Contacts of the helix formed by residues 359 - 380 (chain A) in PDB entry 3CMM
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 ILE 359 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A THR* 3.7 2.2 - - - -
156A THR* 5.3 1.8 - - - +
158A GLY* 3.9 23.9 + - - +
159A LEU* 4.4 5.8 - - + -
357A GLY 4.0 0.4 + - - -
358A ASP* 1.3 79.4 + - - +
360A PRO* 1.3 66.8 - - - +
361A GLY 3.9 8.5 - - - +
362A VAL* 3.0 25.8 + - + +
363A VAL* 3.0 23.5 + - - +
419A ASN 4.2 0.2 - - - +
420A GLN* 4.1 17.3 - - + -
423A VAL* 3.8 20.6 - - + -
424A PHE* 3.5 24.7 - - + -
879A LEU* 4.1 3.4 - - + -
882A TYR* 3.4 31.4 - - + +
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Residues in contact with PRO 360 (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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77A SER 3.8 3.1 - - - +
78A THR* 3.4 21.3 - - + -
358A ASP 3.7 8.3 - - - +
359A ILE* 1.3 88.3 - - + +
361A GLY* 1.3 56.6 + - - +
363A VAL* 3.8 2.4 - - + +
364A ALA* 2.9 32.9 + - - +
420A GLN* 3.8 22.2 - - + +
452A ASN* 3.8 15.9 - - - +
455A LEU* 4.0 20.4 - - + -
456A LEU* 3.5 29.8 - - + -
882A TYR* 4.2 0.2 - - - +
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Residues in contact with GLY 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ILE* 3.3 4.8 - - - +
360A PRO* 1.3 79.5 - - - +
362A VAL* 1.3 59.6 + - - +
365A PHE* 3.3 19.9 + - - +
452A ASN* 3.9 5.5 + - - -
456A LEU* 5.5 0.2 - - - +
875A GLY* 3.4 33.5 - - - +
878A ASN* 4.3 8.3 - - - +
879A LEU* 4.0 16.4 - - - +
882A TYR* 5.0 2.0 + - - -
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR* 3.3 20.2 - - - +
158A GLY 3.6 19.7 - - - +
159A LEU* 3.9 14.6 - - + +
160A PHE 3.7 20.4 - - - +
359A ILE* 3.0 16.2 + - + +
361A GLY* 1.3 74.1 - - - +
363A VAL* 1.3 61.2 + - + +
365A PHE* 3.2 6.6 + - - +
366A PHE* 2.9 40.1 + - + -
391A PHE* 4.7 7.4 - - + -
879A LEU* 3.8 25.4 - - + -
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A GLY* 3.5 31.6 - - - +
47A LEU* 3.7 16.4 - - - +
50A GLU* 3.9 11.2 - - + +
78A THR* 4.1 14.8 - - + +
156A THR* 3.8 22.4 - - + -
358A ASP* 3.8 21.8 - - - +
359A ILE 3.0 18.0 + - - +
360A PRO* 3.8 3.6 - - + +
362A VAL* 1.3 76.1 - - - +
364A ALA* 1.3 52.3 + - - +
366A PHE 3.2 1.6 + - - -
367A GLY* 2.7 34.3 + - - -
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 4.3 18.1 - - - +
360A PRO 2.9 17.8 + - - +
363A VAL* 1.3 75.7 - - - +
365A PHE* 1.3 57.8 + - - +
367A GLY* 3.9 0.2 - - - -
368A GLY* 2.9 27.7 + - - -
451A LYS* 4.8 2.5 - - - +
452A ASN* 4.3 15.0 - - - +
871A SER* 3.6 14.4 - - - +
872A LEU 3.8 6.4 + - - -
875A GLY* 3.6 22.7 - - - +
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Residues in contact with PHE 365 (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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281A SER* 5.0 1.1 - - - -
361A GLY 3.3 12.2 + - - +
362A VAL* 3.2 9.3 + - - +
364A ALA* 1.3 78.1 - - - +
366A PHE* 1.3 89.7 + + - +
369A LEU* 3.2 26.3 + - + +
389A MET* 3.8 26.2 - - + -
391A PHE* 4.0 27.1 - + + -
872A LEU* 3.5 47.3 - - + +
875A GLY* 4.3 1.7 - - - -
876A LEU* 3.8 28.3 - - + -
879A LEU* 5.4 0.7 - - + -
906A PHE* 3.9 28.5 - + + -
908A PHE* 5.4 1.1 - + - -
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Residues in contact with PHE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.7 20.0 - - + -
154A SER* 3.5 17.7 - - - +
155A GLU 5.1 0.9 - - - -
156A THR* 4.4 4.7 - - - +
161A GLY* 3.3 37.7 - - - -
162A ASN* 3.3 22.4 - - - -
163A THR* 3.4 6.7 - - - -
362A VAL* 2.9 25.7 + - + +
365A PHE* 1.3 91.8 - + - +
367A GLY* 1.3 54.4 + - - +
369A LEU* 3.9 12.8 - - + -
370A VAL* 2.8 39.8 + - - +
389A MET* 3.7 22.4 - - + -
391A PHE* 3.6 27.6 - + + -
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Residues in contact with GLY 367 (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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47A LEU* 3.7 3.0 - - - +
50A GLU* 3.9 19.1 - - - -
51A ILE* 3.9 14.6 - - - +
54A ASN* 3.7 6.6 + - - -
363A VAL 2.7 21.0 + - - -
364A ALA 3.9 0.7 - - - -
366A PHE* 1.3 70.1 - - - +
368A GLY* 1.3 65.0 + - - +
371A ALA* 3.0 27.9 + - - +
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Residues in contact with GLY 368 (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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54A ASN* 3.6 13.2 - - - +
364A ALA 2.9 20.2 + - - -
365A PHE 4.0 0.9 - - - -
367A GLY* 1.3 72.3 - - - +
369A LEU* 1.3 56.8 + - - +
372A GLN* 3.2 13.3 + - - +
868A THR* 3.2 45.2 + - - +
871A SER* 4.1 2.9 - - - -
872A LEU* 4.3 3.1 - - - -
901A LEU* 4.1 3.0 - - - +
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Residues in contact with LEU 369 (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 THR* 3.8 25.6 - - + -
365A PHE* 3.2 14.7 + - + +
366A PHE* 3.9 21.8 - - + +
368A GLY* 1.3 75.6 - - - +
370A VAL* 1.3 69.1 + - + +
372A GLN* 3.4 3.0 + - + +
373A GLU* 3.1 42.8 + - + +
385A LEU* 4.2 8.1 - - + -
389A MET* 4.1 8.5 - - + -
872A LEU* 3.6 16.1 - - + +
901A LEU* 4.4 10.8 - - + -
904A PRO* 5.1 1.6 - - + -
906A PHE* 3.7 27.1 - - + -
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Residues in contact with VAL 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 3.8 28.0 - - + -
127A VAL* 4.1 11.9 - - + -
152A ILE* 3.8 20.0 - - + -
154A SER* 3.6 23.1 - - - +
163A THR* 3.3 28.3 - - - +
366A PHE* 2.8 29.2 + - + +
369A LEU* 1.3 72.1 - - + +
371A ALA* 1.3 66.6 + - - +
373A GLU* 3.1 10.3 + - - +
374A VAL* 2.9 22.4 + - + +
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Residues in contact with ALA 371 (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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51A ILE* 4.0 9.8 - - - +
54A ASN* 3.5 29.2 - - + -
55A VAL* 3.9 19.2 - - + +
367A GLY 3.0 21.0 + - - +
368A GLY 3.7 3.6 - - - +
370A VAL* 1.3 77.8 - - - +
372A GLN* 1.3 61.5 + - - +
374A VAL* 3.2 6.4 + - - +
375A LEU* 3.1 25.6 + - + +
868A THR* 3.8 4.5 - - - +
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Residues in contact with GLN 372 (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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26A LEU* 4.3 4.7 - - - +
368A GLY 3.2 14.8 + - - +
369A LEU 3.8 5.6 - - - +
370A VAL 3.2 0.4 - - - -
371A ALA* 1.3 74.2 - - - +
373A GLU* 1.3 60.8 + - - +
375A LEU* 3.1 22.4 + - - +
376A LYS* 2.9 39.6 + - - +
382A PHE* 3.8 29.4 - - + -
571A THR* 4.3 9.1 - - - +
866A ILE* 4.1 9.5 - - - +
868A THR* 2.7 34.3 + - + +
901A LEU* 4.0 26.2 - - + +
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Residues in contact with GLU 373 (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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152A ILE* 3.7 15.4 - - + +
163A THR* 5.3 2.9 - - - +
165A VAL* 4.0 21.1 - - + +
167A LEU* 5.4 1.6 - - - +
369A LEU* 3.1 39.7 + - + +
370A VAL* 3.1 11.7 + - - +
372A GLN* 1.3 76.4 - - - +
374A VAL* 1.3 57.0 + - - +
376A LYS* 2.8 38.0 + - - +
377A ALA* 2.8 30.0 + - - +
384A PRO* 3.5 2.9 - - - +
385A LEU* 2.8 35.3 + - + +
901A LEU* 4.5 0.7 - - - +
904A PRO* 4.0 5.7 - - - +
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Residues in contact with VAL 374 (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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39A VAL* 4.2 21.1 - - + -
51A ILE* 4.4 4.3 - - + -
55A VAL* 4.0 29.6 - - + -
125A VAL* 4.3 6.2 - - + +
127A VAL* 3.7 27.8 - - + -
152A ILE* 3.6 13.7 - - + +
370A VAL* 2.9 21.1 + - + +
371A ALA* 3.2 13.4 + - - +
373A GLU* 1.3 75.2 - - - +
375A LEU* 1.3 64.3 + - + +
377A ALA* 3.0 5.8 + - - +
378A CYS* 3.0 26.7 + - - -
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Residues in contact with LEU 375 (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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26A LEU* 4.5 9.2 - - + -
34A MET* 3.9 20.1 - - + +
54A ASN 5.2 2.2 - - - +
55A VAL* 4.5 11.2 - - + -
58A ALA* 3.7 33.9 - - + -
60A VAL* 4.3 17.7 - - + -
371A ALA* 3.1 13.2 + - + +
372A GLN* 3.1 29.7 + - - +
374A VAL* 1.3 73.8 - - + +
376A LYS* 1.3 58.7 + - - +
378A CYS* 3.2 12.9 + - - +
379A SER* 2.7 28.4 + - - -
866A ILE* 4.1 18.4 - - + -
868A THR* 4.8 4.5 - - - +
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Residues in contact with LYS 376 (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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167A LEU* 5.1 1.1 - - + -
171A PHE* 3.5 7.6 - - - -
372A GLN* 2.9 20.6 + - - +
373A GLU* 2.8 45.4 + - - +
375A LEU* 1.3 76.2 - - - +
377A ALA* 1.3 58.9 + - - +
379A SER* 3.9 0.2 - - - -
380A GLY* 2.9 29.1 + - - -
381A LYS 3.3 25.1 - - - +
382A PHE* 3.7 17.5 - - + +
383A THR 3.0 29.8 + - - +
384A PRO* 3.7 15.0 - - + -
901A LEU 2.8 29.7 + - - -
904A PRO* 3.9 7.7 - - - +
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Residues in contact with ALA 377 (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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124A GLN* 6.1 0.3 - - - +
125A VAL* 4.1 11.9 - - + +
150A ARG* 3.9 24.9 + - + +
152A ILE* 4.5 0.9 - - + -
167A LEU* 3.5 29.4 - - + -
171A PHE* 3.6 24.1 - - - -
373A GLU 2.8 13.4 + - - +
374A VAL* 3.0 10.5 + - - +
376A LYS* 1.3 78.5 - - - +
378A CYS* 1.3 58.6 + - - +
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Residues in contact with CYS 378 (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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33A LYS* 3.7 26.9 + - - +
34A MET* 4.0 16.6 - - + -
37A SER* 3.4 36.1 + - - +
39A VAL* 4.5 11.9 - - - -
60A VAL* 4.6 7.6 - - - -
124A GLN* 5.5 1.6 - - - -
125A VAL* 3.8 16.2 - - - -
374A VAL* 3.0 19.6 + - - +
375A LEU* 3.6 8.7 - - - +
376A LYS 3.2 0.4 - - - -
377A ALA* 1.3 77.9 - - - +
379A SER* 1.3 58.1 + - - +
380A GLY 3.9 0.2 - - - -
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 5.9 1.7 - - - +
30A ALA* 3.6 39.1 - - - +
33A LYS* 3.5 28.4 - - - +
34A MET* 4.4 5.8 - - - +
174A LEU* 3.9 9.5 - - - +
375A LEU 2.7 23.1 + - - -
376A LYS* 3.7 0.9 + - - -
378A CYS* 1.3 79.5 - - - +
380A GLY* 1.3 63.1 + - - +
381A LYS* 3.3 17.0 + - - +
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Residues in contact with GLY 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LYS* 5.5 0.4 - - - -
171A PHE* 3.8 14.5 - - - -
172A THR 3.7 18.4 - - - -
173A VAL* 3.5 4.8 - - - +
174A LEU* 2.7 35.7 + - - +
175A ASP 3.8 1.2 + - - -
376A LYS 2.9 12.7 + - - -
378A CYS 3.9 0.4 - - - -
379A SER* 1.3 77.1 - - - +
381A LYS* 1.3 58.8 + - - +
382A PHE 4.4 3.4 - - - -
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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