Contacts of the helix formed by residues 314 - 346 (chain D) in PDB entry 6D6U
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 GLN 314 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D PHE 2.8 20.3 + - - +
311D THR* 3.7 6.5 - - - -
313D SER* 1.3 87.0 + - - +
315D PRO* 1.3 71.7 - - + +
316D ALA* 4.1 8.6 - - + +
317D ARG* 2.6 71.2 + - + +
318D ALA 4.1 2.3 + - - -
320D LYS* 5.3 8.1 - - - +
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Residues in contact with PRO 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ARG* 5.3 3.3 + - - -
311D THR* 4.2 15.2 + - - +
312D LYS 5.5 1.6 - - - +
313D SER 4.3 4.0 - - - +
314D GLN* 1.3 88.5 - - + +
316D ALA* 1.3 64.5 + - + +
317D ARG 3.4 0.7 + - - -
318D ALA* 3.5 13.7 + - - +
319D ALA* 3.8 8.5 + - - +
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Residues in contact with ALA 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D GLN* 3.5 9.8 - - + +
315D PRO* 1.3 82.6 - - + +
317D ARG* 1.3 60.4 + - - +
318D ALA 3.3 0.2 - - - -
319D ALA* 3.3 9.1 + - + +
320D LYS* 2.9 45.8 + - + +
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Residues in contact with ARG 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D PHE* 3.8 34.3 - - + -
313D SER* 6.1 0.4 - - - -
314D GLN* 2.6 54.7 + - + +
315D PRO 3.3 0.8 - - - -
316D ALA* 1.3 79.1 - - - +
318D ALA* 1.3 57.4 + - - +
320D LYS* 3.3 9.8 + - + +
321D ILE* 2.9 47.3 + - + +
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Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ARG* 4.3 9.6 - - - +
307D VAL* 3.7 26.9 - - + +
310D PHE* 4.9 2.4 - - - +
311D THR* 3.9 27.8 - - - +
314D GLN 4.1 1.8 + - - -
315D PRO 3.5 10.2 + - - +
316D ALA 3.3 0.6 - - - -
317D ARG* 1.3 79.0 - - - +
319D ALA* 1.3 56.9 + - - +
321D ILE* 3.3 7.8 + - - +
322D ASP* 2.9 35.3 + - - +
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ARG* 3.7 34.5 + - - +
315D PRO 3.8 5.7 + - - +
316D ALA* 3.3 13.3 + - + +
318D ALA* 1.3 79.2 - - - +
320D LYS* 1.3 57.9 + - + +
322D ASP* 3.4 1.6 + - - +
323D ARG* 2.9 50.6 + - - +
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Residues in contact with LYS 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D GLN* 5.3 7.2 - - - +
316D ALA* 2.9 33.2 + - + +
317D ARG* 3.6 10.1 - - + +
319D ALA* 1.3 77.0 - - - +
321D ILE* 1.3 57.4 + - + +
323D ARG* 3.3 16.1 + - - +
324D LEU* 2.9 42.3 + - + +
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Residues in contact with ILE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D GLU* 3.3 24.2 - - + +
306D THR* 5.2 7.0 - - + -
307D VAL* 3.7 14.4 - - + -
310D PHE* 3.7 32.8 - - + -
317D ARG* 2.9 33.7 + - + +
318D ALA* 3.3 6.5 + - - +
320D LYS* 1.3 76.9 - - + +
322D ASP* 1.3 57.6 + - - +
324D LEU* 3.3 9.5 + - + +
325D SER* 2.9 35.6 + - - +
408D Y01 4.8 22.4 + - + +
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Residues in contact with ASP 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D PHE* 4.1 14.4 - - + +
249D ARG* 3.2 38.4 - - - +
255D ARG* 4.5 11.7 + - - -
303D GLU* 3.0 25.1 - - - +
307D VAL* 3.6 14.9 - - - +
318D ALA 2.9 15.8 + - - +
319D ALA* 4.0 4.7 - - - +
321D ILE* 1.3 74.9 - - - +
323D ARG* 1.3 57.2 + - - +
325D SER* 3.2 2.6 + - - +
326D ARG* 2.9 47.9 + - - +
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Residues in contact with ARG 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D ALA* 2.9 41.0 + - - +
320D LYS* 3.7 19.7 - - - +
322D ASP* 1.3 78.8 - - - +
324D LEU* 1.3 65.8 + - + +
326D ARG* 3.8 18.1 + - - +
327D ILE* 3.8 29.9 + - + +
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Residues in contact with LEU 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D LYS* 2.9 28.4 + - + +
321D ILE* 3.7 4.9 - - + +
323D ARG* 1.3 78.6 - - + +
325D SER* 1.3 60.6 + - - +
327D ILE* 3.3 8.3 + - + +
328D ALA* 2.9 29.9 + - + +
408D Y01 3.5 33.2 - - + +
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Residues in contact with SER 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D PHE* 3.5 30.2 - - - -
303D GLU* 3.5 19.6 + - - +
321D ILE* 2.9 20.6 + - - +
322D ASP 3.2 2.9 + - - -
324D LEU* 1.3 74.0 - - - +
326D ARG* 1.3 67.2 + - - +
328D ALA* 4.2 6.7 - - - -
329D PHE* 3.0 36.8 + - - +
330D PRO* 3.9 0.2 - - - +
408D Y01 4.1 14.2 - - - +
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Residues in contact with ARG 326 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C TYR* 3.8 20.8 + - - -
245D PHE* 3.1 47.1 + - + -
246D TRP* 3.5 60.6 + - + +
247D LEU 4.8 3.4 + - - -
249D ARG* 5.1 11.3 - - - +
322D ASP* 2.9 29.6 + - - +
323D ARG* 3.9 17.2 - - - +
325D SER* 1.3 76.1 - - - +
327D ILE* 1.3 62.5 + - + +
330D PRO* 3.2 24.8 - - - +
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Residues in contact with ILE 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D ARG* 3.8 21.3 + - + +
324D LEU* 3.3 10.3 + - + +
325D SER 3.1 0.4 - - - -
326D ARG* 1.3 81.8 - - + +
328D ALA* 1.3 65.8 + - - +
330D PRO* 4.2 1.7 - - - +
331D LEU* 3.8 20.4 + - + +
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Residues in contact with ALA 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D LEU* 2.9 19.2 + - + +
325D SER* 3.0 6.9 + - - +
327D ILE* 1.3 77.7 - - - +
329D PHE* 1.3 76.2 + - + +
331D LEU* 3.3 7.0 + - - +
332D LEU* 3.1 32.2 + - + +
408D Y01 5.1 15.3 - - + -
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Residues in contact with PHE 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D GLN* 3.2 24.3 + - + +
245D PHE* 3.3 41.1 - + + -
296D PHE* 5.7 0.5 - - - -
299D SER* 4.7 9.6 - - - -
300D ALA* 4.3 18.4 - - + -
303D GLU* 4.5 8.5 - - + -
325D SER* 3.0 18.7 + - - +
328D ALA* 1.3 85.1 - - + +
330D PRO* 1.3 69.1 - - + +
332D LEU* 3.2 11.4 + - + +
333D PHE* 2.9 19.8 + - - +
408D Y01 3.2 55.9 - - + -
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Residues in contact with PRO 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D GLN* 3.2 26.2 - - + +
325D SER 3.9 0.7 - - - +
326D ARG* 3.2 26.5 - - - +
327D ILE 4.2 2.2 - - - +
328D ALA 3.7 1.1 - - - -
329D PHE* 1.3 92.8 - - + +
331D LEU* 1.3 57.1 + - - +
333D PHE* 3.4 3.8 + - + +
334D GLY* 2.9 26.7 + - - -
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D ILE* 3.8 15.8 + - + +
328D ALA* 3.3 9.6 + - - +
329D PHE 3.2 0.8 - - - -
330D PRO* 1.3 79.6 - - - +
332D LEU* 1.3 63.3 + - + +
334D GLY* 3.3 1.3 + - - -
335D ILE* 2.9 55.3 + - + +
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Residues in contact with LEU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D PHE* 5.0 11.1 - - + -
328D ALA* 3.1 22.2 + - + +
329D PHE* 3.2 14.5 + - + +
331D LEU* 1.3 82.0 - - + +
333D PHE* 1.3 59.1 + - - +
335D ILE* 3.3 16.2 + - + +
336D PHE* 2.9 29.3 + - - +
408D Y01 3.9 32.8 - - + -
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Residues in contact with PHE 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D CYS* 5.1 4.9 - - - -
235D ILE* 4.2 31.0 - - + -
238D VAL* 3.6 41.3 - - + -
239D ILE* 4.9 8.1 - - + -
242D GLN* 4.0 12.3 - - - +
289D PHE* 5.6 1.8 - + - -
292D VAL* 6.1 0.4 - - + -
293D CYS* 5.4 3.8 - - - -
296D PHE* 3.5 35.1 - + + -
329D PHE 2.9 16.3 + - - +
330D PRO* 3.9 4.7 - - + +
332D LEU* 1.3 76.2 - - - +
334D GLY* 1.3 59.8 + - - +
336D PHE* 3.3 8.0 + + - +
337D ASN* 2.8 66.3 + - - +
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Residues in contact with GLY 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D PRO 2.9 16.0 + - - -
331D LEU 3.8 1.1 - - - -
332D LEU 3.3 0.2 - - - -
333D PHE* 1.3 80.6 - - - +
335D ILE* 1.3 56.1 + - - +
337D ASN* 3.3 7.4 + - - +
338D LEU* 2.9 29.3 + - - +
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Residues in contact with ILE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D LEU* 2.9 48.1 + - + +
332D LEU* 3.3 16.1 + - + +
334D GLY* 1.3 75.2 - - - +
336D PHE* 1.3 63.5 + - - +
338D LEU* 3.3 13.2 + - + +
339D VAL* 3.0 34.0 + - + +
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Residues in contact with PHE 336 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D TRP* 4.9 4.3 - - + -
289D PHE* 4.3 22.0 - + - -
292D VAL* 3.5 51.1 - - + -
293D CYS 5.5 0.2 - - - -
296D PHE* 4.9 9.6 - + + -
332D LEU 2.9 16.7 + - - +
333D PHE* 3.6 10.3 - + - +
334D GLY 3.2 0.2 - - - -
335D ILE* 1.3 79.2 - - - +
337D ASN* 1.3 67.8 + - - +
339D VAL* 3.3 9.3 + - + +
340D TYR* 2.9 44.1 + + + +
----------------------------------------------------------
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Residues in contact with ASN 337 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D ILE* 4.8 7.2 - - - +
289D PHE* 3.2 34.6 - - - -
333D PHE* 2.8 58.2 + - - +
334D GLY* 3.9 5.6 - - - +
336D PHE* 1.3 78.5 - - - +
338D LEU* 1.3 63.6 + - - +
340D TYR* 4.4 2.7 - - - -
341D TRP* 2.9 47.6 + - + +
407D Y01 6.4 2.2 - - + -
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Residues in contact with LEU 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D GLY 2.9 14.7 + - - +
335D ILE* 3.4 16.6 - - + +
337D ASN* 1.3 77.1 - - - +
339D VAL* 1.3 66.0 + - + +
341D TRP* 5.2 1.3 - - - -
342D ALA* 2.9 37.6 + - + +
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Residues in contact with VAL 339 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D ILE* 3.0 32.8 + - + +
336D PHE* 3.7 10.3 - - + +
338D LEU* 1.3 77.6 - - + +
340D TYR* 1.3 63.7 + - - +
342D ALA* 4.0 2.6 - - - +
343D THR* 2.7 40.9 + - - +
----------------------------------------------------------
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Residues in contact with TYR 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D PHE 5.2 0.3 + - - -
148D MET* 4.8 4.8 - - + +
231D TYR* 3.3 30.3 + + - -
285D ALA* 3.1 23.1 + - - +
288D TRP* 5.2 4.5 - - + -
289D PHE* 3.6 40.9 - + + +
336D PHE* 2.9 33.8 + + + +
337D ASN* 3.8 5.2 - - - +
339D VAL* 1.3 79.2 - - - +
341D TRP* 1.3 87.3 + + - +
343D THR* 3.7 3.6 - - - -
344D TYR* 3.0 59.6 + + - +
----------------------------------------------------------
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Residues in contact with TRP 341 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D MET* 3.5 28.0 - - + -
223D ILE* 4.3 5.2 - - + -
227D VAL* 5.1 0.7 - - + -
231D TYR* 3.7 48.0 - + + -
235D ILE* 5.0 3.3 - - + +
289D PHE* 4.5 3.9 - + - -
337D ASN* 2.9 55.6 + - + +
338D LEU* 4.4 1.1 - - - +
340D TYR* 1.3 86.5 - + - +
342D ALA* 1.3 64.5 + - - +
344D TYR* 5.1 0.9 - - - -
345D LEU* 2.9 56.8 + - + +
407D Y01 3.9 63.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 342 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D LEU* 2.9 28.9 + - + +
339D VAL* 4.0 2.7 - - - +
341D TRP* 1.3 76.9 - - - +
343D THR* 1.3 63.9 + - - +
345D LEU* 5.3 0.4 - - - -
346D ASN* 2.7 48.3 + - - +
----------------------------------------------------------
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Residues in contact with THR 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D VAL* 2.7 33.8 + - - +
340D TYR* 3.7 3.8 - - - -
342D ALA* 1.3 78.2 - - - +
344D TYR* 1.3 70.3 + - + +
346D ASN* 4.5 1.5 - - - +
347D ARG* 3.3 44.0 + - - +
----------------------------------------------------------
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Residues in contact with TYR 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D GLU 4.8 2.1 + - - -
145D ASP* 4.3 11.7 - - + -
146D PHE 5.7 0.2 - - - -
148D MET* 3.4 31.1 - - + +
285D ALA* 3.4 35.5 + - + +
288D TRP* 4.7 9.6 - - + +
340D TYR* 3.0 55.8 + + - +
341D TRP 4.4 0.2 - - - +
343D THR* 1.3 86.6 - - + +
345D LEU* 1.3 65.2 + - - +
347D ARG* 3.2 50.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D MET* 3.5 30.1 - - + -
223D ILE* 4.6 7.0 - - + -
341D TRP* 2.9 50.5 + - + +
342D ALA* 5.3 0.2 - - - -
344D TYR* 1.3 74.2 - - - +
346D ASN* 1.3 63.6 + - - +
347D ARG 3.2 4.8 + - - -
407D Y01 3.6 37.9 - - + +
----------------------------------------------------------
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Residues in contact with ASN 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D ALA* 2.7 45.5 + - - +
343D THR* 4.6 2.0 - - - +
345D LEU* 1.3 76.5 - - - +
347D ARG* 1.3 64.4 + - - +
----------------------------------------------------------
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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