Contacts of the helix formed by residues 431 - 454 (chain A) in PDB entry 5DO7
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 PRO 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A VAL 3.2 25.1 - - - +
428A GLY 4.5 1.8 - - - -
429A ALA 3.4 3.8 - - - +
430A THR* 1.4 94.4 - - - +
432A TYR* 1.3 59.5 + - - +
433A THR 3.3 0.2 - - - -
434A GLY* 2.8 21.8 + - - -
435A MET* 3.2 9.5 + - - +
509A PRO* 3.6 21.1 - - + +
512A ILE* 5.5 0.2 - - + -
513A GLY* 3.5 14.4 - - - +
538A SER* 3.9 28.0 - - - +
567A PHE* 4.1 21.3 - - + -
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Residues in contact with TYR 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLY 4.6 5.8 - - - +
429A ALA* 2.8 25.1 + - + +
431A PRO* 1.3 74.6 - - - +
433A THR* 1.3 65.7 + - + +
434A GLY 3.0 0.3 + - - -
435A MET* 3.0 29.2 + - + +
436A LEU* 2.8 50.1 + - + +
531A ASN* 4.1 18.1 + - - -
535A ALA* 4.1 22.8 - - + +
538A SER* 4.5 5.4 + - - +
539A ILE* 5.5 6.1 - - + -
461B PHE* 5.4 5.5 - + - -
564B ASN* 5.2 10.3 + - - +
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Residues in contact with THR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLN* 3.8 24.1 + - + -
393A ASN* 4.1 18.6 - - - +
396A MET* 5.1 15.0 - - + -
429A ALA 2.8 18.6 + - - +
430A THR* 3.0 16.6 + - - -
432A TYR* 1.3 74.6 - - + +
434A GLY* 1.3 55.5 + - - +
436A LEU* 3.5 9.2 - - + +
437A ASN* 2.8 34.1 + - - +
510A HIS* 2.6 35.2 + - - -
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Residues in contact with GLY 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A THR 3.9 0.4 + - - -
431A PRO 2.8 13.5 + - - -
433A THR* 1.3 81.1 + - - +
435A MET* 1.3 55.9 + - - -
437A ASN* 2.9 9.2 - - - +
438A ALA* 2.8 21.5 + - - +
510A HIS* 3.6 23.6 - - - -
514A GLU* 3.1 24.2 - - - +
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Residues in contact with MET 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A PRO 3.2 5.0 + - - +
432A TYR* 3.0 38.5 + - + +
434A GLY* 1.3 71.6 - - - +
436A LEU* 1.3 73.4 + - - +
438A ALA 2.8 0.6 + - - +
439A VAL* 2.8 29.3 + - + +
513A GLY 3.9 0.8 - - - -
517A THR* 3.0 36.5 + - + +
531A ASN* 2.8 42.6 - - - +
534A VAL* 3.4 33.4 - - + +
535A ALA* 3.7 18.6 - - - +
538A SER* 4.2 2.7 - - - +
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Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A THR* 5.7 5.2 - - + -
392A GLN* 3.2 26.2 - - + +
432A TYR* 2.8 37.2 + - + +
433A THR* 3.5 10.8 - - + +
435A MET* 1.3 84.0 - - - +
437A ASN* 1.3 66.5 + - - +
439A VAL* 4.2 2.7 - - - -
440A ASN* 2.6 43.7 + - - +
531A ASN* 4.7 1.1 - - - +
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Residues in contact with ASN 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A THR* 5.4 0.5 - - - -
389A ARG* 3.2 43.8 + - - +
392A GLN* 2.7 28.0 + - - +
433A THR 2.8 12.8 + - - +
434A GLY 2.9 14.8 - - - +
436A LEU* 1.3 80.6 - - - +
438A ALA* 1.3 61.3 + - - +
441A LEU* 3.2 26.7 + - - +
467A TYR* 3.9 0.9 - - - -
475A SER* 3.7 3.8 + - - -
510A HIS* 3.5 16.8 + - - -
514A GLU* 3.0 23.5 + - - +
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Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLY 2.8 14.7 + - - +
435A MET 2.8 3.2 + - - -
437A ASN* 1.3 66.0 - - - +
439A VAL* 1.3 58.3 + - - +
440A ASN 2.7 14.2 + - - -
441A LEU 2.8 13.2 + - - -
442A PHE* 2.8 17.4 + - + +
467A TYR* 3.2 20.0 - - + +
514A GLU* 3.7 18.8 - - - +
517A THR* 3.6 25.6 - - + -
518A LEU* 4.6 2.5 - - + +
521A LEU* 4.4 3.8 - - + -
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A MET 2.8 27.2 + - - +
436A LEU* 3.8 5.8 - - - +
438A ALA* 1.3 73.6 - - - +
440A ASN* 1.3 69.7 + - - +
443A PRO* 3.2 23.3 - - - +
517A THR* 3.9 10.8 - - + +
521A LEU* 3.8 13.2 - - + -
527A PRO* 3.6 39.6 - - + +
528A ASN* 5.1 1.1 - - - -
530A VAL* 4.7 2.9 - - + -
531A ASN* 3.6 32.1 - - + +
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Residues in contact with ASN 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A LEU* 2.6 47.6 + - - +
437A ASN 3.5 2.4 + - - +
438A ALA 2.7 5.5 + - - -
439A VAL* 1.3 85.1 - - - +
441A LEU* 1.3 70.9 + - + +
443A PRO* 3.9 4.3 - - - +
444A VAL* 5.3 1.4 - - - +
557B HIS* 5.2 10.2 - - - -
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 3.3 33.7 - - + -
382A ASN* 5.9 0.9 - - - +
385A ALA* 4.4 22.9 - - + +
388A THR* 5.7 2.2 - - - +
389A ARG* 3.3 29.8 - - + +
437A ASN* 3.5 17.5 - - - +
438A ALA 2.8 8.6 + - - +
440A ASN* 1.3 83.7 - - + +
442A PHE* 1.3 58.8 + - - +
443A PRO* 3.3 0.4 - - - +
444A VAL* 2.9 31.4 - - - +
445A LEU* 3.9 8.1 - - + +
467A TYR* 4.3 10.8 - - + +
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA 2.8 23.6 + - - +
441A LEU* 1.3 74.5 - - - +
443A PRO* 1.3 68.8 - - + +
445A LEU* 2.8 30.2 + - + +
446A ARG* 2.8 42.7 + - + -
463A MET* 4.5 6.5 - - + -
464A MET* 4.1 19.7 - - + -
467A TYR* 3.4 50.5 - + + -
518A LEU* 3.6 21.5 - - + -
521A LEU* 4.4 18.2 - - + -
642A PHE* 4.0 19.3 - + - -
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Residues in contact with PRO 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A VAL* 3.2 28.0 - - - +
440A ASN 3.9 5.2 - - - +
441A LEU 3.3 4.7 - - - +
442A PHE* 1.3 93.2 - - + +
444A VAL* 1.3 63.7 + - - +
446A ARG* 3.1 18.3 + - + +
447A ALA* 2.8 28.6 + - - +
521A LEU* 5.0 4.3 - - + -
527A PRO* 4.0 25.4 - - + -
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Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU 5.4 2.7 - - - +
139A LEU* 3.9 27.8 - - + -
140A SER* 5.3 8.3 - - - +
378A ASN* 5.3 4.5 - - - +
440A ASN 5.3 2.0 - - - +
441A LEU* 2.9 23.8 - - - +
443A PRO* 1.3 75.5 - - + +
445A LEU* 1.3 67.0 + - + +
447A ALA* 3.3 3.9 + - - +
448A VAL* 2.8 33.2 + - + +
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Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 4.7 10.1 - - + -
375A VAL* 3.4 35.7 - - + -
378A ASN* 4.9 15.0 - - - +
379A LEU* 6.5 1.1 - - + -
441A LEU* 3.9 21.1 - - + +
442A PHE* 2.8 22.2 + - + +
444A VAL* 1.3 82.1 - - + +
446A ARG* 1.3 58.0 + - - +
448A VAL* 3.3 8.9 - - - +
449A SER* 2.8 35.4 + - - -
463A MET* 3.3 31.4 - - + +
467A TYR* 4.8 13.0 - - + -
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A PHE* 2.8 37.0 + - + +
443A PRO* 3.3 16.6 + - - +
445A LEU* 1.3 75.7 - - - +
447A ALA* 1.3 56.7 + - - +
449A SER* 3.1 9.8 + - - -
450A ASP* 2.8 35.9 + - - +
521A LEU* 3.3 50.5 + - - +
525A GLN* 2.7 53.1 + - - +
527A PRO* 4.1 10.7 - - - +
642A PHE* 4.9 3.1 - - + -
645A ARG* 3.4 29.2 + - - +
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR* 4.9 6.2 + - + +
443A PRO 2.8 18.3 + - - +
444A VAL* 4.0 3.4 - - - +
446A ARG* 1.3 74.8 - - + +
448A VAL* 1.3 61.1 + - - +
450A ASP* 3.1 15.6 - - + +
451A GLN* 2.8 29.5 + - - +
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR* 3.8 37.4 + - - +
138A LEU* 4.6 5.6 - - + -
139A LEU* 4.1 22.7 - - + -
374A ARG* 4.7 0.9 - - - +
444A VAL* 2.8 17.2 + - + +
445A LEU* 3.3 13.0 - - - +
447A ALA* 1.3 74.9 - - - +
449A SER* 1.3 62.5 + - - +
451A GLN* 4.0 2.4 - - - +
452A GLU* 2.8 53.1 + - + +
458A TYR* 3.7 5.6 - - - +
463A MET* 3.7 17.9 - - + -
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Residues in contact with SER 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A LEU 2.8 12.0 + - - -
446A ARG* 3.1 12.3 - - - -
448A VAL* 1.3 71.2 - - - +
450A ASP* 1.3 70.3 + - - +
453A SER* 2.8 26.3 + - - -
458A TYR* 3.6 15.6 - - - -
460A LYS* 4.3 16.4 - - - -
463A MET* 2.8 46.0 - - - +
642A PHE* 6.4 1.8 - - - -
645A ARG* 5.7 0.7 - - - -
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Residues in contact with ASP 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ARG 2.8 14.0 + - - +
447A ALA* 3.1 17.2 + - - +
449A SER* 1.3 80.4 - - - +
451A GLN* 1.3 63.9 + - - +
452A GLU 3.0 0.2 + - - -
453A SER* 3.4 6.4 + - - -
454A GLN* 3.4 17.9 + - - +
460A LYS* 3.5 23.9 + - - +
525A GLN* 5.0 0.2 + - - -
645A ARG* 2.5 50.1 + - - -
649A ILE* 4.6 9.3 - - + +
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Residues in contact with GLN 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.6 31.2 - - + +
135A SER* 3.3 29.5 + - - -
136A ASP* 3.6 2.6 - - - +
137A THR* 2.6 49.5 + - - +
138A LEU* 5.2 0.3 - - - +
202A SER* 5.5 2.1 + - - -
447A ALA 2.8 17.6 + - - +
448A VAL* 4.6 2.5 - - - +
450A ASP* 1.3 73.1 - - - +
452A GLU* 1.3 68.5 + - + +
454A GLN* 3.9 16.7 - - - +
455A ASP* 3.9 11.0 - - - +
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Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR 5.9 0.4 - - - +
138A LEU* 5.9 4.5 - - + +
151A THR* 4.5 11.9 + - - +
154A LEU* 5.9 0.2 - - - +
374A ARG* 2.8 37.9 + - - -
448A VAL* 2.8 40.8 + - + +
449A SER 3.9 0.4 - - - +
451A GLN* 1.3 74.3 - - + +
453A SER* 1.3 68.6 + - - +
454A GLN 3.1 1.6 - - - -
455A ASP* 2.8 22.7 + - - +
456A GLY 3.4 5.0 + - - -
457A LEU* 3.8 24.2 - - + +
458A TYR* 3.4 29.0 + - + +
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Residues in contact with SER 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLN* 5.4 0.2 - - - +
449A SER 2.8 23.0 + - - -
452A GLU* 1.3 73.0 - - - +
454A GLN* 1.3 54.2 + - - +
456A GLY* 2.8 27.2 + - - -
457A LEU 4.3 5.8 - - - +
458A TYR* 2.6 34.6 + - - +
459A GLN* 3.6 9.2 - - - +
460A LYS* 3.8 23.4 + - - +
646A ASP* 5.3 1.2 + - - +
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Residues in contact with GLN 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 3.4 35.0 + - + +
103A LEU* 4.9 2.6 - - - +
126A GLN* 3.7 22.1 + - - +
131A TYR* 5.1 3.5 - - + -
133A LEU* 4.1 18.1 - - + +
450A ASP 3.4 12.6 + - - +
451A GLN* 3.9 13.6 - - - +
452A GLU 3.1 0.2 - - - -
453A SER* 1.3 78.3 - - - +
455A ASP* 1.3 63.0 + - - +
460A LYS* 5.2 6.2 - - - +
649A ILE 4.7 4.0 + - - -
650A SER* 3.1 30.5 + - - +
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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