Contacts of the helix formed by residues 395 - 417 (chain D) in PDB entry 5ED1
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 ALA 395 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D VAL* 3.7 30.1 - - + +
353D ALA* 3.6 19.7 - - + +
372D SER* 2.6 29.7 + - - +
373D THR 4.1 2.7 - - - -
374D GLY 2.8 21.7 + - - +
393D CYS 3.5 0.4 + - - -
394D HIS* 1.3 70.5 - - - +
396D GLU* 1.3 65.3 + - - +
398D ILE* 3.2 4.7 + - - +
399D SER* 2.9 13.9 + - - -
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Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D VAL* 4.6 4.0 - - - +
353D ALA* 4.0 8.5 - - + -
374D GLY 4.9 0.2 - - - +
394D HIS* 3.6 2.1 - - - +
395D ALA* 1.3 82.4 + - - +
397D ILE* 1.3 67.9 + - + +
399D SER* 3.3 4.1 + - - -
400D ARG* 3.0 18.5 + - - +
444D LEU* 4.6 13.8 - - + +
446D ILE* 3.9 33.4 - - + +
450D PRO* 3.7 16.6 - - - +
451D CYS 4.3 0.3 + - - -
455D ARG* 4.9 3.1 + - - -
516D CYS* 3.6 39.9 - - + +
520D ILE* 4.3 11.7 - - + -
523D TRP* 3.6 12.0 - - + -
802D ZN 3.7 4.6 - - - -
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Residues in contact with ILE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D ASP* 3.3 38.8 - - - +
394D HIS 3.4 8.3 - - - +
396D GLU* 1.3 76.0 - - + +
398D ILE* 1.3 63.3 + - - +
400D ARG* 3.3 5.4 + - - +
401D ARG* 3.0 29.3 + - - +
516D CYS* 3.7 25.1 - - + -
519D LYS* 3.5 28.3 - - + -
523D TRP* 3.9 20.9 - - + -
801D IHP 3.5 37.6 + - - +
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Residues in contact with ILE 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372D SER* 3.4 20.6 - - - -
390D LEU* 4.3 16.2 - - + -
392D ASP 3.5 19.1 - - - +
393D CYS* 3.7 23.3 - - - +
394D HIS 3.2 13.4 + - - +
395D ALA* 3.4 8.7 - - - +
397D ILE* 1.3 74.9 - - - +
399D SER* 1.3 55.5 + - - +
401D ARG* 3.1 12.8 + - - +
402D SER* 2.8 36.8 + - - +
599D SER* 3.8 13.5 - - - +
600D VAL 4.0 2.5 - - - +
601D ASN* 3.6 24.9 - - + -
627D LEU* 3.7 7.9 - - + -
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Residues in contact with SER 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ALA* 3.4 2.0 + - - -
354D GLY* 3.3 25.4 + - - -
355D VAL* 4.0 18.3 - - - +
370D SER* 3.3 13.8 + - - -
372D SER* 2.5 24.0 + - - -
395D ALA 2.9 8.3 + - - -
396D GLU* 3.6 11.7 - - - -
397D ILE 3.3 0.2 - - - -
398D ILE* 1.3 75.5 - - - +
400D ARG* 1.3 63.0 + - - +
402D SER* 3.3 4.7 + - - -
403D LEU* 3.0 20.3 + - - +
444D LEU* 4.6 4.5 - - - -
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Residues in contact with ARG 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D VAL* 4.8 2.2 - - - +
396D GLU 3.0 13.1 + - - +
397D ILE 3.6 6.4 + - - +
398D ILE 3.3 0.2 - - - -
399D SER* 1.3 77.4 - - - +
401D ARG* 1.3 69.2 + - - +
403D LEU* 3.0 13.3 + - + +
404D LEU* 2.9 48.2 + - + +
444D LEU* 5.8 0.4 - - - +
523D TRP* 3.4 51.4 - - + +
527D GLY 5.4 0.4 + - - -
528D ILE* 2.7 52.3 + - + +
530D GLY* 4.0 12.9 - - - +
542D PHE* 5.3 5.3 - - + -
801D IHP 3.3 44.0 + - - -
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Residues in contact with ARG 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D LEU* 3.6 18.6 - - - +
392D ASP 5.2 0.9 - - - -
397D ILE* 3.0 20.5 + - - +
398D ILE* 3.1 16.8 + - - +
400D ARG* 1.3 82.8 - - - +
402D SER* 1.3 59.8 + - - +
404D LEU* 3.1 30.1 - - - +
405D ARG* 3.1 6.8 + - - +
627D LEU* 2.7 49.5 + - + +
628D CYS* 3.9 0.8 - - - +
629D LYS* 3.8 16.0 - - - +
632D LEU* 3.6 21.7 - - + +
801D IHP 2.6 73.5 + - - +
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Residues in contact with SER 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D SER* 3.5 17.0 - - - -
371D VAL 5.0 1.3 + - - -
398D ILE* 2.8 15.7 + - - +
399D SER* 3.4 10.2 - - - -
401D ARG* 1.3 74.4 - - - +
403D LEU* 1.3 59.8 + - - +
405D ARG* 3.0 15.1 + - - +
406D PHE 3.1 9.5 + - - -
601D ASN* 4.1 10.6 - - - +
602D TRP 4.2 2.0 + - - -
603D THR* 3.2 33.2 + - - +
627D LEU* 3.6 20.4 - - - +
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Residues in contact with LEU 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D VAL* 4.2 21.3 - - + -
369D ILE* 3.7 25.1 - - + -
370D SER* 4.2 1.3 + - - +
399D SER 3.0 13.1 + - - +
400D ARG* 3.3 11.9 - - + +
402D SER* 1.3 72.9 - - - +
404D LEU* 1.3 60.6 + - + +
406D PHE* 3.1 19.8 + - + +
407D LEU* 3.0 34.8 + - + +
442D PHE* 3.9 23.1 - - + -
528D ILE* 3.6 36.1 - - + +
542D PHE* 4.4 9.2 - - + -
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Residues in contact with LEU 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D ARG* 2.9 44.4 + - - +
401D ARG* 3.1 14.3 + - - +
403D LEU* 1.3 73.9 - - + +
405D ARG* 1.3 65.0 + - - +
407D LEU* 3.0 12.8 + - + +
408D TYR* 3.0 32.9 + - + -
528D ILE 3.5 22.9 - - - +
529D GLN* 3.6 23.6 - - - +
530D GLY* 5.8 0.2 - - - -
533D LEU* 3.9 12.8 - - + -
632D LEU* 4.0 26.5 - - + -
801D IHP 5.3 3.4 - - - +
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Residues in contact with ARG 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D ARG 3.1 14.0 + - - +
402D SER 3.0 8.9 + - - +
404D LEU* 1.3 76.1 - - - +
406D PHE* 1.3 64.5 + - - +
408D TYR* 3.2 9.8 + - - +
409D THR* 3.0 25.0 + - - +
603D THR* 3.3 19.7 + - + +
606D ASP* 2.7 41.6 + - - -
626D ARG* 3.5 39.9 + - - +
627D LEU* 3.6 24.4 - - + +
632D LEU* 4.1 13.9 - - + +
635D ARG* 3.7 25.4 + - + +
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Residues in contact with PHE 406 (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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357D MET* 4.0 13.5 - - + -
367D LYS* 4.8 6.7 - - - -
369D ILE* 3.5 46.9 - - + -
402D SER 3.1 8.4 + - - +
403D LEU* 3.1 20.4 + - + +
405D ARG* 1.3 74.4 - - - +
407D LEU* 1.3 61.4 + - + +
409D THR* 3.0 14.7 + - + -
410D GLN* 2.9 58.5 + - + +
425D ILE* 3.9 20.6 - - + -
442D PHE* 3.9 10.8 - + - -
603D THR* 3.9 9.8 - - + +
604D VAL* 3.7 24.2 - - + -
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Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D LEU* 3.0 27.1 + - + +
404D LEU* 3.0 16.5 + - + +
406D PHE* 1.3 82.4 - - + +
408D TYR* 1.3 64.6 + - - +
410D GLN* 3.1 6.4 + - - +
411D LEU* 3.0 23.1 + - - +
425D ILE* 4.2 15.7 - - + -
426D PHE* 3.7 26.6 - - + -
442D PHE* 4.2 12.8 - - + -
528D ILE* 5.6 1.6 - - + -
529D GLN* 4.3 9.2 - - + -
533D LEU* 3.8 27.4 - - + -
537D VAL* 5.7 0.4 - - + -
540D ILE* 4.1 24.9 - - + -
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Residues in contact with TYR 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D LEU* 3.0 29.8 + - + -
405D ARG* 3.6 7.0 - - - +
407D LEU* 1.3 76.4 - - - +
409D THR* 1.3 62.9 + - - +
411D LEU* 3.3 6.8 + - + +
412D GLU* 3.0 26.0 + - - +
532D LEU* 3.9 11.1 - - - +
533D LEU* 3.7 36.1 + - + +
536D PHE* 4.6 2.5 - + - -
632D LEU* 4.0 28.3 + - + +
635D ARG* 3.4 32.1 - - + +
636D TRP* 3.1 55.5 - + + +
639D VAL* 4.0 19.6 - - + +
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Residues in contact with THR 409 (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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405D ARG 3.0 12.0 + - - -
406D PHE* 3.0 16.0 + - + +
408D TYR* 1.3 75.7 - - - +
410D GLN* 1.3 66.0 + - - +
412D GLU* 3.2 9.1 + - - +
413D LEU* 2.9 29.5 + - + +
635D ARG* 3.0 22.5 + - - +
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Residues in contact with GLN 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D LYS* 5.6 2.4 - - - +
406D PHE* 2.9 44.2 + - + +
407D LEU 3.1 7.4 + - - +
409D THR* 1.3 78.4 - - - +
411D LEU* 1.3 60.7 + - - +
413D LEU* 3.2 18.7 - - - +
414D TYR* 3.0 22.2 + - - +
423D ARG 4.2 1.6 + - - +
424D SER* 3.3 20.6 + - - -
425D ILE* 3.0 49.8 + - + +
426D PHE* 3.6 19.5 - - + -
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D LEU 3.0 14.8 + - - +
408D TYR* 3.7 7.2 - - - +
410D GLN* 1.3 75.0 - - - +
412D GLU* 1.3 66.6 + - - +
414D TYR* 3.1 5.0 + - + +
415D LEU* 2.9 33.7 + - + +
426D PHE* 3.4 29.6 - - + -
434D PHE* 4.0 29.6 - - + -
533D LEU* 4.0 17.9 - - + -
536D PHE* 3.7 37.5 - - + -
537D VAL* 4.0 7.0 - - + -
639D VAL* 4.3 18.6 - - + -
643D VAL* 6.2 0.4 - - + -
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Residues in contact with GLU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D TYR 3.0 10.6 + - - +
409D THR* 3.2 9.9 + - - +
411D LEU* 1.3 75.3 - - - +
413D LEU* 1.3 57.4 + - - +
415D LEU* 3.5 3.7 + - + +
416D ASN* 2.9 37.9 + - - +
635D ARG* 3.6 30.0 + - - +
638D ARG* 3.0 43.4 + - - +
639D VAL* 4.3 12.3 - - + +
642D LYS* 4.2 25.9 - - + +
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Residues in contact with LEU 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D THR* 2.9 16.0 + - + +
410D GLN* 3.2 37.0 - - - +
412D GLU* 1.3 74.4 - - - +
414D TYR* 1.3 66.2 + - - +
416D ASN* 3.3 11.8 + - + +
420D ASP* 3.2 50.3 - - + +
423D ARG* 4.0 23.8 - - + +
424D SER* 3.7 21.1 - - - +
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Residues in contact with TYR 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D GLN 3.0 8.8 + - - +
411D LEU* 3.1 9.4 + - + +
413D LEU* 1.3 75.7 - - - +
415D LEU* 1.3 64.0 + - + +
417D ASN 3.2 21.7 - - - +
421D GLN* 3.0 66.9 + - + +
424D SER* 3.7 15.9 - - - +
426D PHE* 3.6 30.1 - - + -
427D GLN* 4.1 8.9 - - + +
428D LYS* 3.4 37.1 + - + +
434D PHE* 3.7 29.6 - + + -
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D LEU* 2.9 30.1 + - + +
412D GLU* 3.7 5.4 - - - +
414D TYR* 1.3 82.3 - - + +
416D ASN* 1.3 65.1 + - - +
417D ASN* 3.5 1.9 - - - -
421D GLN* 5.5 1.3 - - - +
434D PHE* 4.4 20.2 - - + -
639D VAL* 4.4 9.0 - - + -
642D LYS* 3.7 43.3 + - + +
643D VAL* 3.5 32.8 - - + -
644D PRO* 4.5 8.1 - - + -
647D LEU* 5.1 3.4 - - + -
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Residues in contact with ASN 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D GLU* 2.9 23.0 + - - +
413D LEU* 3.5 11.9 - - + +
414D TYR 3.2 1.2 - - - -
415D LEU* 1.3 78.7 - - - +
417D ASN* 1.3 73.2 + - - +
420D ASP* 3.8 12.8 - - - +
642D LYS* 4.3 16.4 + - - +
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Residues in contact with ASN 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D LEU 4.2 0.2 + - - -
414D TYR 3.2 16.6 - - - +
415D LEU 4.3 2.2 - - - -
416D ASN* 1.3 88.1 + - - +
418D LYS* 1.3 70.6 + - + +
419D ASP* 2.9 33.3 + - - +
420D ASP* 3.2 37.3 + - - +
421D GLN* 3.3 6.9 + - - +
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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