Contacts of the helix formed by residues 325 - 354 (chain D) in PDB entry 7A62
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 ASP 325 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ARG* 2.7 48.6 + - - +
320D VAL 4.5 2.8 + - - +
323D LYS* 3.2 17.4 - - + +
324D GLY* 1.3 74.8 - - - +
326D ALA* 1.3 62.8 + - - +
327D GLY 2.8 23.9 + - - -
328D LEU* 3.1 21.0 + - + +
329D ARG* 3.1 30.0 + - - +
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Residues in contact with ALA 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D GLY 4.1 1.4 + - - -
325D ASP* 1.3 71.5 + - - +
327D GLY* 1.3 61.1 + - - +
329D ARG* 3.3 25.7 + - - +
330D GLU* 2.8 35.4 + - - +
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Residues in contact with GLY 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ARG* 3.9 7.1 - - - +
197D LEU* 3.1 24.2 - - - +
325D ASP* 2.8 9.8 + - - -
326D ALA* 1.3 79.0 - - - +
328D LEU* 1.3 55.1 + - - -
330D GLU* 3.3 8.3 + - - +
331D ALA* 3.0 23.0 + - - +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ARG* 4.2 16.6 - - + +
196D LEU* 3.8 33.7 - - + -
197D LEU* 3.7 31.2 - - + +
200D LEU* 4.4 7.6 - - + +
319D PHE* 4.7 8.5 - - + -
320D VAL* 4.0 25.4 - - + +
323D LYS* 4.8 6.7 - - + -
325D ASP* 3.1 37.0 + - + +
326D ALA 3.3 0.2 - - - -
327D GLY* 1.3 72.4 - - - +
329D ARG* 1.3 62.1 + - - +
331D ALA* 4.0 1.1 - - - +
332D TYR* 2.9 31.2 + - - +
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Residues in contact with ARG 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D VAL* 4.6 12.9 + - + +
321D LEU* 5.4 8.4 + - - +
324D GLY* 3.7 11.3 - - - +
325D ASP 3.1 42.9 + - - +
326D ALA* 3.6 26.4 - - - +
328D LEU* 1.3 75.9 - - - +
330D GLU* 1.3 58.2 + - - +
332D TYR* 3.7 1.0 - - - +
333D ASP* 2.9 35.5 + - - +
400D LEU* 3.7 34.3 - - + -
401D LYS 3.8 21.6 + - - +
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Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D LEU* 5.3 1.8 - - + -
326D ALA* 2.8 19.5 + - - +
327D GLY* 3.7 7.0 - - - +
328D LEU 3.2 0.2 - - - -
329D ARG* 1.3 77.4 - - - +
331D ALA* 1.3 58.0 + - - +
333D ASP* 3.4 6.2 + - - +
334D ALA* 3.0 26.0 + - - +
337D LYS* 5.4 1.7 + - - +
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Residues in contact with ALA 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU* 4.1 10.8 - - + +
200D LEU* 3.8 22.9 - - + +
201D LEU* 3.5 33.4 - - + -
327D GLY 3.0 16.7 + - - +
328D LEU 4.0 2.9 - - - +
330D GLU* 1.3 75.2 - - - +
332D TYR* 1.3 65.6 + - - +
334D ALA* 3.1 12.6 + - - +
335D CYS* 3.2 17.0 + - - -
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Residues in contact with TYR 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D LEU* 4.0 12.9 - - + +
277D LEU* 2.3 56.2 + - + +
279D ILE* 4.5 1.7 - - - +
316D VAL* 4.2 13.9 - - + -
317D ARG* 3.1 54.3 + - + +
320D VAL* 4.3 10.8 - - + -
328D LEU 2.9 18.8 + - - +
329D ARG 3.7 2.7 - - - +
331D ALA* 1.3 75.4 - - - +
333D ASP* 1.3 69.6 + - - +
335D CYS* 3.0 17.7 + - - +
336D VAL* 3.1 29.1 + - + +
398D SER 3.8 4.0 - - - -
400D LEU* 3.6 21.3 - - + -
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Residues in contact with ASP 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D ARG 2.9 19.3 + - - +
330D GLU* 3.7 6.0 - - - +
332D TYR* 1.3 78.7 - - - +
334D ALA* 1.3 63.9 + - - +
336D VAL* 3.0 7.2 + - - +
337D LYS* 2.9 40.0 + - - +
399D LEU* 3.5 20.5 - - + +
400D LEU* 2.9 31.5 + - - +
401D LYS* 3.1 27.2 + - - +
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Residues in contact with ALA 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D LEU* 4.6 9.6 - - + -
204D ALA* 3.6 23.6 - - + +
208D GLU* 4.7 6.7 - - - +
330D GLU 3.0 14.0 + - - +
331D ALA* 3.1 13.6 + - - +
333D ASP* 1.3 76.6 - - - +
335D CYS* 1.3 62.0 + - - +
337D LYS* 3.6 11.4 + - - +
338D ALA* 3.3 18.7 + - - +
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Residues in contact with CYS 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D LEU* 3.1 42.4 - - - -
203D ILE* 3.7 17.5 - - + -
204D ALA* 3.7 15.9 - - - +
207D LEU* 4.5 5.2 - - + +
277D LEU* 3.7 24.3 - - + +
331D ALA 3.2 7.8 + - - -
332D TYR 3.0 9.9 + - - +
334D ALA* 1.3 75.0 - - - +
336D VAL* 1.3 64.5 + - - +
338D ALA* 3.3 3.8 + - - +
339D LEU* 3.2 21.8 + - - +
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Residues in contact with VAL 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D LEU* 4.1 16.4 - - + -
279D ILE* 4.6 5.8 - - + -
332D TYR* 3.1 39.4 + - + +
333D ASP* 3.0 9.0 + - - +
335D CYS* 1.3 74.3 - - - +
337D LYS* 1.3 58.2 + - - +
339D LEU* 3.2 7.1 + - - +
340D VAL* 2.8 34.5 + - + +
395D THR* 3.6 28.2 - - + +
398D SER* 4.5 6.3 - - - +
399D LEU* 3.9 26.2 - - + +
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Residues in contact with LYS 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D GLU 5.4 1.4 + - - -
333D ASP* 2.9 28.2 + - - +
334D ALA* 4.1 8.0 - - - +
336D VAL* 1.3 76.5 - - - +
338D ALA* 1.3 53.5 + - - +
340D VAL* 2.9 10.3 + - + +
341D SER* 2.5 44.0 + - - +
399D LEU* 3.9 31.4 - - + -
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Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ALA* 4.1 11.4 - - - +
207D LEU* 3.5 33.3 - - + +
208D GLU* 4.3 11.0 - - + +
211D LEU* 5.6 0.3 - - - +
334D ALA 3.3 15.4 + - - +
335D CYS 3.3 3.8 + - - +
337D LYS* 1.3 78.6 - - - +
339D LEU* 1.3 57.7 + - - +
341D SER* 3.7 7.5 - - - -
342D LEU* 3.0 35.5 + - - +
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Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LEU* 4.6 7.0 - - + +
270D PHE* 4.0 33.7 - - + +
273D PHE* 4.0 18.6 - - + +
274D ASP* 3.5 39.3 - - - +
277D LEU* 4.6 8.7 - - + -
279D ILE* 4.8 2.0 - - + -
335D CYS 3.2 11.5 + - - +
336D VAL* 3.4 9.0 - - - +
337D LYS 3.1 0.6 - - - -
338D ALA* 1.3 74.7 - - - +
340D VAL* 1.3 64.9 + - - +
342D LEU* 3.4 8.4 + - + +
343D ARG* 3.0 39.4 + - + +
395D THR* 4.2 10.1 - - + -
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Residues in contact with VAL 340 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D VAL* 2.8 27.2 + - + +
337D LYS* 3.3 12.8 - - + +
339D LEU* 1.3 74.3 - - - +
341D SER* 1.3 58.6 + - - +
343D ARG* 3.2 5.7 + - - +
344D SER* 2.8 37.5 + - - +
392D ARG* 4.6 5.5 - - + -
395D THR* 3.5 24.5 - - + -
396D GLU* 3.8 41.7 - - + +
399D LEU* 5.8 2.7 - - + -
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Residues in contact with SER 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 3.8 23.8 - - - +
337D LYS* 2.5 25.7 + - - +
338D ALA* 3.7 7.7 - - - -
340D VAL* 1.3 74.6 - - - +
342D LEU* 1.3 58.2 + - - +
344D SER* 3.2 7.5 + - - -
345D TYR* 2.8 31.2 + - - +
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Residues in contact with LEU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D VAL* 5.6 3.4 - - + -
207D LEU* 4.1 29.8 - - + +
210D ALA* 4.0 9.9 - - + +
211D LEU* 3.5 42.2 - - + +
214D PHE* 4.3 15.5 - - + -
269D VAL* 6.0 2.0 - - + -
270D PHE* 4.1 27.4 - - + -
338D ALA 3.0 24.7 + - - +
339D LEU* 3.7 12.3 - - + +
340D VAL 3.3 0.2 - - - -
341D SER* 1.3 76.1 - - - +
343D ARG* 1.3 52.6 + - - +
345D TYR* 3.1 2.1 + - - +
346D HIS* 2.7 37.7 + - - +
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Residues in contact with ARG 343 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D PHE* 3.2 35.3 - - + +
271D GLN* 4.4 1.4 - - - +
274D ASP* 2.6 42.3 + - - -
281D GLN* 4.1 6.3 - - - +
292D LEU* 5.8 1.8 - - - +
339D LEU* 3.0 35.7 + - - +
340D VAL* 3.8 3.6 - - - +
342D LEU* 1.3 77.5 - - - +
344D SER* 1.3 61.9 + - - +
346D HIS* 3.8 9.7 + - - +
347D LEU* 3.1 23.6 + - - +
388D LEU* 5.8 0.4 - - - +
391D VAL* 3.7 17.7 - - + +
392D ARG* 4.4 18.5 - - + +
395D THR* 3.2 20.6 + - - -
504D HEM 2.6 39.1 + - - +
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Residues in contact with SER 344 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D VAL* 2.8 22.0 + - - +
341D SER* 3.6 7.6 - - - -
343D ARG* 1.3 74.3 - - - +
345D TYR* 1.3 65.1 + - - +
347D LEU* 3.2 5.9 + - - +
348D GLN* 3.2 28.5 + - - +
392D ARG* 3.1 39.3 + - - +
396D GLU* 5.6 0.2 + - - -
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Residues in contact with TYR 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D LEU* 3.5 16.4 - - + -
214D PHE* 3.8 34.8 - + + -
215D HIS* 2.9 43.4 + + - -
218D HIS* 2.9 33.9 + - - -
341D SER 2.8 20.5 + - - +
342D LEU 3.6 1.6 - - - +
344D SER* 1.3 71.3 - - - +
346D HIS* 1.3 66.7 + - - +
348D GLN* 2.9 39.3 + - - +
349D ILE* 3.0 29.3 + - + -
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Residues in contact with HIS 346 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D PHE* 3.9 19.3 - + + -
270D PHE* 4.6 10.0 - + + -
342D LEU 2.7 21.4 + - - +
343D ARG* 3.8 10.3 + - - +
345D TYR* 1.3 72.9 - - - +
347D LEU* 1.3 59.0 + - - +
349D ILE* 3.2 4.5 + - + +
350D VAL* 3.0 38.6 + - + +
388D LEU* 3.7 16.7 - - + +
504D HEM 2.4 94.9 + + + -
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Residues in contact with LEU 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D ARG 3.1 17.1 + - - +
344D SER 3.6 4.0 - - - +
345D TYR 3.0 1.4 - - - -
346D HIS* 1.3 78.4 + - - +
348D GLN* 1.3 64.5 + - + +
350D VAL* 3.2 6.0 + - + +
351D THR* 3.1 37.0 + - + +
385D MET* 4.5 14.4 - - + +
388D LEU* 3.9 33.2 - - + +
389D LYS* 3.7 31.6 - - + +
392D ARG* 3.7 32.3 - - - +
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Residues in contact with GLN 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D HIS* 6.2 0.4 - - + -
344D SER* 3.2 19.3 + - - +
345D TYR* 2.9 30.9 + - + +
347D LEU* 1.3 78.6 - - + +
349D ILE* 1.3 65.4 + - + +
351D THR* 2.8 25.7 + - - +
352D LYS* 3.0 11.5 + - - +
----------------------------------------------------------
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Residues in contact with ILE 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D PHE* 4.0 12.8 - - + -
217D ILE* 3.6 13.0 - - + -
218D HIS* 3.4 38.1 - - + +
345D TYR* 3.0 33.8 + - + +
346D HIS* 3.4 9.6 - - - +
347D LEU 3.2 0.2 - - - -
348D GLN* 1.3 78.3 - - + +
350D VAL* 1.3 59.6 + - - +
352D LYS* 3.2 1.5 + - - -
353D TYR* 2.8 42.0 + - + +
504D HEM 3.6 41.5 - - + -
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Residues in contact with VAL 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D HIS* 3.0 38.6 + - + +
347D LEU* 3.2 8.5 + - + +
349D ILE* 1.3 78.6 - - - +
351D THR* 1.3 57.8 + - + +
354D ILE* 2.7 40.9 + - + +
355D LEU* 3.2 10.1 + - + -
384D LEU* 3.9 28.9 - - + -
385D MET* 6.3 0.4 - - - -
388D LEU* 3.7 16.2 - - + -
504D HEM 3.7 22.9 - - + -
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Residues in contact with THR 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU* 3.1 26.4 + - + +
348D GLN* 2.8 21.2 + - - -
350D VAL* 1.3 78.3 - - + +
352D LYS* 1.3 63.2 + - - +
355D LEU* 3.4 21.9 + - + -
356D ILE* 3.0 37.8 + - - +
385D MET* 5.9 3.1 - - + -
389D LYS* 6.2 1.1 - - - +
----------------------------------------------------------
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Residues in contact with LYS 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A HIS* 5.5 8.3 + - - -
218D HIS* 3.0 44.2 + - + +
223D PRO* 3.6 33.7 - - + +
348D GLN 3.0 13.2 + - - +
349D ILE* 3.7 4.3 - - - +
351D THR* 1.3 83.8 + - - +
353D TYR* 1.3 79.4 + - + +
356D ILE* 4.3 14.0 - - + +
357D PRO* 3.5 13.3 - - - +
----------------------------------------------------------
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Residues in contact with TYR 353 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D ILE* 3.2 23.1 + - + -
218D HIS* 3.6 15.1 - - - -
221D VAL* 2.5 50.0 + - + -
223D PRO* 3.5 31.0 - - + +
226D PHE* 4.0 11.8 - + + -
227D PHE* 3.5 24.4 + - - +
349D ILE* 2.8 41.3 + - + +
352D LYS* 1.3 101.6 + - + +
354D ILE* 1.3 66.1 + - - +
357D PRO* 3.9 3.6 - - - +
504D HEM 4.2 20.0 - - + -
----------------------------------------------------------
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Residues in contact with ILE 354 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D PHE* 3.7 25.8 - - + -
227D PHE* 3.7 15.7 - - + -
231D ARG* 4.4 13.2 - - + +
350D VAL* 2.7 26.4 + - + +
352D LYS 3.6 0.4 - - - -
353D TYR* 1.3 78.9 - - - +
355D LEU* 1.3 68.7 + - + +
356D ILE 3.4 0.9 - - - -
357D PRO* 3.4 1.3 - - - +
358D ALA* 3.1 25.5 + - - +
379D THR* 4.2 22.9 - - + +
384D LEU* 4.1 22.0 - - + -
504D HEM 3.9 29.4 - - + -
----------------------------------------------------------
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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