0 15.3 - - + +
214B VAL* 4.0 33.4 - - + +
216B TRP* 5.5 6.4 - - + -
217B GLN* 3.3 47.6 - - + +
269B TRP* 4.6 8.1 - - + -
273B PHE* 5.3 4.5 - - + -
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Residues in contact with LYS 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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151B ARG 3.4 1.4 + - - -
152B ASP* 3.1 29.9 + - - +
154B LEU* 1.3 78.7 - - - +
156B ASN* 1.3 73.1 + - - +
158B LEU* 3.5 2.6 + - - +
159B VAL* 2.9 42.6 + - + +
182B ILE* 4.4 8.7 - - + -
188B ARG* 4.5 6.9 - - + +
189B LEU* 2.9 33.4 + - - +
190B GLU 4.7 0.8 + - - -
202B ASP* 5.1 0.9 - - - -
209B MET* 4.3 28.3 - - + +
210B TYR* 3.7 38.4 - - + -
213B PRO* 3.9 17.1 - - + +
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Residues in contact with ASN 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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152B ASP* 3.1 43.5 + - - +
153B TRP* 3.9 6.3 - - + +
155B LYS* 1.3 90.3 + - - +
157B VAL* 1.3 59.9 + - - +
159B VAL* 3.6 3.5 - - - +
160B THR* 2.9 35.1 + - + +
188B ARG* 4.6 10.6 + - - -
191B ALA* 3.3 40.6 + - + +
192B GLY 4.7 0.6 - - - +
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Residues in contact with VAL 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 TRP* 3.0 61.8 + - + +
154B LEU* 2.9 9.9 + - + +
156B ASN* 1.3 75.5 - - + +
158B LEU* 1.3 59.0 + - - +
160B THR* 3.0 8.8 + - - +
161B LEU* 2.9 33.3 + - + +
216B TRP* 4.3 22.7 - - + -
217B GLN* 6.3 0.7 - - - +
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Residues in contact with LEU 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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154B LEU 2.9 15.4 + - - +
155B LYS* 3.8 5.8 - - - +
157B VAL* 1.3 77.2 - - - +
159B VAL* 1.3 63.9 + - + +
161B LEU* 3.4 5.5 + - + +
162B TYR* 3.2 16.5 + - - +
171B LEU* 3.7 20.8 - - + +
179B VAL* 3.2 26.9 - - + +
182B ILE* 5.5 0.2 - - + -
212B PHE* 3.6 23.8 - - + -
213B PRO* 3.5 34.8 - - + -
216B TRP* 3.6 43.2 - - + -
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Residues in contact with VAL 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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155B LYS* 2.9 32.4 + - + +
156B ASN* 3.6 7.6 - - - +
157B VAL 3.2 0.2 - - - -
158B LEU* 1.3 75.8 - - - +
160B THR* 1.3 60.7 + - + +
162B TYR* 2.9 21.5 + - - +
163B GLU* 3.0 27.5 + - - +
179B VAL* 3.9 10.3 - - + -
182B ILE* 4.2 24.0 - - + -
183B HIS* 3.9 17.7 - - + -
188B ARG* 3.3 32.3 - - - +
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Residues in contact with THR 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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156B ASN* 2.9 22.5 + - + +
157B VAL* 3.0 15.1 + - - +
159B VAL* 1.3 76.5 - - + +
161B LEU* 1.3 55.9 + - - +
163B GLU* 3.7 19.4 - - + +
164B ARG* 3.0 36.4 + - - +
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Residues in contact with LEU 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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157B VAL* 2.9 24.6 + - + +
158B LEU* 3.5 7.9 - - + +
159B VAL 3.1 0.2 - - - -
160B THR* 1.3 74.9 + - - +
162B TYR* 1.3 56.8 + - - +
164B ARG* 3.2 27.9 + - - +
165B ASP* 2.7 34.5 + - - +
170B LEU* 3.4 32.0 - - + +
171B LEU* 4.2 18.4 - - + -
216B TRP* 3.5 37.9 - - + -
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Residues in contact with TYR 162 (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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158B LEU 3.2 1.4 + - - -
159B VAL 2.9 7.6 + - - +
161B LEU* 1.3 80.2 - - - +
163B GLU* 1.3 72.0 + - + +
165B ASP* 3.3 17.3 + - - +
171B LEU* 3.5 12.3 - - + +
176B LYS* 3.8 46.8 + - - -
179B VAL* 3.5 21.5 - - + -
180B LYS* 3.6 33.8 + - + +
183B HIS* 3.2 40.2 + + + -
184B GLU* 3.5 20.6 + - - -
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Residues in contact with GLU 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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159B VAL* 3.0 24.1 + - - +
160B THR* 3.9 18.4 - - + +
161B LEU 3.2 0.2 - - - -
162B TYR* 1.3 90.3 - - + +
164B ARG* 1.3 61.6 + - + +
165B ASP 3.6 4.2 + - - +
183B HIS* 2.9 29.6 + - + +
188B ARG* 5.5 1.2 + - - -
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Residues in contact with ARG 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 THR* 3.0 21.0 + - - +
161B LEU* 3.3 30.5 - - - +
163B GLU* 1.3 75.8 - - + +
165B ASP* 1.3 64.5 + - - +
166B GLU* 3.7 3.8 + - - +
169B ASN* 4.4 5.2 + - - +
170B LEU* 3.6 31.9 - - + +
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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