Contacts of the helix formed by residues 140 - 164 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A CYS 3.4 1.8 + - - -
139A LEU* 1.3 70.4 - - - +
141A SER* 1.3 64.8 + - - +
143A LEU* 3.2 16.6 + - - +
144A THR* 3.5 11.1 + - - +
251A ARG* 2.6 37.4 + - - +
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Residues in contact with SER 141 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A LEU* 2.8 14.7 + - - +
140A ASP* 1.3 78.0 - - - +
142A GLU* 1.3 67.8 + - - +
144A THR* 2.9 25.0 + - - -
145A GLU* 3.5 11.2 + - - +
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Residues in contact with GLU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 2.7 57.8 + - + +
141A SER* 1.3 76.4 + - - +
143A LEU* 1.3 56.8 + - - +
145A GLU* 3.3 2.6 + - - -
146A PHE* 2.8 30.1 + - - +
245A MET* 3.5 38.6 - - + +
247A HIS* 2.7 34.5 + - - -
248A CYS* 3.6 9.0 - - - -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A CYS* 3.9 15.9 - - - -
139A LEU 3.1 5.7 + - - +
140A ASP 3.4 10.5 - - - +
141A SER 3.1 0.8 + - - -
142A GLU* 1.3 77.8 - - - +
144A THR* 1.3 66.6 + - + +
146A PHE* 3.2 13.5 + - + +
147A PRO* 3.3 12.1 - - - +
248A CYS* 4.0 2.1 - - + +
251A ARG* 3.5 52.3 - - + +
252A PHE* 3.6 32.7 - - + +
255A THR* 4.6 11.7 - - - +
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Residues in contact with THR 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ASP 3.5 7.7 + - - +
141A SER* 2.9 17.4 + - - -
143A LEU* 1.3 81.2 - - + +
145A GLU* 1.3 58.6 + - - +
147A PRO* 3.5 10.8 - - - +
148A LEU* 3.6 13.2 - - - +
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Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A SER* 3.9 12.0 + - - +
142A GLU* 3.3 8.7 + - - +
143A LEU 3.2 0.6 - - - -
144A THR* 1.3 79.3 + - - +
146A PHE* 1.3 64.4 + - - +
147A PRO 3.6 0.4 - - - -
148A LEU* 3.5 9.8 + - - +
149A ARG* 2.8 67.0 + - + +
196A VAL* 3.7 29.4 - - + +
245A MET* 3.2 24.4 - - - +
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU 2.8 12.1 + - - +
143A LEU* 3.3 13.0 - - - +
145A GLU* 1.3 74.6 - - - +
147A PRO* 1.3 74.0 - - + +
149A ARG* 2.9 7.4 + - - +
150A MET* 2.9 58.9 + - + +
243A ILE* 4.3 2.5 - - + -
244A PRO 3.2 27.4 - - - -
245A MET* 3.5 23.8 - - + -
248A CYS* 3.8 10.1 - - + -
249A THR* 3.5 26.5 - - - -
252A PHE* 3.3 45.5 - + + -
253A PHE* 4.5 0.2 - + - -
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Residues in contact with PRO 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU 3.3 14.8 - - - +
144A THR* 3.5 12.1 - - - +
145A GLU 3.6 0.2 - - - -
146A PHE* 1.3 95.3 - - + +
148A LEU* 1.3 61.6 + - + +
150A MET 4.0 0.2 - - - -
151A ARG* 3.0 40.6 + - - +
252A PHE* 3.3 26.9 - - + -
272A CYS 4.5 11.7 - - - +
273A PHE* 4.1 14.2 - - + -
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A THR 3.6 22.7 - - - +
145A GLU 3.8 4.9 - - - +
146A PHE 3.2 0.4 - - - -
147A PRO* 1.3 80.6 - - + +
149A ARG* 1.3 64.4 + - - +
151A ARG* 3.6 24.3 + - - +
152A ASP* 3.3 23.9 + - - +
196A VAL* 3.5 32.3 - - + +
199A LEU* 3.8 16.5 - - + +
200A ALA* 3.4 39.5 - - + +
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A GLU* 2.8 59.0 + - - +
146A PHE* 2.9 11.8 + - - +
148A LEU* 1.3 78.7 - - - +
150A MET* 1.3 57.9 + - - +
152A ASP* 3.7 4.7 + - - +
153A TRP* 3.3 20.6 + - - +
193A ASP* 4.4 19.4 + - - -
194A HIS 3.7 20.8 + - - +
195A PRO* 4.9 1.4 - - - +
196A VAL* 3.9 13.7 - - - +
199A LEU* 4.0 15.8 - - - +
244A PRO* 3.8 30.8 - - + +
245A MET* 4.4 12.1 - - + +
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Residues in contact with MET 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE* 2.9 53.8 + - + +
147A PRO 4.3 1.1 - - - +
149A ARG* 1.3 69.8 - - - +
151A ARG* 1.3 68.1 + - - +
152A ASP 3.2 1.6 - - - -
153A TRP* 3.1 30.1 + - + +
154A LEU* 3.0 31.1 + - - +
238A LEU* 3.9 31.6 - - + -
243A ILE* 4.3 8.3 - - + -
244A PRO* 4.6 8.1 - - + +
253A PHE* 4.0 9.2 - - + -
269A TRP* 5.2 1.6 - - - -
273A PHE* 3.4 27.1 - - + -
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Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PRO* 3.0 22.2 + - - +
148A LEU* 3.6 37.8 + - - +
150A MET* 1.3 80.3 - - - +
152A ASP* 1.3 63.1 + - - +
154A LEU* 3.2 23.1 + - - +
155A LYS 3.4 4.9 + - - -
199A LEU 4.6 2.0 + - - -
200A ALA* 5.2 0.2 - - - +
203A PHE* 3.3 57.8 - - - +
210A TYR* 3.9 22.4 - - + -
214A VAL* 4.2 15.9 - - + -
273A PHE* 2.7 52.0 + - + +
274A GLY* 4.1 1.6 - - - -
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU 3.3 14.7 + - - +
149A ARG 3.8 5.1 - - - +
150A MET 3.2 0.2 - - - -
151A ARG* 1.3 76.8 - - - +
153A TRP* 1.3 68.2 + - - +
154A LEU 3.1 0.9 + - - -
155A LYS* 3.1 30.7 + - - +
156A ASN* 3.1 37.0 + - - -
189A LEU* 4.8 5.5 - - - +
190A GLU 5.2 0.3 - - - +
192A GLY 4.5 10.6 - - - +
194A HIS* 4.7 3.3 - - - -
199A LEU* 4.0 27.7 - - + +
210A TYR* 4.3 13.9 + - - +
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Residues in contact with TRP 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ARG 3.3 13.0 + - - +
150A MET* 3.1 23.8 + - + +
152A ASP* 1.3 82.7 + - - +
154A LEU* 1.3 76.0 + - + +
156A ASN* 3.5 6.0 + - + +
157A VAL* 3.0 54.3 + - + +
217A GLN* 3.2 31.6 - - - -
237A PRO 5.4 0.2 - - - -
238A LEU* 3.6 16.2 - - + -
242A LEU* 4.4 17.8 + - + +
243A ILE* 3.6 33.7 - - + -
244A PRO* 3.7 26.5 - - + -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A MET* 3.0 24.6 + - + +
151A ARG* 3.3 14.6 - - + +
152A ASP 3.1 0.2 - - - -
153A TRP* 1.3 86.0 - - + +
155A LYS* 1.3 68.6 + - - +
157A VAL* 3.0 17.2 + - + +
158A LEU* 3.0 14.6 + - - +
213A PRO* 4.0 26.0 - - + +
214A VAL* 4.0 22.2 - - + +
216A TRP* 5.5 5.4 - - + -
217A GLN* 3.3 46.4 - - + +
269A TRP* 4.6 8.5 - - + -
273A PHE* 5.3 4.3 - - + -
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Residues in contact with LYS 155 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ARG 3.4 1.6 + - - -
152A ASP* 3.1 29.8 + - - +
154A LEU* 1.3 77.8 - - - +
156A ASN* 1.3 72.0 + - - +
158A LEU* 3.5 1.9 + - - +
159A VAL* 2.9 43.4 + - + +
182A ILE* 4.4 9.0 - - + -
188A ARG* 4.5 6.0 - - + +
189A LEU* 2.8 34.7 + - - +
190A GLU 4.7 0.4 + - - -
202A ASP* 5.1 0.9 - - - -
209A MET* 4.3 28.9 - - + +
210A TYR* 3.7 37.7 - - + -
213A PRO* 4.0 17.1 - - + +
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Residues in contact with ASN 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ASP* 3.1 42.6 + - - +
153A TRP* 4.0 6.2 - - + +
155A LYS* 1.3 88.4 + - - +
157A VAL* 1.3 60.2 + - + +
159A VAL* 3.7 4.0 - - - +
160A THR* 2.8 35.1 + - + +
188A ARG* 4.6 10.7 + - - -
190A GLU 4.6 0.2 - - - -
191A ALA* 3.3 40.0 + - + +
192A GLY 4.7 0.6 - - - +
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Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A TRP* 3.0 63.3 + - + +
154A LEU* 3.0 9.7 + - + +
156A ASN* 1.3 73.4 - - + +
158A LEU* 1.3 61.9 + - - +
160A THR* 3.0 8.7 + - - +
161A LEU* 2.9 33.5 + - + +
216A TRP* 4.3 22.0 - - + -
217A GLN* 6.3 0.9 - - - +
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LEU 3.0 13.5 + - - +
155A LYS* 3.8 5.6 - - - +
157A VAL* 1.3 80.5 - - - +
159A VAL* 1.3 61.0 + - + +
161A LEU* 3.4 5.4 + - + +
162A TYR 3.2 16.8 + - - -
171A LEU* 3.7 21.2 - - + +
179A VAL* 3.3 24.7 - - + +
182A ILE* 5.5 0.7 - - + -
212A PHE* 3.5 31.2 - - + -
213A PRO* 3.5 26.5 - - + -
216A TRP* 3.5 43.1 - - + -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A LYS* 2.9 32.2 + - + +
156A ASN* 3.7 8.5 - - - +
157A VAL 3.2 0.2 - - - -
158A LEU* 1.3 75.6 - - + +
160A THR* 1.3 60.3 + - + +
162A TYR* 2.9 21.9 + - - +
163A GLU* 3.0 27.5 + - - +
179A VAL* 3.9 9.4 - - + -
182A ILE* 4.2 23.6 - - + -
183A HIS* 3.9 17.3 - - + -
188A ARG* 3.3 32.8 - - - +
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASN* 2.8 19.2 + - + +
157A VAL* 3.0 14.7 + - - +
159A VAL* 1.3 79.9 - - + +
161A LEU* 1.3 56.0 + - - +
163A GLU* 3.4 20.0 + - - +
164A ARG* 2.9 36.4 + - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A VAL* 2.9 22.1 + - + +
158A LEU* 3.5 10.5 - - + +
159A VAL 3.0 0.4 + - - -
160A THR* 1.3 74.6 - - - +
162A TYR* 1.3 55.3 + - - +
164A ARG* 3.1 28.5 + - - +
165A ASP* 2.8 34.8 + - - +
170A LEU* 3.4 30.0 - - + +
171A LEU* 4.2 17.9 - - + -
216A TRP* 3.5 38.1 - - + -
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Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU 3.2 1.0 + - - -
159A VAL 2.9 7.4 + - - +
161A LEU* 1.3 79.7 - - - +
163A GLU* 1.3 74.1 + - + +
165A ASP* 3.4 15.9 + - - +
171A LEU* 3.5 12.8 - - + +
176A LYS* 3.8 47.4 + - - -
179A VAL* 3.6 20.6 - - + -
180A LYS* 3.6 32.9 + - + +
183A HIS* 3.3 37.1 + + + -
184A GLU* 3.5 20.1 + - - -
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A VAL* 3.0 23.3 + - - +
160A THR* 3.8 19.4 - - - +
162A TYR* 1.3 90.8 - - + +
164A ARG* 1.3 60.6 + - + +
165A ASP 3.6 4.2 + - - +
183A HIS* 2.9 30.6 + - + +
188A ARG* 5.4 1.2 + - - -
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A THR* 2.9 21.0 + - - +
161A LEU* 3.2 31.1 - - - +
163A GLU* 1.3 75.4 - - - +
165A ASP* 1.3 64.1 + - - +
166A GLU* 3.7 4.2 + - - +
169A ASN* 4.4 5.4 + - - +
170A LEU* 3.6 31.0 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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