Contacts of the helix formed by residues 289 - 316 (chain B) in PDB entry 2GFP
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 TRP 289 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B VAL* 5.9 3.6 - - + -
240B LEU* 6.4 2.7 - - + -
243B MET* 6.1 6.3 - - + -
244B THR* 5.5 5.2 - - + -
287B LEU 2.8 10.8 + - - +
288B MET* 1.3 84.2 - - + +
290B ILE* 1.3 68.2 + - + +
293B TRP* 2.8 76.8 - + - -
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 3.8 22.4 - - + -
286B LEU* 3.5 39.9 - - + -
287B LEU 4.3 5.6 - - - +
289B TRP* 1.3 79.1 - - + +
291B PRO* 1.3 80.4 - - + +
293B TRP* 5.0 0.4 - - - -
294B PHE* 2.8 28.8 + - + +
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Residues in contact with PRO 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 4.7 3.3 - - - +
282B LEU* 3.0 40.1 - - + +
283B LEU* 4.2 13.2 - - + +
285B GLY 5.0 0.2 - - - +
286B LEU 4.0 15.9 - - - +
287B LEU 4.3 1.8 - - - +
288B MET* 2.8 30.3 - - - +
289B TRP 3.1 0.2 - - - -
290B ILE* 1.3 99.4 - - + +
292B ASP* 1.3 67.9 + - - +
294B PHE* 3.4 6.8 - - - +
295B GLY* 3.2 11.6 + - - -
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Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 4.9 3.4 - - + +
227B GLU* 3.0 35.3 - - + +
230B SER* 3.1 34.5 + - - +
279B ILE* 5.8 2.0 - - - -
283B LEU* 5.2 7.0 - - + +
288B MET* 4.7 2.4 - - - +
291B PRO* 1.3 82.0 - - - +
293B TRP* 1.3 85.0 + - - +
295B GLY* 2.8 23.4 + - - +
296B VAL* 3.2 12.8 + - - +
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Residues in contact with TRP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B SER* 5.0 7.8 + - - -
231B GLY* 6.3 1.8 - - - -
237B VAL* 3.6 35.0 - - + -
244B THR* 4.7 33.9 - - + +
245B VAL* 6.1 0.2 - - - -
248B LEU* 5.6 0.8 - - - +
288B MET* 3.9 32.6 + - - +
289B TRP* 2.8 84.4 + + - +
290B ILE* 5.0 0.4 - - - -
291B PRO 3.2 0.4 - - - -
292B ASP* 1.3 101.7 + - - +
294B PHE* 1.3 61.9 + - - +
296B VAL* 3.4 16.9 + - - +
297B MET* 3.4 10.0 + - - +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TRP* 3.3 40.4 - + - -
278B VAL* 3.9 15.5 - - + -
279B ILE* 3.4 36.6 - - + +
282B LEU* 3.9 25.4 - - + -
290B ILE* 2.8 24.7 + - + +
291B PRO 3.4 1.6 - - - +
293B TRP* 1.3 74.4 - - - +
295B GLY* 1.3 66.8 + - - +
297B MET* 2.9 46.7 - - + +
298B ASN* 3.0 21.0 + - + -
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Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU* 3.1 19.1 - - - +
279B ILE* 3.4 29.2 - - - +
291B PRO 3.2 6.8 + - - -
292B ASP* 2.8 13.9 + - - -
294B PHE* 1.3 79.9 - - - +
296B VAL* 1.3 60.3 + - - -
298B ASN* 3.4 3.1 + - - +
299B VAL* 3.2 17.0 + - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B GLU* 3.4 49.0 + - + +
228B ALA* 4.2 10.5 - - + +
241B SER* 5.9 2.7 - - - +
245B VAL* 3.3 37.4 - - + +
249B PHE* 5.4 0.4 - - + -
292B ASP 3.2 8.3 + - - +
293B TRP* 3.7 10.5 - - - +
294B PHE 3.3 0.2 - - - -
295B GLY* 1.3 73.1 - - - +
297B MET* 1.3 67.2 + - - +
299B VAL* 3.1 12.9 + - + +
300B TRP* 3.2 12.3 + - - +
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Residues in contact with MET 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 5.4 3.5 - - - +
248B LEU* 3.3 59.0 - - + +
249B PHE* 5.9 0.2 - - - -
251B LEU* 5.2 8.5 - - + -
252B PRO* 4.6 8.4 - - + +
275B TRP* 5.9 3.6 - - + -
293B TRP 3.4 4.8 + - - +
294B PHE* 2.9 52.7 + - + +
296B VAL* 1.3 80.4 - - - +
298B ASN* 1.3 64.3 + - - +
300B TRP* 3.4 5.5 + - - +
301B THR* 2.9 23.2 + - - +
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Residues in contact with ASN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TRP* 3.1 48.9 - - - +
276B GLN* 3.4 13.0 + - - +
279B ILE* 3.4 31.3 - - + +
294B PHE* 3.0 10.5 + - + +
297B MET* 1.3 81.7 - - - +
299B VAL* 1.3 66.8 + - - +
301B THR* 2.9 26.4 + - - -
302B LEU* 3.0 33.0 + - - +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 3.5 41.7 - - + +
223B ILE* 4.2 6.1 - - + -
224B ALA* 5.4 3.4 - - + -
227B GLU* 3.0 37.9 - - - +
276B GLN* 6.2 0.4 - - + -
279B ILE* 6.3 1.1 - - + -
295B GLY 3.2 3.1 + - - +
296B VAL* 3.1 10.6 + - + +
298B ASN* 1.3 81.4 - - - +
300B TRP* 1.3 65.2 + - + +
302B LEU* 3.3 10.0 + - + +
303B LEU* 3.1 36.1 + - + +
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Residues in contact with TRP 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 4.8 14.2 + + - -
136B LEU* 4.6 19.7 - - + -
140B GLY* 6.2 1.8 - - - -
248B LEU 4.5 0.4 - - - -
249B PHE* 2.8 92.4 - + + -
252B PRO* 4.4 4.3 - - + -
253B ILE* 3.8 28.3 - - + -
296B VAL 3.2 5.2 + - - +
297B MET 3.8 6.3 - - - +
299B VAL* 1.3 78.0 - - + +
301B THR* 1.3 75.7 + - - +
303B LEU* 3.2 15.2 + - + +
304B VAL* 3.1 45.4 + - + +
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Residues in contact with THR 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO* 3.1 43.0 - - + +
255B ALA* 5.9 2.5 - - + -
256B ALA* 6.2 0.2 - - + -
268B LYS* 6.5 0.2 - - + -
271B SER* 5.5 4.3 - - - +
275B TRP* 5.0 10.5 - - + +
297B MET* 2.9 17.3 + - - +
298B ASN* 2.9 22.1 + - - +
300B TRP* 1.3 82.9 - - - +
302B LEU* 1.3 61.2 + - + +
305B PRO* 2.6 40.0 - - + +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 4.2 9.9 - - + -
220B LEU* 3.9 23.1 - - + -
268B LYS* 3.8 3.4 - - + +
271B SER* 4.8 2.2 - - - +
272B THR* 3.3 41.5 - - + +
275B TRP* 4.3 4.3 - - + -
276B GLN* 3.1 28.9 - - + +
298B ASN* 3.0 45.1 - - - +
299B VAL* 3.5 4.5 - - - +
301B THR* 1.3 75.5 - - + +
303B LEU* 1.3 64.7 + - - +
305B PRO* 3.8 5.4 - - - +
306B ALA* 3.0 27.8 + - - +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 4.4 25.4 - - + +
53B LEU* 6.3 2.9 - - + -
213B LEU* 5.6 0.7 - - - -
216B LEU* 4.5 1.3 - - + -
217B ILE* 3.9 21.1 - - + -
220B LEU* 3.4 25.8 - - + -
299B VAL* 3.1 28.8 + - + +
300B TRP* 3.3 22.0 - - + +
302B LEU* 1.3 79.1 - - - +
304B VAL* 1.3 59.2 + - + +
306B ALA* 3.5 4.5 - - - +
307B ALA* 3.0 31.8 + - - +
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 6.1 2.7 - - - +
132B HIS* 5.1 6.3 - - + -
136B LEU* 3.6 27.4 - - + -
253B ILE* 3.6 17.0 - - + -
256B ALA* 3.9 4.7 - - + -
300B TRP* 3.3 50.3 - - + +
301B THR 3.0 6.1 + - - +
303B LEU* 1.3 72.4 - - + +
305B PRO* 1.3 78.0 - - + +
306B ALA 3.0 2.1 + - - -
307B ALA* 3.0 7.4 + - - +
308B LEU* 2.9 21.4 + - + +
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Residues in contact with PRO 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PRO 6.0 0.2 - - - -
256B ALA* 3.5 26.5 - - + -
259B GLY* 4.1 23.1 - - - +
260B ALA* 4.8 0.6 - - - -
263B ALA* 4.6 2.6 - - - +
268B LYS* 3.0 28.7 + - + +
301B THR* 2.6 37.0 - - + +
302B LEU 3.8 2.0 - - - +
304B VAL* 1.3 83.1 - - + +
306B ALA* 1.3 62.9 + - - +
308B LEU* 3.0 24.3 + - + +
309B PHE* 3.2 9.2 + - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B LEU* 3.5 38.1 - - + -
216B LEU* 5.5 0.7 - - + -
268B LYS* 2.8 19.0 - - - +
272B THR* 6.1 0.4 - - + -
302B LEU 3.0 20.4 + - - +
303B LEU 3.5 3.4 - - - +
304B VAL 3.0 0.6 - - - -
305B PRO* 1.3 74.2 - - - +
307B ALA* 1.3 60.4 + - - +
308B LEU 3.0 5.4 + - - -
309B PHE* 3.0 17.9 - - - -
310B PHE* 3.0 20.6 - - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 4.9 12.1 - - - +
118B ARG* 4.9 15.1 + - - +
132B HIS* 5.4 2.6 + - - -
213B LEU* 5.6 0.2 - - - +
303B LEU 3.0 19.5 + - - +
304B VAL* 3.6 5.2 - - - +
306B ALA* 1.3 75.5 - - - +
308B LEU* 1.3 56.0 + - - +
310B PHE* 3.9 10.1 - - - -
311B PHE* 2.9 32.5 + - + +
327B PRO* 6.4 0.2 - - - -
331B LEU* 6.5 0.7 - - + -
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 3.2 33.5 + - - +
131B ARG* 4.2 6.3 - - + +
132B HIS* 3.6 40.6 - - + +
253B ILE* 6.0 0.2 - - + -
256B ALA* 3.7 17.5 - - + +
257B PHE* 5.1 2.5 - - - -
260B ALA* 3.3 32.8 - - + -
304B VAL* 2.9 11.1 + - + +
305B PRO* 3.1 15.3 - - + +
306B ALA 3.0 2.0 - - - -
307B ALA* 1.3 75.0 - - - +
309B PHE* 1.3 65.3 + - - +
310B PHE 3.0 0.9 - - - -
311B PHE* 3.0 14.4 + - + +
312B GLY* 3.3 9.5 + - - -
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Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 4.0 25.1 - + - -
212B TYR* 3.5 37.9 - + - -
213B LEU* 4.6 0.4 - - + -
260B ALA* 5.2 3.6 - - + +
263B ALA* 4.0 28.0 - - + +
268B LYS* 4.3 2.7 - - + -
305B PRO 3.2 11.8 + - - -
306B ALA* 3.0 34.5 - - + -
308B LEU* 1.3 79.2 - - - +
310B PHE* 1.3 85.8 + + - +
312B GLY* 4.1 0.6 - - - -
313B ALA* 3.1 36.3 + - + +
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 4.2 24.5 - - + -
210B ASN* 5.7 1.8 - - - -
212B TYR* 5.6 0.2 - + - -
213B LEU* 3.3 43.3 - - + -
306B ALA 3.0 20.5 + - - +
307B ALA* 3.9 8.1 - - - -
309B PHE* 1.3 98.4 - + - +
311B PHE* 1.3 60.6 + - - +
314B GLY* 2.8 34.9 + - - +
315B MET* 3.7 1.6 + - - +
326B GLU* 3.6 25.4 - - + -
327B PRO* 3.8 29.2 - - + +
331B LEU* 4.0 16.8 - - + -
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 3.7 22.0 - - - -
118B ARG* 4.0 29.6 - - + -
119B THR* 4.6 16.6 - - + -
122B ARG* 4.0 36.6 - - + -
132B HIS* 4.1 9.9 - + + -
307B ALA 2.9 23.8 + - - +
308B LEU* 3.0 8.3 + - + +
310B PHE* 1.3 74.7 - - - +
312B GLY* 1.3 58.7 + - - +
315B MET* 3.0 65.8 + - + +
316B LEU* 5.6 0.7 - - - +
327B PRO* 6.3 0.2 - - - -
328B PHE* 4.9 4.5 - + - -
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Residues in contact with GLY 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 4.9 13.6 - - - +
308B LEU 3.3 8.0 + - - -
309B PHE 4.1 0.7 - - - -
311B PHE* 1.3 80.4 - - - +
313B ALA* 1.3 59.4 + - - +
314B GLY 2.8 10.1 + - - -
316B LEU* 3.3 32.1 + - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B PHE* 3.1 23.5 + - + +
310B PHE* 5.4 0.2 - - - -
312B GLY* 1.3 70.6 - - - +
314B GLY* 1.3 56.7 + - - +
317B PHE* 3.2 33.6 - - + -
319B LEU* 5.4 3.1 - - - +
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 2.8 23.4 + - - +
312B GLY 2.8 1.0 + - - -
313B ALA* 1.3 79.4 - - - +
315B MET* 1.3 57.6 + - - -
316B LEU 3.2 3.3 + - - -
317B PHE* 3.7 5.2 + - - +
319B LEU* 2.5 32.4 - - - +
323B GLY* 4.6 3.4 - - - -
326B GLU* 4.9 16.4 - - - -
327B PRO* 5.8 1.8 - - - -
----------------------------------------------------------
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 5.0 4.5 - - - +
310B PHE 3.7 1.1 + - - +
311B PHE* 3.0 54.1 + - + +
314B GLY* 1.3 73.4 - - - +
316B LEU* 1.3 63.3 + - + +
317B PHE 3.6 0.7 - - - -
319B LEU 3.9 4.7 - - - -
320B ALA* 3.4 31.9 - - + +
323B GLY 5.1 2.2 - - - -
324B ALA* 5.1 10.5 - - + +
327B PRO* 5.4 4.0 - - + -
328B PHE* 3.8 31.4 - - + -
----------------------------------------------------------
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B GLY* 3.3 23.1 + - - +
314B GLY 3.2 0.4 + - - -
315B MET* 1.3 80.4 - - + +
317B PHE* 1.3 68.7 + - + +
320B ALA* 5.0 0.4 - - - -
----------------------------------------------------------
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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