Contacts of the helix formed by residues 473 - 495 (chain B) in PDB entry 3EE6
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 GLY 473 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 6.1 0.4 - - - -
360B ASP* 3.5 17.7 - - - -
407B ILE* 3.9 7.5 - - - +
456B SER* 2.7 23.5 + - - -
472B SER* 1.3 76.1 - - - +
474B THR* 1.3 58.8 + - - -
475B SER* 3.0 9.0 - - - -
476B ALA* 2.9 27.3 + - - +
477B SER 3.7 0.2 + - - -
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Residues in contact with THR 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ALA* 3.5 9.9 - - - +
358B SER* 3.7 12.8 - - - +
359B GLY* 3.1 32.5 + - - +
360B ASP* 2.7 22.9 + - - +
388B VAL 3.8 10.8 - - - -
389B GLY 3.7 2.9 - - - -
390B GLY* 3.7 28.9 - - - +
407B ILE* 4.6 1.5 - - + +
408B SER* 4.3 5.8 - - - -
456B SER* 4.5 1.1 - - - -
473B GLY* 1.3 68.5 - - - -
475B SER* 1.3 56.1 + - - +
476B ALA 3.0 5.2 - - - -
477B SER* 3.2 7.5 + - - -
478B THR* 2.8 34.1 + - - -
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Residues in contact with SER 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLU* 3.6 20.9 + - - -
275B LEU* 3.7 17.4 - - - +
276B ASP* 4.2 5.5 - - - +
324B SER* 2.7 29.4 + - - -
357B ALA* 4.0 4.8 - - - +
360B ASP* 4.7 7.0 + - - -
473B GLY* 3.0 3.3 - - - -
474B THR* 1.3 78.1 + - - +
476B ALA* 1.3 57.1 + - - +
478B THR* 4.6 1.6 - - - -
479B PRO* 2.9 24.0 - - - +
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 3.6 23.3 - - + +
279B TYR* 4.9 1.0 - - - +
455B LEU 4.1 1.6 - - - +
456B SER* 4.4 0.7 - - - -
459B TYR* 3.7 37.6 + - + -
471B VAL 5.1 1.3 - - - +
473B GLY 2.9 19.8 + - - +
475B SER* 1.3 80.3 - - - +
477B SER* 1.3 61.5 + - - +
478B THR 3.3 0.4 - - - -
479B PRO* 3.2 13.5 - - - +
480B VAL* 3.6 15.9 + - - +
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Residues in contact with SER 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B VAL* 3.8 3.4 - - - +
389B GLY 3.0 19.7 + - - -
454B ALA* 3.2 36.6 + - - +
455B LEU 3.3 9.9 - - - -
456B SER* 3.8 4.2 - - - -
459B TYR* 4.4 1.1 - - - -
474B THR* 3.2 22.5 + - - -
476B ALA* 1.3 78.5 - - - +
478B THR* 1.3 57.6 + - - +
480B VAL* 3.3 3.1 + - - +
481B PHE* 2.9 30.7 + - - +
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Residues in contact with THR 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B THR* 3.5 11.7 - - - +
323B VAL 4.1 6.1 - - - +
355B LEU* 3.7 41.9 - - + +
356B PHE* 3.9 7.4 - - - +
357B ALA* 3.2 20.5 - - - +
388B VAL* 3.6 15.4 - - + +
474B THR 2.8 20.6 + - - -
475B SER* 4.8 1.8 - - - -
477B SER* 1.3 78.6 - - - +
479B PRO* 1.3 64.0 - - - +
481B PHE* 3.9 1.6 - - - +
482B GLY* 2.9 22.3 + - - -
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Residues in contact with PRO 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU 4.7 4.0 - - - +
276B ASP* 3.6 33.2 - - + +
279B TYR* 4.5 2.7 - - + -
280B LEU* 3.6 24.6 - - + +
283B ALA* 4.3 0.2 - - - +
322B THR* 3.8 19.5 - - + +
475B SER 2.9 29.6 - - - +
476B ALA* 3.2 14.1 - - - +
478B THR* 1.3 90.0 - - + +
480B VAL* 1.3 63.0 + - - +
483B GLY* 3.0 20.3 + - - -
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 3.4 49.8 - - + -
209B TYR* 3.9 20.4 - - + -
279B TYR* 4.3 12.8 - - + +
283B ALA* 3.4 13.5 - - + +
454B ALA* 4.3 7.0 - - + -
459B TYR* 3.7 11.9 - - + +
476B ALA 3.7 13.2 - - - +
477B SER* 3.3 8.2 + - - +
478B THR 3.3 0.8 - - - -
479B PRO* 1.3 79.8 - - - +
481B PHE* 1.3 65.7 + - - +
483B GLY 3.3 0.2 + - - -
484B ILE* 3.3 23.1 + - + +
551B PRO* 5.2 0.2 - - + -
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Residues in contact with PHE 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 4.1 10.1 - - + -
386B THR* 5.5 0.4 - - + -
388B VAL* 4.3 8.1 - - + -
452B VAL* 3.5 45.3 - - + -
453B ALA 3.6 19.3 - - - -
454B ALA* 4.7 0.9 - - + -
477B SER 2.9 17.4 + - - +
478B THR 4.0 2.9 - - - +
480B VAL* 1.3 80.6 - - - +
482B GLY* 1.3 63.5 + - - +
484B ILE* 3.4 5.9 + - + +
485B LEU* 3.2 49.6 + - + +
503B LEU* 4.9 4.9 - - + -
507B LEU* 6.1 0.4 - - + -
515B LEU* 3.6 22.4 - - + -
549B GLY 4.1 0.7 - - - -
551B PRO* 3.8 31.0 - - + -
556B LEU* 4.5 4.0 - - + -
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Residues in contact with GLY 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 4.3 2.0 - - - -
320B VAL* 3.7 11.4 - - - +
322B THR* 3.6 18.2 - - - -
355B LEU* 4.1 11.2 - - - -
478B THR 2.9 18.2 + - - -
480B VAL 3.2 0.2 - - - -
481B PHE* 1.3 76.0 - - - +
483B GLY* 1.3 55.7 + - - +
485B LEU* 3.0 7.0 + - - +
486B SER* 2.9 26.7 + - - -
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Residues in contact with GLY 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLN* 3.9 7.4 - - - -
280B LEU* 3.7 14.4 - - - +
283B ALA 3.6 7.2 - - - -
284B GLY* 3.4 26.4 - - - -
479B PRO 3.0 15.6 + - - -
480B VAL 3.3 1.5 + - - -
482B GLY* 1.3 72.7 - - - +
484B ILE* 1.3 59.7 + - - +
486B SER* 3.2 1.4 + - - -
487B LEU* 3.0 23.4 + - - +
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Residues in contact with ILE 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ILE* 5.4 1.8 - - + -
209B TYR* 4.1 24.7 - - + -
211B LEU* 4.1 15.7 - - + -
283B ALA* 3.7 16.4 + - + +
480B VAL* 3.3 17.4 + - + +
481B PHE* 3.7 8.5 - - + +
482B GLY 3.2 0.6 - - - -
483B GLY* 1.3 76.8 - - - +
485B LEU* 1.3 61.7 + - + +
487B LEU* 3.5 6.5 + - - +
488B ILE* 3.3 21.8 + - + +
551B PRO* 3.6 32.8 - - + +
553B PHE* 3.9 20.6 - - + -
556B LEU* 4.2 23.8 - - + -
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B VAL* 4.6 8.5 - - + -
353B THR* 4.2 15.3 - - + +
355B LEU* 3.9 28.5 - - + -
386B THR* 5.9 0.2 - - - +
481B PHE* 3.2 26.7 + - + +
482B GLY 3.0 10.7 + - - +
484B ILE* 1.3 76.4 - - - +
486B SER* 1.3 58.6 + - - +
487B LEU 3.1 1.8 - - - -
488B ILE* 3.1 9.3 + - + +
489B ASN* 2.9 28.6 + - - +
500B LEU* 4.3 19.9 - - + +
503B LEU* 3.8 30.7 - - + -
556B LEU* 4.6 9.9 - - + -
560B LEU* 4.4 10.5 - - + -
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Residues in contact with SER 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ASN* 2.9 35.7 + - - -
224B SER 4.4 3.6 + - - -
225B GLN* 3.0 39.5 + - - +
287B ILE* 3.7 6.6 - - - +
320B VAL* 4.0 21.5 - - - +
482B GLY 2.9 11.5 + - - -
483B GLY 3.2 3.8 + - - -
485B LEU* 1.3 77.7 - - - +
487B LEU* 1.3 61.4 + - - +
489B ASN* 3.3 10.6 + - - +
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Residues in contact with LEU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 5.4 0.2 - - - +
211B LEU* 3.6 21.1 - - + -
215B ASP 3.4 24.5 - - - +
216B VAL* 3.8 29.8 - - - +
217B GLY* 4.2 4.5 - - - +
283B ALA 4.3 9.9 - - - +
284B GLY* 5.2 2.0 - - - -
287B ILE* 3.9 14.3 - - + +
483B GLY 3.0 14.8 + - - +
484B ILE* 3.6 7.4 - - - +
486B SER* 1.3 77.9 - - - +
488B ILE* 1.3 61.4 + - - +
490B GLU* 3.2 17.3 + - + +
491B HIS* 3.2 30.1 + - + -
553B PHE* 3.8 19.5 - - + -
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Residues in contact with ILE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ILE 3.3 13.9 + - - +
485B LEU* 3.1 11.8 + - + +
487B LEU* 1.3 75.3 - - - +
489B ASN* 1.3 64.6 + - - +
490B GLU 3.1 0.4 - - - -
491B HIS* 3.2 17.7 + - - +
492B ARG* 3.3 20.9 + - + +
500B LEU* 4.0 19.3 - - + -
553B PHE* 4.0 17.9 - - + -
556B LEU* 4.0 25.4 - - + -
557B LEU* 4.0 38.1 - - + +
560B LEU* 4.3 21.5 - - + +
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Residues in contact with ASN 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ASN* 4.0 11.2 - - - +
319B HIS* 3.6 26.8 - - + +
320B VAL* 3.7 19.8 - - - +
353B THR* 4.1 7.7 - - - +
485B LEU 2.9 11.3 + - - +
486B SER* 3.4 12.1 - - - +
487B LEU 3.2 0.2 - - - -
488B ILE* 1.3 77.4 - - - +
490B GLU* 1.3 56.2 + - - +
492B ARG* 3.2 5.6 + - - +
493B ILE* 3.0 38.0 + - + +
499B PRO* 3.6 13.7 - - - +
500B LEU* 3.0 35.2 + - - +
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Residues in contact with GLU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL 5.2 0.2 - - - +
217B GLY* 3.8 18.5 - - - -
218B SER* 3.4 34.0 + - - +
219B GLY* 4.4 9.4 + - - -
221B SER* 5.2 7.5 + - - -
223B ASN* 3.0 36.0 + - + +
287B ILE* 4.1 13.9 - - + +
486B SER 3.4 2.3 + - - +
487B LEU* 3.2 15.5 + - + +
488B ILE 3.1 0.6 - - - -
489B ASN* 1.3 80.1 - - - +
491B HIS* 1.3 60.1 + - + +
493B ILE* 4.4 5.8 - - + -
494B LEU* 3.0 46.6 + - + +
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Residues in contact with HIS 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B ASP* 5.6 5.9 + - - -
216B VAL 5.7 2.2 - - - -
487B LEU* 3.2 40.9 + - + -
488B ILE* 3.2 10.5 + - - +
490B GLU* 1.3 81.0 - - + +
492B ARG* 1.3 60.9 + - - +
494B LEU* 4.6 4.2 - - + +
495B SER* 3.3 21.6 + - - -
553B PHE* 4.7 11.0 - + - -
557B LEU* 4.3 22.7 - - + +
561B LEU* 3.8 25.3 - - + +
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Residues in contact with ARG 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 4.1 10.5 + - - -
488B ILE* 3.3 16.8 + - + +
489B ASN* 3.2 11.8 + - - +
490B GLU 3.1 0.4 - - - -
491B HIS* 1.3 79.8 - - - +
493B ILE* 1.3 58.1 - - + +
495B SER* 3.0 14.5 + - - +
497B ARG* 2.9 43.9 + - + +
498B PRO* 2.8 48.2 + - - +
499B PRO 4.2 1.6 + - - -
500B LEU* 4.0 28.6 - - - +
506B ARG* 3.7 17.5 - - - +
560B LEU 3.1 26.2 + - - +
561B LEU* 4.0 16.6 - - + -
580B CL 3.9 21.6 - - - +
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Residues in contact with ILE 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B SER* 3.2 28.3 - - - +
222B ASN* 4.9 1.1 - - + +
223B ASN* 3.7 31.2 - - + +
319B HIS* 4.5 9.9 - - + +
489B ASN* 3.0 19.3 + - + +
490B GLU* 3.9 6.1 - - - +
492B ARG* 1.3 72.6 - - + +
494B LEU* 1.3 61.2 + - + +
495B SER 2.6 18.6 - - - +
497B ARG 3.4 14.8 - - - +
499B PRO* 4.4 25.8 - - + -
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B SER* 3.7 23.8 - - - +
220B THR 6.1 0.9 - - - -
221B SER* 4.4 20.0 - - - +
490B GLU* 3.0 37.7 + - + +
491B HIS* 4.6 4.3 - - + +
493B ILE* 1.3 76.6 - - + +
495B SER* 1.3 65.8 + - - +
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Residues in contact with SER 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B HIS 3.3 16.9 + - - -
492B ARG* 3.0 16.1 + - - +
493B ILE 2.6 22.9 - - - +
494B LEU* 1.3 81.0 - - - +
496B GLY* 1.3 62.7 + - - +
497B ARG* 3.3 19.9 + - - -
561B LEU* 5.4 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