Contacts of the helix formed by residues 397 - 419 (chain R) in PDB entry 1HI0
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 397 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135R PHE* 6.4 1.1 - - + -
283R ILE* 4.4 2.5 - - + -
287R ALA* 4.1 15.5 - - + -
291R ARG* 4.3 0.7 - - - +
357R PHE* 4.4 20.0 - - + -
395R GLN* 2.9 16.6 + - - +
396R GLY* 1.3 74.6 - - - +
398R THR* 1.3 67.8 + - - +
399R ASP* 2.9 11.7 + - - -
400R LEU* 2.9 23.9 + - + -
401R MET* 3.0 14.7 + - + +
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Residues in contact with THR 398 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F C 5.3 1.7 + - - -
329R ASP* 6.1 0.2 - - - -
391R LEU* 3.1 45.4 - - + +
392R SER 2.9 35.2 - - - +
393R SER* 3.1 21.2 + - - +
395R GLN* 3.3 18.8 + - + +
397R ALA* 1.3 75.4 - - - +
399R ASP* 1.3 59.1 + - - +
401R MET 4.0 0.7 - - - -
402R GLY* 3.1 9.2 + - - -
667R GTP 3.8 23.9 + - - -
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Residues in contact with ASP 399 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291R ARG* 2.7 48.2 + - - +
295R TYR* 4.1 9.7 + - - -
397R ALA 3.5 5.5 - - - +
398R THR* 1.3 75.0 + - - +
400R LEU* 1.3 70.8 + - - +
402R GLY 3.4 0.3 + - - -
403R THR* 2.9 34.9 + - - +
451R LYS* 5.1 14.1 + - - -
452R SER* 3.6 11.6 + - - +
629R GLN 6.1 1.6 - - - +
667R GTP 4.2 8.1 - - - +
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Residues in contact with LEU 400 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R MET* 4.8 8.6 - - + +
135R PHE* 5.3 5.4 - - + -
287R ALA* 3.6 39.7 - - + +
290R VAL* 3.7 30.7 - - + -
291R ARG* 4.2 14.4 - - + -
294R ILE* 4.0 23.6 - - + -
295R TYR* 5.7 1.1 - - - +
397R ALA* 2.9 11.6 + - + +
399R ASP* 1.3 92.3 + - - +
401R MET* 1.3 69.6 + - + +
403R THR* 3.1 4.1 + - - +
404R LEU* 2.7 37.2 + - - +
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Residues in contact with MET 401 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R MET* 6.4 0.2 - - - -
135R PHE* 4.6 15.7 - - + -
332R TRP* 3.0 44.2 + - + -
337R ARG* 5.9 0.2 - - - -
340R ILE* 3.9 23.1 - - + -
357R PHE* 3.6 33.2 - - + -
361R LEU* 4.3 4.5 - - + -
391R LEU* 3.7 21.1 - - + -
395R GLN* 4.4 6.7 - - - +
397R ALA* 3.0 18.7 + - + +
398R THR 4.1 0.4 - - - +
400R LEU* 1.3 89.0 - - + +
402R GLY* 1.3 63.0 + - - +
404R LEU* 3.8 6.9 - - + +
405R LEU 3.0 15.6 + - - -
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Residues in contact with GLY 402 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328R HIS* 3.4 27.4 - - - -
332R TRP* 4.0 2.0 - - - -
391R LEU* 3.8 1.5 - - - +
398R THR 3.1 13.0 + - - -
399R ASP 3.8 2.5 - - - -
400R LEU 3.2 0.2 - - - -
401R MET* 1.3 79.7 - - - +
403R THR* 1.3 56.8 + - - +
405R LEU* 3.6 0.9 - - - +
406R MET* 2.9 35.0 + - - +
452R SER* 3.9 11.2 - - - -
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Residues in contact with THR 403 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134R MET* 4.2 9.6 - - + -
294R ILE* 5.0 3.9 - - + +
302R PHE* 3.4 41.1 - - + -
399R ASP* 2.9 25.1 + - - +
400R LEU* 3.6 7.4 - - - +
402R GLY* 1.3 72.4 - - - +
404R LEU* 1.3 62.2 + - - +
406R MET 3.3 0.4 + - - +
407R SER* 2.7 37.4 + - - +
450R SER* 4.9 2.7 - - - +
451R LYS* 4.2 6.8 - - - +
452R SER* 3.2 24.4 + - - +
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Residues in contact with LEU 404 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R PHE* 4.4 11.7 - - + +
130R ALA* 3.5 35.0 - - + -
131R VAL* 3.9 8.3 - - + +
134R MET* 3.2 35.6 - - - +
135R PHE* 5.1 4.3 - - + -
336R LEU* 4.2 14.1 - - + -
340R ILE* 3.9 28.0 - - + -
400R LEU 2.7 21.6 + - - +
401R MET* 3.8 8.5 - - + +
403R THR* 1.3 72.7 - - - +
405R LEU* 1.3 65.5 + - - +
407R SER* 4.5 2.2 - - - -
408R ILE* 3.6 18.0 + - - +
440R TRP* 5.9 1.1 - - - -
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Residues in contact with LEU 405 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R PHE* 4.0 11.9 - - + -
328R HIS* 3.8 7.4 - - + -
332R TRP* 3.5 31.9 - - + +
333R PRO* 4.0 16.8 - - + -
335R TRP* 5.2 1.3 - - + -
336R LEU* 3.4 28.5 - - + +
401R MET 3.0 7.9 + - - +
402R GLY 3.6 1.3 - - - +
404R LEU* 1.3 80.9 - - - +
406R MET* 1.3 82.9 + - - +
408R ILE* 3.9 1.7 - - - +
409R THR* 3.0 38.7 + - - +
485R TYR* 5.1 4.7 - - + -
486R MET* 3.8 22.2 - - + -
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Residues in contact with MET 406 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325R VAL* 3.2 31.6 - - + -
328R HIS* 3.7 19.5 - - + +
402R GLY 2.9 16.3 + - - +
403R THR 4.3 0.2 - - - +
405R LEU* 1.3 98.0 - - - +
407R SER* 1.3 59.8 + - - +
409R THR* 3.5 6.9 - - + -
410R TYR* 2.8 55.7 + - + +
452R SER 3.1 29.8 - - - +
453R ASP* 4.1 1.6 - - - -
486R MET* 3.6 13.2 - - + -
488R ILE* 3.9 15.5 - - + -
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Residues in contact with SER 407 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302R PHE* 3.7 13.9 - - - -
403R THR* 2.7 22.7 + - - +
404R LEU 4.5 0.9 - - - -
406R MET* 1.3 72.6 - - - +
408R ILE* 1.3 63.2 + - - +
410R TYR* 4.3 1.3 - - - -
411R LEU* 3.0 21.3 + - - +
439R TYR* 4.9 0.2 - - - -
440R TRP* 2.9 31.5 + - - -
448R GLN* 2.6 41.5 + - - +
450R SER* 4.4 3.7 + - - -
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Residues in contact with ILE 408 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123R ASP 4.9 0.2 - - - +
126R LEU* 3.8 35.7 - - + +
127R PHE* 3.5 41.3 - - + -
130R ALA* 3.7 24.5 - - + -
404R LEU 3.6 13.6 + - - +
405R LEU 3.5 1.2 + - - -
407R SER* 1.3 75.2 - - - +
409R THR* 1.3 66.5 + - - +
411R LEU* 3.1 6.9 + - + +
412R VAL* 2.8 31.4 + - + +
436R LEU* 3.9 25.8 - - + -
440R TRP* 4.4 4.9 - - + -
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Residues in contact with THR 409 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R PHE* 4.5 2.1 - - - -
405R LEU* 3.0 39.1 + - - +
406R MET* 3.5 25.3 - - + -
408R ILE* 1.3 78.2 - - - +
410R TYR* 1.3 59.5 + - + +
412R VAL* 3.3 7.7 + - - +
413R MET* 2.8 26.4 + - + +
483R SER* 3.5 27.9 + - - +
485R TYR* 3.8 20.2 - - + +
486R MET* 4.7 2.0 - - - +
488R ILE* 4.6 8.5 - - + -
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Residues in contact with TYR 410 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323R THR* 3.4 24.7 + - - -
325R VAL* 3.2 14.9 - - - +
406R MET* 2.8 56.0 + - + +
407R SER* 4.3 1.6 - - - -
409R THR* 1.3 70.0 - - + +
411R LEU* 1.3 67.6 + - - +
413R MET* 3.1 29.4 + - + +
414R GLN* 2.9 27.6 + - - +
448R GLN* 3.6 13.2 - - - +
450R SER* 4.8 2.2 - - - -
452R SER 4.1 3.8 - - - -
453R ASP 2.8 24.6 + - - -
455R ALA* 3.5 24.9 - - + -
457R LEU* 3.5 24.6 - - + +
488R ILE* 4.3 7.4 - - + -
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Residues in contact with LEU 411 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R LEU* 3.9 31.6 - - + -
407R SER 3.0 15.1 + - - +
408R ILE* 3.5 12.1 - - + +
410R TYR* 1.3 74.7 - - - +
412R VAL* 1.3 60.1 + - - +
414R GLN* 2.9 7.4 + - - +
415R LEU* 2.8 35.1 + - + +
435R PHE* 4.0 20.9 - - + -
436R LEU* 4.0 21.1 - - + -
439R TYR* 3.7 39.9 - - + -
446R ILE* 3.9 14.6 - - + -
448R GLN* 4.1 0.6 + - - -
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Residues in contact with VAL 412 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ARG* 3.7 14.1 - - - +
123R ASP* 3.5 37.7 - - + +
126R LEU* 4.1 18.8 - - + -
408R ILE* 2.8 25.8 + - + +
409R THR* 3.5 9.9 - - - +
411R LEU* 1.3 74.9 - - - +
413R MET* 1.3 67.3 + - - +
415R LEU* 3.1 7.4 + - - +
416R ASP* 2.8 34.9 + - - +
483R SER* 5.7 0.4 - - - +
484R PRO* 5.3 4.0 - - + -
485R TYR* 4.3 12.6 - - + -
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Residues in contact with MET 413 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323R THR* 5.2 1.1 - - - -
409R THR* 2.8 14.3 + - + +
410R TYR* 3.3 41.1 - - + +
412R VAL* 1.3 76.5 - - - +
414R GLN* 1.3 61.3 + - + +
416R ASP* 4.6 1.6 - - - -
417R HIS* 3.2 32.9 + - + +
457R LEU* 4.0 11.4 - - + -
471R LEU* 4.1 18.9 - - + +
475R LEU* 5.1 4.3 - - - -
482R PRO* 3.5 52.9 - - + +
483R SER* 4.6 4.7 + - - -
488R ILE* 3.8 24.0 - - + -
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Residues in contact with GLN 414 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410R TYR 2.9 13.4 + - - +
411R LEU* 3.2 8.0 - - - +
413R MET* 1.3 76.1 - - - +
415R LEU* 1.3 68.9 + - - +
418R THR* 2.8 38.6 + - - +
419R ALA* 3.2 2.0 + - - -
439R TYR* 2.7 36.6 + - - -
446R ILE* 3.8 17.5 - - + +
447R ARG 3.4 10.8 + - - -
457R LEU* 3.9 15.1 - - + +
458R GLY 3.3 24.7 + - - -
459R TRP* 3.5 31.0 - - + -
471R LEU* 4.9 1.8 - - + -
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Residues in contact with LEU 415 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ARG* 3.5 43.3 - - - +
126R LEU* 3.9 19.3 - - + -
411R LEU* 2.8 37.3 + - + +
412R VAL* 3.6 6.5 - - - +
414R GLN* 1.3 76.2 - - - +
416R ASP* 1.3 63.5 + - - +
418R THR 3.5 0.2 + - - -
419R ALA* 3.2 21.9 + - + +
420R PRO* 3.6 12.5 - - - +
422R LEU* 4.0 28.0 - - + -
423R ASN* 4.1 5.2 + - - +
426R ILE* 3.9 10.3 - - + -
435R PHE* 4.5 5.8 - - + -
446R ILE* 4.3 10.1 - - + -
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Residues in contact with ASP 416 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ARG* 2.6 34.2 + - - +
123R ASP* 5.2 0.5 - - - +
412R VAL* 2.8 32.2 + - - +
413R MET* 4.0 1.3 - - - +
415R LEU* 1.3 75.4 - - - +
417R HIS* 1.3 78.4 + - + +
420R PRO* 5.2 3.1 - - - +
482R PRO 5.2 2.1 - - - +
484R PRO* 4.8 12.0 - - - +
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Residues in contact with HIS 417 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413R MET* 3.2 27.3 + - + +
416R ASP* 1.3 89.5 + - + +
418R THR* 1.3 70.7 + - + +
420R PRO* 5.2 1.6 - - - -
467R GLY* 3.7 12.3 - - - +
470R ARG* 4.2 12.3 + - + +
471R LEU* 4.0 21.5 - - + +
474R MET* 3.1 37.1 - - + +
480R VAL* 5.8 0.9 - - + -
482R PRO* 3.0 30.4 + - + +
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Residues in contact with THR 418 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414R GLN 2.8 25.5 + - - +
415R LEU 3.5 0.8 + - - -
416R ASP 3.7 0.2 - - - -
417R HIS* 1.3 87.9 - - + +
419R ALA* 1.3 60.8 + - - +
420R PRO* 3.5 8.2 - - - +
421R HIS* 4.0 2.1 - - - -
446R ILE* 4.0 1.7 - - - +
459R TRP* 3.1 25.8 + - + +
463R ARG 4.6 0.9 - - - +
464R ALA* 3.1 37.6 - - - +
467R GLY* 3.2 9.8 - - - +
468R GLY* 3.2 27.1 - - - +
470R ARG* 5.6 0.9 - - - +
471R LEU* 4.3 5.2 - - + -
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Residues in contact with ALA 419 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414R GLN 3.2 3.8 + - - +
415R LEU* 3.2 18.8 + - + +
418R THR* 1.3 87.9 + - - +
420R PRO* 1.3 53.6 - - - +
421R HIS* 3.0 17.5 - - + -
422R LEU* 2.7 56.5 + - + +
423R ASN 3.9 1.2 + - - -
446R ILE* 4.6 5.4 - - + -
464R ALA* 4.0 6.5 - - + -
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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