Contacts of the strand formed by residues 423 - 445 (chain D) in PDB entry 2C11
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 LYS 423 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D HIS* 3.4 2.9 - - - +
415D PHE* 3.0 60.4 + - + +
419D SER* 3.5 25.8 + - - +
421D ALA* 3.7 10.7 + - - +
422D PRO* 1.3 77.8 - - - +
424D THR* 1.3 67.4 + - - +
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Residues in contact with THR 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ARG* 5.3 4.5 - - - +
412D ASP* 3.6 24.7 - - + -
413D TRP 3.6 6.3 - - - +
414D HIS* 2.7 40.9 + - + +
415D PHE* 4.2 2.9 - - - -
423D LYS* 1.3 78.7 + - - +
425D ILE* 1.3 68.7 + - - +
426D ARG* 3.8 9.3 + - + +
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Residues in contact with ILE 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D GLY 4.1 2.2 - - - +
393D LYS 4.2 6.5 - - - +
395D THR* 3.1 37.5 - - + +
397D PRO* 3.9 20.4 - - + -
412D ASP* 3.3 2.9 - - - +
413D TRP* 2.9 65.0 + - + +
415D PHE* 3.6 19.5 - - + -
424D THR* 1.3 72.8 - - - +
426D ARG* 1.3 73.3 + - - +
428D ALA* 4.0 11.8 + - + -
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Residues in contact with ARG 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728C ASP* 5.4 11.1 + - - +
397D PRO* 2.9 33.1 - - + +
412D ASP* 3.0 16.6 - - - +
424D THR* 3.8 10.1 + - + +
425D ILE* 1.3 73.0 - - - +
427D ASP* 1.3 78.3 + - - +
428D ALA 3.4 0.5 + - - -
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Residues in contact with ASP 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D PRO* 4.8 0.7 - - + -
398D LEU* 2.8 43.8 + - - +
400D ARG* 2.7 39.5 + - - +
410D TYR* 3.4 22.9 - - + +
411D VAL 3.1 16.5 + - - -
412D ASP* 3.3 5.6 + - - +
426D ARG* 1.3 89.9 - - - +
428D ALA* 1.3 63.4 + - - +
429D PHE 3.3 7.0 - - - -
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Residues in contact with ALA 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D LEU* 4.9 0.9 - - + -
395D THR* 3.7 25.0 - - + +
396D THR 4.7 1.1 - - - -
398D LEU* 3.5 6.2 - - - +
411D VAL 2.9 5.4 + - - +
413D TRP* 3.5 32.8 - - + -
425D ILE* 4.1 11.0 - - + +
426D ARG 3.3 2.0 - - - -
427D ASP* 1.3 78.0 - - - +
429D PHE* 1.3 70.4 + - + +
464D SER* 3.5 23.9 + - - -
465D MET 4.0 2.4 + - - -
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Residues in contact with PHE 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ASP* 5.5 0.2 - - - -
339D PHE* 4.0 33.0 - + + -
340D GLY* 3.5 31.2 - - - -
341D LEU* 3.7 34.5 - - + -
347D PRO* 5.5 1.3 - - + -
398D LEU* 3.7 3.5 - - - +
410D TYR* 3.5 4.0 - - - +
411D VAL* 2.9 41.4 + - + +
412D ASP 3.9 15.7 - - - -
413D TRP* 4.0 9.9 - + - -
427D ASP 4.0 3.8 - - - -
428D ALA* 1.3 86.4 - - + +
430D CYS* 1.3 63.9 + - - +
431D VAL* 5.4 0.7 - - + -
462D VAL* 5.0 10.8 - - + -
463D ARG 3.1 9.2 - - - +
464D SER* 4.0 15.3 - - - -
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Residues in contact with CYS 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D LEU* 3.7 3.3 - - + +
404D CYS* 2.0 53.6 - - + -
408D ALA* 4.5 1.1 - - + -
409D THR 3.0 13.7 - - - +
410D TYR* 3.9 9.4 - - + -
411D VAL* 4.9 0.4 - - - +
429D PHE* 1.3 77.2 - - - +
431D VAL* 1.3 62.6 + - - +
432D PHE* 3.6 18.2 - - - -
461D VAL 3.7 1.0 - - - +
462D VAL* 3.4 2.3 - - - -
463D ARG* 2.8 38.3 + - - -
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Residues in contact with VAL 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D PHE* 3.3 28.0 - - + -
325D VAL* 4.0 13.5 - - + -
330D VAL* 4.0 30.1 - - + -
339D PHE* 4.3 10.5 - - + -
409D THR* 2.9 28.8 + - - +
411D VAL* 5.5 2.7 - - + +
429D PHE* 5.4 1.6 - - + -
430D CYS* 1.3 80.3 - - - +
432D PHE* 1.3 65.9 + - - +
460D LEU* 4.2 9.0 - - + -
461D VAL 3.2 9.6 - - - +
462D VAL* 3.7 27.6 - - + -
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Residues in contact with PHE 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C GLY 3.9 1.8 - - - -
317D TYR* 3.4 15.5 - - - +
323D PHE* 3.6 8.5 - - - -
405D PRO* 3.8 29.6 - - + -
408D ALA* 3.5 19.5 - - + -
430D CYS* 3.6 28.5 - - - -
431D VAL* 1.3 81.2 - - - +
433D GLU* 1.3 72.1 + - - +
434D GLN* 3.7 26.0 - - + -
460D LEU* 3.5 5.1 - - - +
461D VAL* 2.8 67.0 + - + -
463D ARG* 3.8 17.9 - - - -
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Residues in contact with GLU 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C PRO* 4.0 7.2 - - + +
315D GLN* 4.1 6.1 - - - +
317D TYR* 3.0 32.0 + - + -
322D ARG* 3.0 64.1 + - - +
323D PHE* 4.0 16.4 - - + -
405D PRO* 5.8 0.7 - - - +
432D PHE* 1.3 80.4 - - - +
434D GLN* 1.3 62.1 + - - +
435D ASN 4.2 0.2 - - - -
458D THR* 3.5 14.9 - - + +
459D VAL 3.1 11.0 - - - +
460D LEU* 4.1 8.7 - - + +
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Residues in contact with GLN 434 (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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434C GLN* 3.8 0.6 - - - +
435C ASN 3.2 25.3 + - - -
436C GLN* 3.7 19.0 + - - +
437C GLY* 3.9 2.2 - - - +
315D GLN* 3.5 22.0 - - - +
405D PRO* 3.5 26.5 - - - +
432D PHE* 3.7 16.1 + - + -
433D GLU* 1.3 76.4 - - - +
435D ASN* 1.3 79.1 + - - +
436D GLN* 3.3 17.8 + - - +
458D THR* 4.2 2.5 - - - -
459D VAL* 2.9 47.4 + - + +
461D VAL* 4.9 2.2 - - + -
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Residues in contact with ASN 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C PRO* 4.5 6.5 - - - +
313C PRO* 2.7 33.6 + - + +
314C LEU* 4.5 5.4 - - - +
434C GLN* 3.2 18.7 + - - -
315D GLN* 3.5 21.2 + - - +
434D GLN* 1.3 79.1 + - - +
436D GLN* 1.3 65.4 + - - +
437D GLY* 3.4 13.2 + - - -
456D ALA* 4.7 14.8 + - - +
457D GLU 3.7 7.9 - - - +
458D THR* 3.4 19.5 + - - -
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Residues in contact with GLN 436 (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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432C PHE* 5.6 0.5 - - - -
434C GLN* 3.9 16.9 - - - +
436C GLN* 5.2 1.7 - - - +
463C ARG* 5.6 0.7 + - - -
434D GLN* 3.9 17.5 - - - +
435D ASN* 1.3 72.4 - - - +
437D GLY* 1.3 56.0 + - - +
438D LEU* 3.0 24.1 + - + +
457D GLU* 3.1 35.8 + - + +
459D VAL* 3.0 35.7 - - + +
478D VAL* 4.7 2.6 - - - +
480D HIS* 4.3 8.5 - - - -
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Residues in contact with GLY 437 (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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402C VAL 4.0 4.1 - - - +
403C ASP 3.8 0.9 - - - +
404C CYS* 3.8 14.9 - - - -
405C PRO* 4.0 14.9 - - - +
432C PHE* 4.9 2.9 - - - -
434C GLN* 4.0 14.8 - - - -
463C ARG* 2.9 27.3 + - - -
435D ASN* 3.4 14.7 + - - -
436D GLN* 1.3 75.9 - - - +
438D LEU* 1.3 54.5 + - - +
456D ALA* 5.8 1.8 - - - -
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Residues in contact with LEU 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C VAL 4.4 1.3 - - - -
463C ARG* 3.3 25.8 - - - +
474C VAL* 4.1 9.6 - - + -
476C ASP* 3.8 11.9 - - - +
490C TYR* 3.5 44.2 - - + +
696C THR* 3.8 13.0 - - + +
436D GLN* 3.0 15.0 + - + +
437D GLY* 1.3 79.1 + - - +
439D PRO* 1.3 79.8 - - + +
456D ALA* 4.0 1.1 - - - -
457D GLU* 3.1 32.7 + - - +
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Residues in contact with PRO 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C VAL* 3.7 25.1 - - + +
403C ASP 3.9 10.8 - - - +
463C ARG* 4.1 0.4 - - - +
465C MET* 3.6 24.5 - - + -
474C VAL* 4.8 2.9 - - + -
696C THR* 2.9 36.5 + - + +
438D LEU* 1.3 100.0 - - + +
440D LEU* 1.3 60.3 + - - +
441D ARG 4.2 11.0 - - - +
442D ARG* 4.3 10.3 - - + -
455D LEU 3.6 9.0 - - - +
456D ALA* 3.8 4.9 - - - -
457D GLU* 3.9 1.1 - - - +
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Residues in contact with LEU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695C VAL* 2.9 27.8 - - + +
696C THR* 2.9 31.2 + - - +
697C VAL* 3.5 31.9 - - + -
439D PRO* 1.3 71.9 - - - +
441D ARG* 1.3 57.7 + - + +
455D LEU* 2.5 30.9 + - + +
457D GLU* 3.4 18.1 - - + +
481D PRO* 3.4 31.0 - - + -
482D SER* 4.1 6.3 - - - +
716D SER* 3.6 31.9 - - - +
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Residues in contact with ARG 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 4.1 19.7 + - - +
492C THR* 3.6 7.4 - - - +
692C PRO* 4.8 5.3 - - - +
693C ASN* 3.6 37.0 - - + -
694C THR 4.4 0.4 - - - +
695C VAL* 4.3 10.8 - - + -
696C THR* 6.0 0.2 - - - -
439D PRO* 4.2 2.4 - - - +
440D LEU* 1.3 80.0 - - + +
442D ARG* 1.3 65.5 + - - +
453D GLY 4.5 0.7 - - - -
454D GLY* 3.2 17.6 + - - +
455D LEU* 3.0 38.5 + - + +
714D ASP* 3.7 5.0 + - - +
716D SER* 2.7 46.8 + - - +
717D PHE* 3.7 11.5 + - - +
722D SER* 2.5 39.2 + - - -
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Residues in contact with ARG 442 (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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396C THR* 2.9 25.9 + - - -
397C PRO 2.9 29.9 + - - -
398C LEU* 4.5 0.2 - - - +
402C VAL* 4.8 0.9 - - + -
403C ASP* 3.0 36.6 + - - +
465C MET* 3.1 29.6 - - + +
467C THR* 3.3 2.4 + - - -
472C ASP* 2.7 51.9 + - - +
492C THR* 3.1 27.8 + - + +
493C GLY 3.2 3.1 + - - -
693C ASN* 3.6 4.8 + - - -
439D PRO* 4.3 13.5 - - + -
441D ARG* 1.3 79.5 - - - +
443D HIS* 1.3 56.0 + - - +
444D HIS* 3.4 17.8 + - - +
452D PHE* 3.5 13.1 - - + -
453D GLY 3.7 6.5 - - - -
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Residues in contact with HIS 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C PHE* 4.2 6.1 - - - -
302C LEU* 5.2 2.2 - - + -
467C THR* 3.5 13.0 - - + -
469C LEU 3.4 17.8 + - - -
470C ASN* 3.3 20.3 + - - -
472C ASP* 3.0 25.6 + - - +
493C GLY* 3.8 2.5 - - - -
494C TYR* 3.5 31.2 - + + -
693C ASN* 3.7 13.0 - - - +
442D ARG* 1.3 78.6 - - - +
444D HIS* 1.3 62.1 + - - +
445D SER* 3.9 11.4 + - - -
451D TYR* 3.8 26.7 + + - +
452D PHE* 3.2 19.1 - - - -
453D GLY 3.2 19.8 + - - +
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Residues in contact with HIS 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C THR* 3.3 44.3 - - - +
397C PRO* 3.3 35.8 + - + +
399C THR* 4.4 5.1 + - - -
467C THR* 3.4 21.5 - - - +
472C ASP* 3.2 7.3 + - - -
442D ARG* 3.4 9.3 - - - +
443D HIS* 1.3 71.9 - - - +
445D SER* 1.3 61.6 + - - +
446D ASP* 3.5 18.6 + - - -
451D TYR 4.1 1.6 - - - -
452D PHE* 3.6 23.3 - + + +
725D PHE* 5.3 3.1 - + - -
727D GLY 3.9 15.0 + - - -
728D ASP* 5.7 1.1 - - - -
1749D CU 3.0 18.8 - - - -
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Residues in contact with SER 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C PHE* 6.0 1.2 - - - -
443D HIS* 3.9 10.0 + - - -
444D HIS* 1.3 73.6 - - - +
446D ASP* 1.3 67.5 + - - +
447D LEU* 3.4 15.1 + - - +
449D SER 3.0 12.1 + - - -
450D HIS* 3.0 21.5 - - - +
451D TYR* 2.9 57.9 + - - +
727D GLY* 5.9 0.2 - - - -
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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