Contacts of the helix formed by residues 210 - 237 (chain A) in PDB entry 6NHY
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 SER 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLY* 1.4 74.7 - - - -
211A LEU* 1.4 69.6 + - - +
212A SER* 3.3 4.5 - - - +
213A GLY* 3.4 16.4 + - - +
214A ILE* 3.9 6.9 + - - +
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Residues in contact with LEU 211 (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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209A GLY* 5.7 2.0 - - - -
210A SER* 1.4 77.6 - - - +
212A SER* 1.3 64.1 + - - +
213A GLY 3.2 2.8 + - - -
214A ILE* 3.5 19.7 - - + +
215A ILE* 3.2 27.2 - - + +
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Residues in contact with SER 212 (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* 3.3 1.3 - - - -
211A LEU* 1.3 77.4 - - - +
213A GLY* 1.3 60.2 + - - +
215A ILE* 4.3 6.0 - - - +
216A ILE* 3.2 37.8 + - - +
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Residues in contact with GLY 213 (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* 3.4 10.4 + - - +
211A LEU 3.2 0.8 - - - -
212A SER* 1.3 77.6 - - - +
214A ILE* 1.4 63.4 + - - +
216A ILE* 3.6 6.3 + - - +
217A TYR* 3.2 24.5 + - - +
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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 3.9 6.0 + - - +
211A LEU* 3.5 28.7 - - + +
213A GLY* 1.4 72.1 - - - +
215A ILE* 1.4 69.2 + - + +
217A TYR* 4.4 16.8 - - + -
218A VAL* 2.9 40.0 + - + +
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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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211A LEU* 3.2 22.1 + - + +
212A SER* 4.4 6.1 - - - +
213A GLY 3.4 0.4 - - - -
214A ILE* 1.4 83.9 - - + +
216A ILE* 1.4 63.2 + - + +
218A VAL* 3.4 20.4 - - + +
219A THR* 3.6 11.8 - - - +
215B ILE* 5.8 0.3 - - - +
216C ILE* 4.4 34.5 - - + -
219C THR* 5.5 1.9 - - + +
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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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212A SER* 3.2 25.3 + - - +
213A GLY* 3.6 6.8 + - - +
214A ILE 3.4 0.4 - - - -
215A ILE* 1.4 79.0 - - + +
217A TYR* 1.4 58.6 + - - +
219A THR* 2.7 27.3 + - - -
220A VAL* 3.6 12.7 - - + +
215B ILE* 4.9 35.8 - - + +
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Residues in contact with TYR 217 (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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213A GLY 3.2 18.3 + - - +
214A ILE* 3.5 17.5 + - + +
216A ILE* 1.4 75.5 - - - +
218A VAL* 1.4 56.5 + - - +
219A THR 3.2 2.5 - - - -
220A VAL* 3.2 13.8 + - + +
221A ALA* 2.8 53.6 + - + -
224A VAL* 6.0 2.1 - - + +
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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* 2.9 29.2 + - + +
215A ILE* 3.4 23.8 - - + +
217A TYR* 1.4 75.5 - - - +
219A THR* 1.4 64.6 + - + +
221A ALA* 3.6 9.8 - - + +
222A ALA* 3.5 19.2 + - - +
219C THR* 4.2 26.7 - - + +
220C VAL* 5.2 8.1 - - + -
223C VAL* 4.0 24.5 - - + +
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Residues in contact with THR 219 (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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215A ILE 3.6 19.1 - - - +
216A ILE* 2.7 19.5 + - - +
218A VAL* 1.4 74.3 - - - +
220A VAL* 1.4 73.5 + - - +
222A ALA* 3.4 18.5 + - - +
223A VAL* 3.6 13.1 - - - +
215B ILE* 4.9 10.5 + - + +
218B VAL* 4.1 20.9 - - - +
219B THR* 3.9 16.3 - - + +
222B ALA* 5.3 1.0 - - - +
219C THR* 3.9 31.6 - - + +
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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* 3.6 16.2 - - + +
217A TYR* 3.2 15.8 + - + +
219A THR* 1.4 89.3 + - - +
221A ALA* 1.4 65.2 + - - +
223A VAL* 3.3 9.9 + - + +
224A VAL* 3.3 36.6 + - + +
218B VAL* 5.4 8.1 - - + -
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Residues in contact with ALA 221 (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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217A TYR* 2.8 39.4 + - + +
218A VAL* 3.6 13.0 - - + +
219A THR 3.3 0.2 - - - -
220A VAL* 1.4 77.2 - - - +
222A ALA* 1.4 60.1 + - - +
224A VAL* 3.3 21.8 - - - +
225A LEU* 3.4 13.5 - - - +
223C VAL* 5.9 2.0 - - + -
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Residues in contact with ALA 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 VAL 3.5 7.9 + - - +
219A THR* 3.4 12.5 + - - +
220A VAL 3.2 0.4 - - - -
221A ALA* 1.4 78.6 - - - +
223A VAL* 1.4 63.2 + - - +
225A LEU* 3.6 12.8 + - - +
226A ILE* 3.5 24.5 + - + +
222B ALA* 4.7 14.6 - - + -
219C THR 5.5 0.4 - - - +
222C ALA* 4.8 11.0 - - + -
223C VAL* 4.4 17.7 - - + +
226C ILE* 4.6 11.6 - - + +
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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 15.7 - - - +
220A VAL* 3.3 10.0 + - + +
222A ALA* 1.4 73.9 - - - +
224A VAL* 1.4 66.2 + - + +
225A LEU 3.5 0.3 + - - -
226A ILE* 3.5 17.6 + - - +
227A VAL* 3.8 18.7 + - + +
218B VAL* 4.2 28.0 - - + +
222B ALA* 4.2 11.7 - - + +
225B LEU* 5.8 7.4 - - + +
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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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217A TYR* 6.0 1.8 - - - +
220A VAL* 3.3 26.4 + - + +
221A ALA* 3.3 20.9 - - - +
223A VAL* 1.4 77.4 - - + +
225A LEU* 1.4 60.9 + - - +
227A VAL* 3.3 11.4 - - + +
228A ALA* 3.1 33.3 + - + +
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Residues in contact with LEU 225 (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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221A ALA 3.4 16.8 - - - +
222A ALA* 3.6 7.6 - - - +
223A VAL 3.3 0.4 - - - -
224A VAL* 1.4 83.3 - - + +
226A ILE* 1.4 59.9 + - - +
228A ALA* 4.2 6.3 - - + +
229A VAL* 3.5 23.8 + - + +
223C VAL* 5.9 7.0 - - + -
226C ILE* 4.1 37.7 - - + -
227C VAL* 5.8 5.2 - - + -
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Residues in contact with ILE 226 (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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222A ALA* 3.5 19.1 - - + +
223A VAL* 3.5 9.5 + - - +
224A VAL 3.4 0.6 - - - -
225A LEU* 1.4 75.6 - - - +
227A VAL* 1.4 62.4 + - + +
229A VAL* 3.1 24.1 - - - +
230A PHE* 3.7 19.5 - - + -
222B ALA* 4.2 11.9 - - + +
225B LEU* 4.0 35.4 - - + -
226B ILE* 4.0 29.8 - - + -
226C ILE* 4.4 14.1 - - + -
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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* 3.8 16.6 + - + +
224A VAL* 3.3 18.4 - - + +
226A ILE* 1.4 79.6 - - + +
228A ALA* 1.4 68.5 + - + +
230A PHE* 3.3 9.7 + - - +
231A VAL* 3.1 31.9 + - + +
225B LEU* 5.6 6.3 - - + -
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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 3.1 21.7 + - - +
225A LEU* 4.2 8.5 - - + +
226A ILE 3.4 0.4 - - - -
227A VAL* 1.4 78.3 - - + +
229A VAL* 1.4 56.4 + - - +
231A VAL* 3.3 7.8 + - - +
232A CYS* 3.0 29.8 + - - +
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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* 3.5 15.3 + - + +
226A ILE* 3.1 23.1 - - - +
228A ALA* 1.4 76.7 - - - +
230A PHE* 1.4 68.8 + - + +
232A CYS* 3.5 9.0 + - + +
233A LYS* 3.4 46.1 + - + +
230C PHE* 6.5 0.9 - - + -
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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 26.0 - - + +
227A VAL* 3.3 12.6 + - - +
229A VAL* 1.4 86.3 - - + +
231A VAL* 1.4 64.8 + - + +
233A LYS* 3.5 10.7 + - + +
234A SER* 3.2 21.7 + - - -
229B VAL* 6.5 0.9 - - + -
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Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A VAL* 3.1 26.2 + - + +
228A ALA* 3.8 7.2 - - - +
230A PHE* 1.4 74.0 - - + +
232A CYS* 1.4 62.7 + - - +
234A SER* 2.6 25.7 + - - +
235A LEU* 3.5 9.7 + - - +
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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 17.3 + - - +
229A VAL* 3.6 12.6 - - + +
230A PHE 3.3 0.2 - - - -
231A VAL* 1.4 77.4 - - - +
233A LYS* 1.4 61.5 + - + +
235A LEU* 3.7 19.1 - - - +
236A LEU* 3.7 9.9 + - - +
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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* 3.4 34.0 + - + +
230A PHE* 3.5 12.3 + - + +
231A VAL 3.4 0.2 - - - -
232A CYS* 1.4 74.2 - - + +
234A SER* 1.4 57.1 + - - +
235A LEU 3.1 4.9 - - - -
236A LEU* 3.1 9.8 + - + +
237A TRP* 2.8 48.0 + - + +
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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 3.2 14.1 + - - -
231A VAL* 2.6 30.9 + - - +
233A LYS* 1.4 75.6 - - - +
235A LEU* 1.4 58.8 + - - +
236A LEU 3.5 0.2 - - - -
237A TRP* 4.0 5.2 - - - +
238A LYS* 3.4 20.8 + - - +
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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 3.5 8.3 + - - +
232A CYS* 3.7 14.1 - - - +
234A SER* 1.4 83.0 + - - +
236A LEU* 1.4 56.7 + - - +
237A TRP 3.5 0.2 - - - -
238A LYS* 3.2 41.8 - - + +
240A VAL 4.4 3.8 - - - +
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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 3.7 10.3 + - - +
233A LYS* 3.1 12.2 + - + +
235A LEU* 1.4 77.1 - - + +
237A TRP* 1.4 70.0 + - + +
238A LYS 3.4 3.8 - - - -
240A VAL 4.9 2.0 - - - -
241A LEU* 3.6 21.2 - - - +
242A PRO* 3.8 29.8 - - + -
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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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233A LYS* 2.8 34.7 + - + +
234A SER* 4.0 6.1 - - - -
236A LEU* 1.4 91.9 - - + +
238A LYS* 1.4 66.0 + - - +
241A LEU* 4.9 6.7 - - - +
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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
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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