Contacts of the helix formed by residues 207 - 239 (chain A) in PDB entry 1M5I
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 CYS 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TYR* 5.5 4.3 - - - -
206A THR* 1.3 77.3 - - - +
208A GLN* 1.3 79.1 + - - +
210A MET* 3.9 18.3 - - + +
211A GLU* 3.4 27.8 + - - +
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Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 3.2 10.2 + - - +
207A CYS* 1.3 92.6 + - - +
209A ASP* 1.3 58.6 + - - +
211A GLU* 2.9 41.6 + - - +
212A LYS* 3.2 26.8 + - - +
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Residues in contact with ASP 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLY* 3.3 11.5 - - - -
206A THR* 2.6 49.1 + - - +
208A GLN* 1.3 74.0 - - - +
210A MET* 1.3 59.0 + - - +
212A LYS* 3.8 10.3 - - - +
213A ARG* 3.1 39.6 + - - +
216A ARG* 4.5 3.0 + - - +
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Residues in contact with MET 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 3.8 19.7 - - - +
155A LYS* 3.4 45.1 - - + +
159A TYR* 3.9 16.8 - - - +
200A MET* 4.3 4.7 - - + -
204A LEU* 3.6 36.3 - - + +
205A GLY 5.0 1.1 - - - +
206A THR 3.0 20.4 - - - +
207A CYS* 3.9 17.9 - - + +
208A GLN 3.2 0.8 - - - -
209A ASP* 1.3 81.7 + - - +
211A GLU* 1.3 60.9 + - - +
213A ARG* 3.8 8.8 + - - +
214A ALA* 3.7 17.2 + - - +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A CYS* 3.4 13.0 + - - +
208A GLN* 2.9 49.3 + - - +
210A MET* 1.3 80.0 - - - +
212A LYS* 1.3 71.3 + - + +
213A ARG 3.3 0.4 - - - -
214A ALA* 3.7 7.3 + - - +
215A GLN* 3.6 23.2 + - - +
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Residues in contact with LYS 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLN* 3.2 30.3 + - - +
209A ASP* 4.3 7.2 - - - +
211A GLU* 1.3 86.7 + - + +
213A ARG* 1.3 64.2 + - - +
214A ALA 3.3 0.2 - - - -
215A GLN* 3.3 16.9 + - + +
216A ARG* 3.3 28.1 + - - +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLU* 3.2 40.1 + - - +
203A GLN 5.7 0.2 - - - -
204A LEU* 3.0 40.1 + - - +
205A GLY* 4.2 2.4 - - - +
209A ASP* 3.1 33.1 + - - +
210A MET* 3.8 11.0 - - - +
211A GLU 3.3 0.2 - - - -
212A LYS* 1.3 78.4 - - - +
214A ALA* 1.3 60.1 + - - +
216A ARG* 2.9 28.1 + - - +
217A ARG* 3.3 44.0 + - - +
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Residues in contact with ALA 214 (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* 4.0 21.5 - - + -
151A GLU* 5.2 4.3 - - - +
152A GLU* 5.2 8.7 - - - +
210A MET 3.7 9.7 + - - +
211A GLU* 3.7 9.8 + - - +
212A LYS 3.3 0.4 - - - -
213A ARG* 1.3 77.7 - - - +
215A GLN* 1.3 60.7 + - - +
217A ARG* 3.9 4.9 - - - +
218A ILE* 3.0 40.5 + - + +
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Residues in contact with GLN 215 (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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211A GLU 3.6 13.8 + - - +
212A LYS* 3.3 15.2 + - + +
213A ARG 3.2 0.4 - - - -
214A ALA* 1.3 78.6 - - - +
216A ARG* 1.3 62.7 - - + +
218A ILE* 3.5 22.1 + - - +
219A ALA* 2.8 30.6 + - - +
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Residues in contact with ARG 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 4.5 3.6 + - - +
212A LYS* 3.3 14.8 + - - +
213A ARG* 2.9 48.6 + - - +
215A GLN* 1.3 76.9 - - + +
217A ARG* 1.3 60.1 + - - +
219A ALA* 3.6 7.1 - - + +
220A ARG* 2.8 32.7 + - - +
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.9 23.5 - - + +
147A ASP* 3.2 48.4 + - - +
148A LEU* 3.7 31.3 - - + +
151A GLU* 3.4 36.8 + - - +
152A GLU* 5.6 0.2 + - - -
213A ARG* 3.3 31.6 + - + +
214A ALA* 3.9 1.3 - - - +
215A GLN 3.2 0.4 - - - -
216A ARG* 1.3 79.5 - - - +
218A ILE* 1.3 57.5 + - - +
220A ARG* 3.3 5.0 + - - +
221A ILE* 2.8 36.8 + - - +
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Residues in contact with ILE 218 (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* 4.1 22.9 - - + -
214A ALA* 3.0 23.1 + - + +
215A GLN* 3.9 23.8 - - - +
217A ARG* 1.3 76.5 - - - +
219A ALA* 1.3 63.4 + - - +
221A ILE* 3.5 7.7 + - - +
222A GLN* 3.0 46.7 + - + +
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Residues in contact with ALA 219 (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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215A GLN* 2.8 20.2 + - - +
216A ARG* 3.6 8.5 - - + +
218A ILE* 1.3 77.4 - - - +
220A ARG* 1.3 56.5 + - - +
222A GLN* 3.3 12.5 + - - +
223A GLN* 2.8 29.3 + - - +
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Residues in contact with ARG 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 5.0 5.5 + - - -
137A LEU* 4.0 11.7 - - - +
140A GLU* 3.0 33.4 + - - +
144A LEU* 3.3 27.1 - - + -
216A ARG 2.8 21.7 + - - +
217A ARG* 3.7 1.6 - - - +
219A ALA* 1.3 70.9 - - - +
221A ILE* 1.3 54.9 + - - +
223A GLN* 3.1 27.5 + - - +
224A ILE* 2.7 54.8 + - + +
227A ASP* 4.1 6.7 + - - -
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 4.2 18.8 - - + +
144A LEU* 3.5 33.7 - - + -
145A LEU* 3.6 35.2 - - + +
148A LEU* 3.9 15.7 - - + -
217A ARG 2.8 25.1 + - - +
218A ILE* 3.9 6.7 - - - +
220A ARG* 1.3 73.2 - - - +
222A GLN* 1.3 58.4 + - + +
224A ILE* 3.4 6.7 + - - +
225A GLU* 2.8 53.4 + - - +
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Residues in contact with GLN 222 (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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218A ILE* 3.0 41.9 + - + +
219A ALA* 3.6 9.1 - - - +
221A ILE* 1.3 77.9 - - + +
223A GLN* 1.3 63.5 + - - +
225A GLU* 3.5 18.1 + - - +
226A LYS* 3.3 30.8 + - - +
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Residues in contact with GLN 223 (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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219A ALA 2.8 18.0 + - - +
220A ARG* 3.6 26.2 - - - +
222A GLN* 1.3 75.5 - - - +
224A ILE* 1.3 64.4 + - - +
226A LYS* 3.2 42.6 + - - +
227A ASP* 2.9 34.2 + - - +
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Residues in contact with ILE 224 (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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137A LEU* 3.6 27.6 - - + +
140A GLU* 3.4 39.9 - - + +
141A ARG* 4.0 15.3 - - + +
144A LEU* 3.9 10.3 - - + -
220A ARG* 2.7 49.5 + - + +
221A ILE* 3.6 4.9 - - - +
223A GLN* 1.3 74.0 - - - +
225A GLU* 1.3 58.2 + - - +
227A ASP* 3.2 9.5 + - - +
228A ILE* 3.0 42.9 + - + +
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Residues in contact with GLU 225 (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 ARG* 2.9 42.1 + - - +
221A ILE* 2.8 32.8 + - - +
222A GLN* 3.7 21.2 - - - +
223A GLN 3.3 0.6 - - - -
224A ILE* 1.3 78.8 - - - +
226A LYS* 1.3 60.4 + - - +
228A ILE* 3.8 7.6 + - - +
229A LEU* 3.5 28.6 + - + +
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Residues in contact with LYS 226 (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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222A GLN* 3.3 24.6 + - - +
223A GLN* 3.2 47.8 + - - +
225A GLU* 1.3 76.8 - - - +
227A ASP* 1.3 66.7 + - - +
229A LEU* 3.5 9.6 + - + +
230A ARG* 3.2 29.8 + - + +
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Residues in contact with ASP 227 (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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133A TYR* 5.6 2.0 + - + -
137A LEU* 4.1 20.5 - - + +
220A ARG* 4.1 8.7 + - - -
223A GLN* 2.9 39.3 + - - +
224A ILE* 3.2 13.6 + - - +
226A LYS* 1.3 78.4 - - - +
228A ILE* 1.3 62.0 + - - +
230A ARG* 3.2 7.5 + - - +
231A ILE* 2.9 31.8 + - + +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.8 15.0 - - + +
137A LEU* 3.9 19.7 - - + +
138A GLU* 3.7 27.4 - - + +
141A ARG* 4.6 11.2 - - - -
224A ILE* 3.0 36.1 + - + +
225A GLU* 3.9 8.1 - - - +
226A LYS 3.3 0.2 - - - -
227A ASP* 1.3 76.7 - - - +
229A LEU* 1.3 64.9 + - + +
231A ILE* 3.2 3.6 + - - +
232A ARG* 3.0 62.5 + - - +
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Residues in contact with LEU 229 (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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225A GLU* 3.5 16.1 + - + +
226A LYS* 3.5 12.5 + - + +
227A ASP 3.3 0.2 - - - -
228A ILE* 1.3 80.3 - - + +
230A ARG* 1.3 59.5 + - + +
232A ARG* 3.3 22.2 + - + +
233A GLN* 2.9 47.3 + - - +
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Residues in contact with ARG 230 (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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226A LYS* 3.2 17.0 + - + +
227A ASP* 3.2 9.3 + - - +
229A LEU* 1.3 77.2 - - - +
231A ILE* 1.3 58.2 + - + +
233A GLN* 3.3 29.1 + - - +
234A LEU* 2.8 28.8 + - - +
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 3.9 22.4 - - + -
134A LEU* 3.9 22.0 - - + +
137A LEU* 3.5 32.1 - - + -
227A ASP* 2.9 22.6 + - + +
228A ILE 3.2 4.2 + - - +
230A ARG* 1.3 75.2 - - + +
232A ARG* 1.3 64.0 + - - +
234A LEU* 3.5 14.7 + - + +
235A LEU* 3.1 36.0 + - + +
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Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 4.0 18.7 - - + +
138A GLU* 2.5 31.7 + - - +
228A ILE* 3.0 41.0 + - - +
229A LEU* 3.6 20.3 - - + +
231A ILE* 1.3 74.0 - - - +
233A GLN* 1.3 59.3 + - + +
235A LEU* 3.4 7.2 + - - +
236A GLN* 2.7 43.7 + - - +
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Residues in contact with GLN 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 2.9 43.0 + - - +
230A ARG* 3.5 29.1 + - - +
232A ARG* 1.3 78.3 - - + +
234A LEU* 1.3 52.0 + - - +
236A GLN* 3.1 8.5 + - - +
237A SER* 2.7 40.5 + - - +
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG 2.8 17.4 + - - +
231A ILE* 3.5 16.8 - - + +
233A GLN* 1.3 75.4 - - - +
235A LEU* 1.3 71.5 + - + +
237A SER* 3.3 20.7 - - - -
238A GLN* 3.2 31.5 + - + +
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Residues in contact with LEU 235 (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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131A THR 6.1 0.4 - - - +
134A LEU* 4.5 18.6 - - + -
231A ILE* 3.1 29.9 + - + +
232A ARG* 3.8 6.3 - - - +
233A GLN 3.3 0.2 - - - -
234A LEU* 1.3 83.2 - - + +
236A GLN* 1.3 66.7 + - - +
238A GLN* 3.1 19.4 + - - +
239A ALA* 3.3 23.4 + - - +
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Residues in contact with GLN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 2.7 42.2 + - - +
233A GLN* 3.1 9.6 + - - +
235A LEU* 1.3 80.2 - - - +
237A SER* 1.3 68.0 + - - +
239A ALA* 3.1 25.6 + - + +
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLN* 2.7 24.7 + - - +
234A LEU* 3.3 15.9 - - - -
236A GLN* 1.3 73.2 - - - +
238A GLN* 1.3 66.2 + - - +
239A ALA 4.4 1.7 - - - -
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Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 3.3 29.5 + - + +
235A LEU* 3.1 40.4 + - - +
236A GLN 3.1 0.2 - - - -
237A SER* 1.3 84.5 - - - +
239A ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU 3.3 14.4 + - - +
236A GLN* 3.1 18.7 + - + +
237A SER 4.4 1.8 - - - -
238A GLN* 1.3 84.8 - - - +
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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