Contacts of the helix formed by residues 369 - 396 (chain D) in PDB entry 6V3O
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 GLU 369 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002C SO4 4.0 8.3 + - - -
330D LEU 5.1 0.7 - - - +
331D SER* 3.8 23.9 - - - +
332D MET 4.3 2.9 - - - +
366D PRO* 3.0 31.1 - - - +
367D PRO 3.0 5.0 + - - -
368D ASN* 1.3 92.3 + - - +
370D PRO* 1.3 68.2 - - - +
371D TYR 3.4 2.5 - - - -
372D ARG* 3.2 56.7 + - + +
373D VAL* 3.2 15.4 + - - +
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Residues in contact with PRO 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D MET 3.5 19.5 - - - +
333D TRP* 3.6 18.6 - - - +
335D CYS* 3.9 17.9 - - + -
339D LEU* 3.5 24.6 - - + +
340D ARG* 5.4 2.0 - - + +
343D ALA* 4.1 15.6 - - + +
367D PRO 4.7 4.0 - - - +
368D ASN 3.6 7.2 - - - +
369D GLU* 1.3 86.9 - - - +
371D TYR* 1.3 62.0 + - + +
373D VAL* 3.0 17.6 + - + +
374D ILE* 3.2 17.2 + - - +
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Residues in contact with TYR 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D LEU* 3.9 32.5 - - + +
332D MET* 3.6 35.0 - - + -
334D ARG 2.9 29.0 + - - -
335D CYS* 3.6 8.1 - - + -
339D LEU* 3.5 23.1 - - + -
369D GLU 3.4 0.4 - - - -
370D PRO* 1.3 78.0 - - + +
372D ARG* 1.3 57.4 + - - +
374D ILE* 3.2 7.4 - - + +
375D LEU* 3.1 37.2 + - + +
419D CYS* 3.9 19.5 - - + -
422D SER* 3.0 20.3 + - - -
423D LEU* 3.5 37.8 + - + +
426D CYS* 4.5 0.9 - - - +
428D ASP* 5.6 0.2 + - - -
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Residues in contact with ARG 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C SER* 3.4 23.4 + - - +
1002C SO4 3.1 29.4 + - - -
327D MET* 2.9 48.1 + - + +
328D PHE* 3.2 32.0 + - - +
330D LEU 3.5 14.0 + - - +
331D SER* 4.3 6.5 - - - +
365D ILE 6.0 4.3 - - - +
366D PRO* 5.4 5.9 - - + +
369D GLU* 3.2 44.2 + - + +
371D TYR* 1.3 76.5 - - - +
373D VAL* 1.3 60.0 + - + +
376D GLY* 2.9 25.8 + - - -
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Residues in contact with VAL 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D ALA* 3.6 30.5 - - + +
346D LEU* 4.1 16.6 - - + +
347D HIS* 4.2 20.0 - - + +
365D ILE 5.5 2.7 - - - +
366D PRO 4.0 16.6 - - - +
367D PRO 4.4 2.2 - - - +
369D GLU 3.4 16.6 - - - +
370D PRO* 3.0 9.7 + - + +
372D ARG* 1.3 79.5 - - + +
374D ILE* 1.3 61.6 + - - +
376D GLY* 3.5 0.9 + - - -
377D HIS* 3.2 20.1 + - - +
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Residues in contact with ILE 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D LEU* 3.6 34.8 - - + -
342D ARG* 4.9 8.1 - - + +
343D ALA* 4.3 17.3 - - - +
346D LEU* 4.1 20.9 - - + -
370D PRO 3.2 6.0 + - - +
371D TYR* 3.2 17.5 - - - +
373D VAL* 1.3 76.6 - - - +
375D LEU* 1.3 62.5 + - + +
377D HIS* 3.2 5.7 + - - +
378D VAL* 3.0 31.6 + - - +
415D PRO* 4.9 9.8 - - + +
418D LEU* 5.2 6.7 - - + -
419D CYS* 3.4 33.0 - - - +
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Residues in contact with LEU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D ILE* 3.5 25.7 - - + +
326D LEU* 3.9 32.5 - - + +
327D MET* 3.6 28.9 - - + +
330D LEU* 4.1 15.9 - - + -
371D TYR* 3.1 23.3 + - + +
374D ILE* 1.3 76.8 - - + +
376D GLY* 1.3 61.3 + - - +
378D VAL* 3.4 7.0 + - + +
379D ARG* 3.0 22.7 + - - +
415D PRO* 5.7 0.4 - - + +
416D LEU* 3.9 28.5 - - + -
419D CYS* 4.4 13.2 - - - -
436D LEU* 5.5 0.7 - - + -
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Residues in contact with GLY 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D MET* 3.8 18.0 - - - +
372D ARG 2.9 18.5 + - - -
373D VAL* 3.9 2.2 - - - -
375D LEU* 1.3 76.7 - - - +
377D HIS* 1.3 60.7 + - - +
379D ARG* 3.3 11.5 + - - +
380D ASP* 3.0 31.0 + - - +
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Residues in contact with HIS 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D ARG* 4.5 10.3 + - - -
346D LEU* 3.8 43.0 - - + +
373D VAL 3.2 7.2 + - - +
374D ILE 3.2 10.4 + - - +
376D GLY* 1.3 76.9 - - - +
378D VAL* 1.3 67.4 + - + +
380D ASP* 3.1 24.7 + - + +
381D LYS* 3.1 35.3 + - + +
406D PHE* 6.0 1.3 - + - -
415D PRO* 5.9 4.0 - - + -
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Residues in contact with VAL 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D ILE* 4.4 10.1 - - + -
374D ILE 3.0 17.4 + - - +
375D LEU* 3.8 14.1 - - + +
376D GLY 3.3 0.4 - - - -
377D HIS* 1.3 79.1 - - + +
379D ARG* 1.3 62.3 + - - +
381D LYS 3.4 1.0 + - - -
382D LEU* 3.0 28.1 + - + +
406D PHE* 3.6 20.3 - - + -
412D PHE* 3.6 32.5 - - + +
415D PRO* 3.6 33.7 - - + -
416D LEU* 5.0 2.9 - - + -
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Residues in contact with ARG 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ILE* 4.3 9.4 - - + +
323D ILE* 4.3 9.3 - - + +
324D GLU* 3.1 42.9 + - - +
327D MET* 4.0 24.6 - - - +
375D LEU 3.0 13.8 + - - +
376D GLY* 3.5 11.9 - - - +
377D HIS 3.2 0.2 - - - -
378D VAL* 1.3 77.9 - - - +
380D ASP* 1.3 82.2 + - - +
382D LEU* 3.2 12.1 + - - +
383D TYR* 3.0 47.0 + - + -
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Residues in contact with ASP 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376D GLY 3.0 20.6 + - - +
377D HIS* 3.1 18.8 + - + +
379D ARG* 1.3 95.6 + - - +
381D LYS* 1.3 62.8 + - - +
383D TYR* 3.2 11.0 + - - +
384D ASN* 3.1 27.3 + - - +
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Residues in contact with LYS 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D HIS* 3.1 30.7 + - + +
378D VAL 4.0 0.9 - - - +
380D ASP* 1.3 79.3 - - - +
382D LEU* 1.3 52.3 + - - +
384D ASN* 2.9 6.5 + - - +
385D THR* 2.7 39.5 + - - +
403D GLU 3.2 19.7 + - - -
404D SER* 3.1 17.0 - - - +
405D SER* 2.8 28.9 - - - +
406D PHE* 3.6 31.4 - - + +
411D GLU* 2.7 29.4 + - - +
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Residues in contact with LEU 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D ALA* 4.0 11.8 - - + +
319D TYR* 3.8 43.7 - - + -
320D ILE* 3.7 17.3 - - + +
323D ILE* 4.1 15.9 - - + -
378D VAL* 3.0 28.6 + - + +
379D ARG* 3.2 6.5 + - - +
381D LYS* 1.3 76.4 - - - +
383D TYR* 1.3 61.6 + - - +
385D THR* 2.3 31.8 + - + +
386D ARG* 3.0 10.0 + - - +
406D PHE* 4.0 19.3 - - + -
412D PHE* 4.3 11.4 - - + -
448D LEU* 5.1 6.5 - - + -
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Residues in contact with TYR 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ILE* 3.9 22.2 - - + +
324D GLU* 4.0 10.3 + - - -
379D ARG* 3.0 57.0 + - + -
380D ASP* 3.2 11.0 + - - +
382D LEU* 1.3 74.2 - - - +
384D ASN* 1.3 60.0 + - - +
386D ARG* 3.3 41.2 + - - +
387D GLU* 3.0 36.6 + - + +
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Residues in contact with ASN 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380D ASP* 3.1 15.5 + - - +
381D LYS* 2.9 8.7 + - - +
383D TYR* 1.3 76.7 - - - +
385D THR* 1.3 66.8 + - - +
387D GLU* 3.3 3.6 + - - +
388D ARG* 3.0 26.7 + - - +
400D ILE* 3.9 12.2 - - + +
404D SER* 2.8 49.4 + - - +
405D SER* 4.1 2.0 - - - -
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Residues in contact with THR 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ARG 5.9 0.4 - - - -
316D ALA* 3.7 12.3 - - - +
381D LYS 2.7 25.5 + - - +
382D LEU* 2.3 35.0 + - + +
384D ASN* 1.3 73.6 - - - +
386D ARG* 1.3 63.8 + - - +
388D ARG* 3.5 4.7 + - - +
389D ALA* 3.2 21.5 + - - +
405D SER* 3.5 8.9 - - - -
406D PHE* 3.1 48.5 - - + +
448D LEU* 6.0 1.1 - - + -
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Residues in contact with ARG 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D ARG 5.3 0.9 - - - -
313D MET* 3.9 25.0 - - + +
316D ALA* 3.8 12.3 - - + -
317D ASN* 2.9 39.9 + - - +
320D ILE* 4.5 6.8 - - + +
382D LEU 3.0 11.7 + - - +
383D TYR* 3.3 40.3 + - - +
384D ASN 3.2 0.2 - - - -
385D THR* 1.3 81.6 + - - +
387D GLU* 1.3 90.1 + - - +
389D ALA* 3.2 8.1 + - - +
390D ARG* 2.9 39.1 + - - +
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Residues in contact with GLU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D TYR* 3.0 22.5 + - + +
384D ASN* 4.0 2.5 - - - +
386D ARG* 1.3 114.8 + - - +
388D ARG* 1.3 57.5 + - - +
390D ARG* 3.1 30.3 + - - +
391D HIS* 2.8 39.1 + - - +
400D ILE* 3.6 23.6 - - + -
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Residues in contact with ARG 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384D ASN 3.0 17.7 + - - +
385D THR* 3.7 4.9 - - - +
387D GLU* 1.3 77.1 - - - +
389D ALA* 1.3 57.1 + - - +
391D HIS* 3.2 2.8 + - - +
392D LEU* 2.9 56.5 + - + +
398D SER* 3.4 30.8 + - - +
400D ILE* 2.4 43.4 + - + +
401D SER* 3.4 1.2 - - - +
402D ALA* 3.2 30.1 - - - +
405D SER* 4.0 17.5 - - - +
407D THR* 6.4 0.4 - - - -
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Residues in contact with ALA 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D LEU* 4.0 29.5 - - + +
312D ARG* 4.6 13.0 - - + -
313D MET* 3.7 19.4 - - + +
385D THR 3.2 9.3 + - - +
386D ARG* 3.2 9.4 + - - +
388D ARG* 1.3 75.3 - - - +
390D ARG* 1.3 66.4 + - - +
392D LEU* 3.8 4.4 - - - +
393D LEU* 2.9 25.6 + - - +
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Residues in contact with ARG 390 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D MET* 3.2 38.6 - - + +
317D ASN* 5.2 4.8 - - - +
386D ARG* 2.9 36.9 + - - +
387D GLU* 3.2 44.8 + - - +
389D ALA* 1.3 76.1 - - - +
391D HIS* 1.3 61.7 + - + +
393D LEU* 3.3 6.6 + - + +
394D ALA* 3.0 30.8 + - + +
----------------------------------------------------------
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Residues in contact with HIS 391 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLU* 2.8 41.0 + - - +
387D GLU* 2.8 26.2 + - - +
389D ALA 3.2 0.2 - - - -
390D ARG* 1.3 83.2 - - + +
392D LEU* 1.3 60.2 + - - +
394D ALA* 3.0 5.4 + - + +
395D SER* 2.8 31.8 + - - -
396D GLY 3.7 1.6 + - - -
397D VAL 3.7 4.3 - - - +
398D SER* 3.6 19.7 + - - -
399D GLU 4.6 0.4 + - - -
400D ILE* 4.1 24.5 - - + +
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Residues in contact with LEU 392 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D ARG* 3.1 20.8 + - - +
309D LEU* 3.9 25.1 - - + -
388D ARG* 2.9 50.8 + - + +
389D ALA* 3.8 5.2 - - - +
391D HIS* 1.3 75.2 - - - +
393D LEU* 1.3 58.4 + - - +
396D GLY 3.0 24.5 + - - +
397D VAL* 3.6 29.6 - - + +
398D SER* 3.8 10.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 393 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D GLU* 5.3 0.5 - - - +
305D ARG* 3.9 8.5 + - - +
306D ASP* 3.4 45.2 - - + +
309D LEU* 3.8 15.0 - - + +
310D LEU* 3.7 29.4 - - + -
313D MET* 4.2 16.4 - - + -
389D ALA 2.9 18.1 + - - +
390D ARG* 3.4 6.1 - - + +
392D LEU* 1.3 79.2 - - - +
394D ALA* 1.3 60.9 + - + +
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Residues in contact with ALA 394 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D ARG* 3.0 18.4 + - + +
391D HIS* 3.9 5.6 - - + +
393D LEU* 1.3 79.3 - - - +
395D SER* 1.3 66.0 + - - +
----------------------------------------------------------
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Residues in contact with SER 395 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLU* 4.5 15.5 + - - +
391D HIS* 2.8 12.3 + - - -
394D ALA* 1.3 83.0 + - - +
396D GLY* 1.3 60.9 + - - +
397D VAL* 3.2 23.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 396 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305D ARG* 4.3 15.5 + - - +
392D LEU* 3.0 30.0 + - - +
393D LEU 4.7 0.2 - - - -
394D ALA 3.9 0.4 - - - -
395D SER* 1.3 75.9 - - - +
397D VAL* 1.3 62.3 + - - +
----------------------------------------------------------
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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