Contacts of the strand formed by residues 400 - 422 (chain A) in PDB entry 1PO3
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 SER 400 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A MET* 3.3 3.3 - - - -
397A ILE* 2.3 71.8 + - - +
398A GLY 2.8 6.4 + - - +
399A PRO* 1.3 83.0 - - - +
401A ALA* 1.3 59.8 + - - +
402A HIS* 3.2 13.7 + - - -
455A ILE* 4.1 6.7 - - - -
456A ASP 3.1 12.1 - - - -
457A ILE* 4.4 8.1 - - - -
620B LYS 5.5 0.2 - - - -
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ILE* 5.6 3.4 - - + -
396A MET* 4.4 2.9 - - - +
399A PRO 4.4 0.2 + - - -
400A SER* 1.3 71.2 - - - +
402A HIS* 1.3 68.7 + - - +
454A LYS 3.4 1.1 - - - +
455A ILE* 3.2 2.6 - - - -
456A ASP* 2.7 58.3 + - + +
620B LYS* 3.6 37.2 - - + +
621B GLY* 5.5 0.4 - - - -
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Residues in contact with HIS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ILE* 3.3 7.2 - - - +
395A PHE* 3.0 63.6 + - + +
397A ILE* 3.7 29.3 - - + +
400A SER* 3.2 24.2 + - - -
401A ALA* 1.3 87.1 - - - +
403A GLU* 1.3 60.6 + - - +
404A VAL* 3.8 0.8 - - - +
453A ASP* 3.3 15.6 + - - +
454A LYS 3.3 3.1 - - - -
455A ILE* 3.2 33.0 - - + +
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Residues in contact with GLU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 5.7 1.0 - - - +
392A SER* 5.3 8.8 + - - -
393A GLN 3.4 7.0 - - - +
394A ILE* 3.3 38.8 - - + +
402A HIS* 1.3 74.2 - - - +
404A VAL* 1.3 66.5 + - - +
405A GLY* 3.5 2.4 + - - -
452A ASP* 3.9 1.9 - - - +
453A ASP* 3.4 2.4 - - - -
454A LYS* 2.8 69.8 + - + +
456A ASP* 5.8 0.6 + - - +
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TYR* 4.2 2.9 - - + +
392A SER* 3.5 4.9 - - - -
393A GLN* 3.0 36.0 + - + +
395A PHE* 3.6 30.1 - - + -
402A HIS* 3.8 0.6 - - - +
403A GLU* 1.3 73.3 - - - +
405A GLY* 1.3 63.5 + - - +
406A VAL* 4.8 4.3 - - + +
451A LEU* 4.2 20.9 - - + -
452A ASP 3.5 4.3 - - - +
453A ASP* 3.0 29.4 - - + +
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Residues in contact with GLY 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A TYR 4.0 4.3 - - - -
392A SER* 4.3 9.2 - - - -
403A GLU* 3.5 1.2 + - - -
404A VAL* 1.3 75.0 - - - +
406A VAL* 1.3 59.9 + - - -
450A TYR* 4.0 1.3 - - - +
451A LEU* 3.2 8.1 - - - +
452A ASP* 2.8 50.7 + - - +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ARG* 3.4 14.8 - - - +
391A TYR* 3.1 45.4 + - + +
392A SER* 5.4 0.3 + - - -
404A VAL* 4.1 4.2 - - + -
405A GLY* 1.3 75.2 - - - -
407A GLY* 1.3 62.4 + - - +
450A TYR* 3.6 10.2 - - - +
451A LEU* 3.8 21.8 - - + -
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Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A PRO 3.7 9.2 - - - -
390A ARG* 3.9 2.0 - - - -
406A VAL* 1.3 80.3 - - - +
408A TYR* 1.3 60.7 + - - +
449A TRP* 3.5 4.5 - - - +
450A TYR* 2.9 60.0 + - - +
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Residues in contact with TYR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ILE* 5.1 3.8 - - + -
388A GLU* 3.0 22.7 - - - +
389A PRO* 3.0 40.1 + - + +
407A GLY* 1.3 75.1 - - - +
409A ARG* 1.3 73.0 + - - +
410A TYR* 3.5 26.1 - - + +
447A HIS* 2.9 28.2 + - - -
448A ALA 2.8 31.0 - - - -
449A TRP* 3.6 45.0 - + + -
450A TYR* 3.8 3.5 - - - -
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Residues in contact with ARG 409 (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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163A LEU* 5.5 4.6 - - - +
166A GLY 5.4 3.0 + - - -
168A PRO* 4.2 20.8 - - - +
173A PRO* 5.3 4.9 - - - +
174A TYR* 3.9 23.6 + - - -
202A ARG 5.9 1.3 + - - -
204A GLY 3.3 24.7 + - - -
205A PRO* 4.4 2.2 - - - +
359A PHE* 4.8 8.7 - - + -
386A GLY* 5.7 0.2 - - - -
387A ILE 3.9 4.3 - - - -
388A GLU* 3.0 43.7 + - + +
408A TYR* 1.3 84.2 - - - +
410A TYR* 1.3 66.4 + - - +
411A LEU* 3.9 30.5 - - - +
446A ALA 3.3 4.3 - - - +
447A HIS* 3.9 0.9 - - - -
448A ALA* 3.1 32.3 + - + +
450A TYR* 4.3 9.0 - - + -
467A ARG* 4.2 9.9 - - - +
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Residues in contact with TYR 410 (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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385A ARG* 5.6 4.9 - - + -
386A GLY* 3.3 6.4 - - - -
387A ILE* 3.2 46.9 + - + +
408A TYR* 3.5 21.6 - - + +
409A ARG* 1.3 78.2 - - - +
411A LEU* 1.3 64.7 + - - +
412A ASN* 4.1 27.0 + - + +
445A GLU* 3.4 34.0 + - + +
446A ALA 3.5 4.0 - - - -
447A HIS* 3.3 34.8 - + - -
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Residues in contact with LEU 411 (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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168A PRO* 4.5 0.7 - - + -
173A PRO* 4.4 14.4 - - + -
174A TYR* 3.9 33.2 - - + -
359A PHE* 3.9 20.9 - - + -
384A VAL* 3.8 16.2 - - + -
385A ARG 3.4 12.1 - - - +
409A ARG* 3.9 28.7 - - - +
410A TYR* 1.3 83.8 - - - +
412A ASN* 1.3 88.7 + - - +
413A GLU* 3.9 10.1 - - + +
444A THR 4.0 0.6 - - - +
445A GLU* 3.6 3.1 - - - -
446A ALA 3.0 31.4 + - - +
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Residues in contact with ASN 412 (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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383A TRP* 3.6 1.3 + - - +
384A VAL* 3.2 3.6 - - - -
385A ARG* 2.8 46.1 + - + +
410A TYR* 4.1 25.3 + - + +
411A LEU* 1.3 79.3 - - - +
413A GLU* 1.3 64.9 + - - +
414A SER* 4.4 13.1 - - - +
444A THR 3.3 14.6 + - - +
445A GLU* 4.3 9.0 - - - +
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Residues in contact with GLU 413 (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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171A PHE 5.0 1.1 - - - +
172A ALA* 2.9 34.8 - - + -
173A PRO* 3.0 6.9 - - - +
174A TYR* 3.0 16.4 + - - +
175A GLY* 2.6 24.7 + - - -
383A TRP 3.3 4.3 - - - +
384A VAL* 3.9 17.7 - - + -
411A LEU* 4.2 6.5 - - + +
412A ASN* 1.3 76.3 - - - +
414A SER* 1.3 60.3 + - - +
415A THR* 4.5 2.9 - - + +
443A GLY* 3.1 4.9 - - - -
444A THR* 2.9 43.0 + - + +
520A TYR* 2.2 29.5 + - - +
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Residues in contact with SER 414 (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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382A TYR* 4.4 0.2 - - - +
383A TRP* 2.9 55.5 + - - +
412A ASN* 4.2 12.1 + - - +
413A GLU* 1.3 72.5 - - - +
415A THR* 1.3 68.8 + - - +
442A SER 3.9 6.5 - - - -
443A GLY* 4.3 1.1 - - - -
474A TYR* 4.8 8.9 + - - -
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Residues in contact with THR 415 (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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171A PHE 5.1 0.7 - - - +
172A ALA* 5.2 0.9 - - + -
381A ASN 3.4 5.2 - - - -
382A TYR* 3.2 39.7 - - + -
383A TRP* 4.3 5.0 - - - -
413A GLU* 4.5 2.7 - - + +
414A SER* 1.3 81.8 + - - +
416A HIS* 1.3 63.9 + - - +
417A GLU* 3.3 13.9 + - - -
441A ARG* 3.3 22.5 - - - +
442A SER* 3.1 26.5 + - - +
520A TYR* 3.5 26.0 - - + +
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Residues in contact with HIS 416 (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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379A PRO 4.1 0.2 - - - +
380A ARG* 3.4 2.1 - - - -
381A ASN* 2.9 45.2 + - + +
382A TYR* 6.2 0.2 - - - -
383A TRP* 4.3 19.2 - - + -
415A THR* 1.3 77.9 - - - +
417A GLU* 1.3 64.9 + - - +
418A MET* 3.7 27.5 - - + +
439A ASP* 3.5 18.0 + - - -
440A THR 2.9 28.3 - - - -
441A ARG* 3.9 31.1 + - + +
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Residues in contact with GLU 417 (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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176A GLN* 5.0 3.8 - - - +
379A PRO 3.4 3.8 - - - -
380A ARG* 3.3 35.6 + - + +
382A TYR* 3.6 18.5 + - + +
415A THR* 3.3 21.1 + - - -
416A HIS* 1.3 73.7 - - - +
418A MET* 1.3 62.5 + - - +
438A ARG* 3.8 8.6 - - - +
439A ASP* 3.6 0.3 - - - -
440A THR* 3.0 65.3 + - + +
442A SER* 3.8 9.7 + - - -
475A GLN* 5.3 0.7 - - - -
520A TYR* 4.8 10.5 - - - +
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Residues in contact with MET 418 (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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378A SER* 3.5 8.5 - - - -
379A PRO* 3.1 34.0 + - + +
380A ARG* 5.0 1.7 + - - +
416A HIS* 3.7 27.8 - - + +
417A GLU* 1.3 80.9 - - - +
419A ARG* 1.3 62.7 + - - +
420A TYR* 2.8 42.4 - - + +
436A TYR* 5.2 9.6 - - + -
438A ARG* 2.8 11.8 - - - +
439A ASP* 3.7 29.4 - - - +
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Residues in contact with ARG 419 (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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371A GLN* 4.2 12.4 + - - +
374A ARG* 4.9 8.5 - - - +
376A THR* 3.8 26.8 - - - +
377A LEU 3.4 3.1 - - - -
378A SER* 3.7 20.2 - - - +
380A ARG* 6.2 0.2 - - - +
418A MET* 1.3 76.0 - - - +
420A TYR* 1.3 63.7 + - - +
421A TYR* 5.2 0.4 - - - +
436A TYR* 3.0 4.4 - - - +
437A ASP* 2.5 68.7 + - - +
438A ARG* 2.8 58.4 + - + +
570A GLN 5.7 0.6 + - - -
573A ASP* 4.7 7.9 - - - +
742A FLC 3.2 21.2 + - + +
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Residues in contact with TYR 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A THR* 3.1 6.6 - - - -
377A LEU* 2.6 58.0 + - + +
379A PRO* 4.1 14.8 - - + -
418A MET* 2.8 51.6 - - + +
419A ARG* 1.3 74.8 - - - +
421A TYR* 1.3 61.3 + - - +
430A PRO* 4.2 2.2 - - + -
431A SER 3.6 20.6 - - - +
432A GLY* 4.2 14.9 - - - -
433A SER 4.6 3.1 - - - -
434A SER* 3.0 26.5 - - - +
435A PRO 3.2 7.2 - - - +
436A TYR* 3.7 18.2 - + + -
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Residues in contact with TYR 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 3.1 49.1 + - + +
375A ILE 3.3 5.2 - - - -
376A THR* 3.5 20.4 - - + -
419A ARG* 5.2 0.4 - - - +
420A TYR* 1.3 76.4 - - - +
422A THR* 1.3 74.7 + - - +
423A ALA 5.5 0.7 - - - -
430A PRO* 4.2 0.6 - - - +
434A SER* 3.4 6.9 + - - -
435A PRO* 2.9 55.6 + - + +
436A TYR 3.6 1.6 + - - -
437A ASP* 3.5 38.8 - - + +
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Residues in contact with THR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 3.1 5.4 - - - -
375A ILE* 2.6 44.7 + - - +
421A TYR* 1.3 85.9 - - - +
423A ALA* 1.3 62.2 + - - +
424A THR 3.2 0.2 + - - -
426A SER* 4.6 4.7 - - - -
428A GLN* 3.1 26.7 + - + +
429A LEU 4.3 3.4 - - - +
430A PRO* 3.4 32.2 - - + +
434A SER* 3.7 7.4 - - - +
435A PRO* 5.7 1.1 - - + -
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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
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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) + - + + + + + -
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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