Contacts of the helix formed by residues 213 - 237 (chain A) in PDB entry 6NHW
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 GLY 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A SER* 3.2 17.8 + - - -
211A LEU 3.1 2.0 - - - -
212A SER* 1.3 78.3 - - - +
214A ILE* 1.4 61.8 + - - +
215A ILE* 3.3 0.4 - - - -
216A ILE* 3.3 24.6 - - - +
217A GLY 4.2 0.3 + - - -
210D SER* 6.4 1.1 - - - -
213D GLY* 3.7 20.7 - - - -
216D ILE* 3.7 13.0 - - - +
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Residues in contact with ILE 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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210A SER 5.3 1.1 - - - +
211A LEU* 3.5 26.5 - - + +
213A GLY* 1.4 74.3 - - - +
215A ILE* 1.4 74.2 + - + +
216A ILE 3.4 0.2 - - - -
217A GLY* 3.2 13.0 + - - -
218A VAL* 3.5 13.3 + - - +
216D ILE* 3.8 17.9 - - + +
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Residues in contact with ILE 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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212A SER* 3.4 23.1 - - - +
213A GLY 4.9 0.2 - - - +
214A ILE* 1.4 85.2 - - + +
216A ILE* 1.4 81.8 + - + +
218A VAL* 3.1 25.3 - - - +
219A THR* 3.5 10.5 - - + +
215B ILE* 6.0 7.2 - - + -
216B ILE* 5.6 17.0 - - + -
216C ILE* 5.2 17.0 - - + -
219C THR* 4.1 9.1 - - + +
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Residues in contact with ILE 216 (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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213A GLY* 3.3 18.6 - - - +
215A ILE* 1.4 89.1 - - + +
217A GLY* 1.4 64.1 + - - +
219A THR* 2.6 39.9 + - + +
220A VAL* 3.7 10.6 - - + +
215B ILE* 3.9 36.1 - - + +
218B VAL* 4.2 7.4 - - + -
213D GLY* 3.6 22.9 - - - +
214D ILE* 4.6 12.8 - - + +
217D GLY* 6.2 0.4 - - - -
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Residues in contact with GLY 217 (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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213A GLY 4.2 0.6 + - - -
214A ILE* 3.2 10.1 + - - -
216A ILE* 1.4 83.3 - - - +
218A VAL* 1.4 61.2 + - - +
220A VAL* 3.3 20.6 + - - +
221A ALA 4.0 2.4 + - - -
213D GLY 5.4 0.7 - - - -
216D ILE* 5.6 2.9 - - - -
217D GLY* 4.1 24.0 - - - -
220D VAL* 4.2 17.0 - - - +
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Residues in contact with VAL 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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214A ILE 3.5 9.1 + - - +
215A ILE* 3.1 28.5 - - - +
217A GLY* 1.4 74.0 - - - +
219A THR* 1.4 62.9 + - - +
220A VAL 3.4 0.3 + - - -
221A ALA* 3.4 13.8 + - + +
219C THR* 4.0 24.2 - - + +
220C VAL* 5.1 6.1 - - + -
223C VAL* 3.7 42.7 - - + +
220D VAL* 5.8 0.9 - - - -
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Residues in contact with THR 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 ILE* 3.5 20.6 - - + +
216A ILE* 2.6 31.4 + - + +
218A VAL* 1.4 77.0 - - - +
220A VAL* 1.4 64.6 + - - +
222A ALA* 3.3 22.4 + - - +
223A VAL* 3.6 13.9 + - - +
215B ILE 5.7 0.4 - - - +
216B ILE* 6.4 1.1 - - - -
218B VAL* 3.8 19.8 - - + +
219B THR* 3.7 33.7 - - - +
219C THR* 4.3 8.1 - - + -
223C VAL* 5.7 0.4 - - - -
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Residues in contact with VAL 220 (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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216A ILE* 3.7 22.7 - - + +
217A GLY* 3.5 14.4 - - - +
218A VAL 3.3 0.4 - - - -
219A THR* 1.4 83.7 + - - +
221A ALA* 1.4 61.5 + - - +
223A VAL* 3.5 22.5 - - + +
224A VAL* 3.5 16.4 - - + +
217D GLY* 4.2 17.7 - - - +
220D VAL* 5.1 1.3 - - + -
221D ALA* 4.2 30.1 - - + +
224D VAL* 5.5 0.2 - - - +
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Residues in contact with ALA 221 (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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217A GLY 4.0 1.6 + - - -
218A VAL* 3.4 12.8 + - - +
219A THR 3.3 0.8 - - - -
220A VAL* 1.4 79.6 - - - +
222A ALA* 1.4 62.9 + - - +
224A VAL 4.0 0.3 + - - -
225A LEU* 3.8 19.1 + - - +
223C VAL* 4.6 9.0 - - + -
226C ILE* 5.1 1.1 - - - +
220D VAL* 4.1 22.3 - - + +
224D VAL* 4.4 22.2 - - + +
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Residues in contact with ALA 222 (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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218A VAL 4.0 0.8 + - - -
219A THR* 3.3 14.1 + - - +
221A ALA* 1.4 76.4 - - - +
223A VAL* 1.4 65.2 + - - +
225A LEU* 3.5 11.8 + - - +
226A ILE* 3.6 19.0 + - + +
222B ALA* 4.3 20.2 - - + -
222C ALA* 4.5 11.0 - - + -
223C VAL* 4.1 18.0 - - + +
226C ILE* 4.2 17.8 - - + +
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Residues in contact with VAL 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 THR* 3.6 11.6 + - - +
220A VAL* 3.5 21.5 - - + +
222A ALA* 1.4 74.9 - - - +
224A VAL* 1.4 70.1 + - + +
225A LEU 3.5 0.3 + - - -
226A ILE* 3.5 20.7 + - + +
227A VAL* 3.6 14.8 - - - +
218B VAL* 4.9 14.4 - - + +
221B ALA* 6.0 2.2 - - + -
222B ALA* 4.7 17.9 - - + +
225B LEU* 6.5 0.7 - - + -
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Residues in contact with VAL 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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220A VAL* 3.5 24.6 + - + +
221A ALA 4.6 2.0 - - - +
222A ALA 3.5 1.0 - - - -
223A VAL* 1.4 82.2 - - + +
225A LEU* 1.4 61.7 + - - +
227A VAL* 3.4 23.1 + - + +
228A ALA* 3.6 6.8 + - - +
221D ALA* 5.5 4.7 - - + +
224D VAL* 4.2 29.2 - - + +
225D LEU* 3.6 32.8 - - + +
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Residues in contact with LEU 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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221A ALA 3.8 10.7 + - - +
222A ALA 3.5 10.2 + - - +
223A VAL 3.3 0.8 - - - -
224A VAL* 1.4 79.5 - - - +
226A ILE* 1.4 63.1 + - + +
228A ALA* 3.3 22.3 + - + +
229A VAL* 3.7 16.1 - - + +
226C ILE* 4.0 40.6 - - + +
227C VAL* 5.7 4.5 - - + +
230C PHE* 6.2 5.2 - - + -
224D VAL* 5.0 10.9 - - + +
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Residues in contact with ILE 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 ALA 3.6 15.9 - - - +
223A VAL* 3.5 15.7 + - + +
224A VAL 3.4 0.6 - - - -
225A LEU* 1.4 79.0 - - + +
227A VAL* 1.4 61.4 + - + +
229A VAL* 3.4 23.7 + - + +
230A PHE* 3.7 5.9 + - - +
222B ALA* 4.4 16.6 - - + +
225B LEU* 3.9 41.7 - - + -
226B ILE* 5.7 4.5 - - + -
229B VAL* 6.4 2.2 - - + -
226C ILE* 5.8 8.5 - - + -
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Residues in contact with VAL 227 (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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223A VAL 3.6 15.7 - - - +
224A VAL* 3.6 13.7 - - + +
225A LEU 3.3 0.6 - - - -
226A ILE* 1.4 77.9 - - + +
228A ALA* 1.4 63.0 - - - +
230A PHE* 3.1 21.8 + - + +
231A VAL* 3.3 22.9 + - + +
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Residues in contact with ALA 228 (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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224A VAL 3.6 6.0 + - - +
225A LEU* 3.3 17.6 + - + +
227A VAL* 1.4 77.3 - - - +
229A VAL* 1.4 58.3 + - + +
231A VAL* 3.5 10.9 + - - +
232A CYS* 3.0 31.1 + - - -
228D ALA* 4.6 21.5 - - + -
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Residues in contact with VAL 229 (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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225A LEU* 3.7 24.5 - - + +
226A ILE* 3.5 14.1 - - + +
227A VAL 3.2 0.6 - - - -
228A ALA* 1.4 77.7 - - + +
230A PHE* 1.4 61.1 + - - +
232A CYS* 3.5 19.9 + - + +
233A LYS* 3.6 29.7 - - - +
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Residues in contact with PHE 230 (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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226A ILE 3.7 4.8 + - - +
227A VAL* 3.1 17.1 + - + +
229A VAL* 1.4 76.2 - - - +
231A VAL* 1.4 64.9 + - + +
233A LYS* 3.4 18.4 + - + +
234A SER* 3.1 32.5 + - - -
237A TRP* 5.2 17.9 - + - -
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Residues in contact with VAL 231 (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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227A VAL* 3.3 24.4 + - + +
228A ALA* 3.6 13.2 - - - +
229A VAL 3.4 0.2 - - - -
230A PHE* 1.4 79.9 - - + +
232A CYS* 1.4 64.5 + - - +
234A SER* 2.7 24.6 + - - +
235A LEU* 3.1 31.3 + - + +
232D CYS* 5.1 13.7 - - - -
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Residues in contact with CYS 232 (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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228A ALA* 3.0 25.7 + - - -
229A VAL* 3.6 11.9 - - + +
230A PHE 3.4 0.4 - - - -
231A VAL* 1.4 76.6 - - - +
233A LYS* 1.4 59.9 + - + +
235A LEU* 3.9 5.8 + - - +
236A LEU* 3.3 26.2 + - - +
231D VAL* 6.1 4.5 - - - -
232D CYS* 5.7 8.7 - - - -
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Residues in contact with LYS 233 (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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229A VAL* 3.6 29.4 - - - +
230A PHE* 3.4 19.7 + - + +
231A VAL 3.2 0.6 - - - -
232A CYS* 1.4 77.4 - - + +
234A SER* 1.4 58.5 + - - +
236A LEU* 3.2 9.5 + - + +
237A TRP* 2.9 61.5 + - + +
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Residues in contact with SER 234 (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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230A PHE* 3.1 23.5 + - - -
231A VAL* 2.7 26.4 + - - +
233A LYS* 1.4 74.5 - - - +
235A LEU* 1.4 78.6 + - - +
236A LEU 3.4 0.2 + - - -
237A TRP* 3.2 30.8 + - - +
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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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231A VAL* 3.1 28.3 + - + +
232A CYS* 4.1 5.6 - - - +
234A SER* 1.4 106.8 + - - +
236A LEU* 1.4 59.5 + - - +
237A TRP 3.5 0.7 - - - -
238A LYS* 3.6 25.6 + - - +
232D CYS* 5.3 14.6 - - + -
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Residues in contact with LEU 236 (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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232A CYS 3.3 18.6 + - - +
233A LYS* 3.2 13.2 + - + +
235A LEU* 1.4 75.3 - - - +
237A TRP* 1.4 71.2 + - + +
238A LYS* 3.4 16.3 + - - +
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Residues in contact with TRP 237 (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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230A PHE* 5.2 18.4 - + - -
233A LYS* 2.9 49.0 + - + +
234A SER* 3.2 22.2 + - - +
235A LEU 4.7 0.3 - - - -
236A LEU* 1.4 84.5 - - + +
238A LYS* 1.4 64.2 + - - +
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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