Contacts of the helix formed by residues 198 - 224 (chain R) in PDB entry 6VMS
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 PHE 198 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ILE* 4.3 13.1 - - + +
194R SER 3.4 11.3 + - - +
196R VAL 3.4 0.8 - - - -
197R SER* 1.3 80.8 - - - +
199R TYR* 1.3 84.7 + + - +
200R VAL 3.4 1.1 - - - -
201R PRO* 3.4 3.6 - - - +
202R PHE* 2.6 52.3 + + + +
382R PHE* 4.1 17.0 - + - -
383R ILE* 5.7 0.7 - - - -
386R TRP* 3.9 20.4 - - + -
387R LEU* 3.3 43.3 - - + -
390R PHE* 3.3 46.7 - + + -
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Residues in contact with TYR 199 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194R SER* 2.9 46.9 + - - -
195R ILE* 3.4 23.0 + - + +
198R PHE* 1.3 99.2 - + - +
200R VAL* 1.3 62.0 + - - +
202R PHE* 3.5 11.5 - + - +
203R ILE* 2.9 38.4 + - + +
387R LEU* 5.2 4.3 - - + -
390R PHE* 3.4 14.9 + - + +
391R ILE* 4.4 7.1 + - + +
394R ILE* 3.4 36.1 - - + +
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Residues in contact with VAL 200 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195R ILE* 3.0 34.5 + - + +
196R VAL* 4.3 7.2 - - + +
199R TYR* 1.3 75.7 - - - +
201R PRO* 1.3 69.0 - - + +
203R ILE* 3.2 6.9 + - - +
204R VAL* 2.9 40.4 + - + +
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Residues in contact with PRO 201 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ILE* 3.7 17.7 - - + -
123R LEU* 4.1 11.4 - - + -
126R CYS* 4.0 22.7 - - + -
196R VAL 3.3 16.6 - - - +
197R SER 3.4 25.8 - - - +
198R PHE 3.4 8.3 - - - +
200R VAL* 1.3 99.2 - - + +
202R PHE* 1.3 54.8 + - - -
204R VAL* 4.2 7.2 - - + -
205R ILE* 2.9 38.4 + - + +
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Residues in contact with PHE 202 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198R PHE* 2.6 44.4 + + + +
199R TYR* 3.5 14.6 - + - +
201R PRO* 1.3 71.6 - - - +
203R ILE* 1.3 83.9 + - + +
205R ILE* 3.9 1.3 - - - +
206R LEU* 2.9 43.2 + - + +
379R LEU* 5.6 1.0 - - + +
382R PHE* 4.0 27.1 - + + -
383R ILE* 3.4 38.1 - - + -
387R LEU* 4.9 12.8 - - + -
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Residues in contact with ILE 203 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199R TYR* 2.9 24.3 + - + +
200R VAL* 3.8 4.9 - - - +
202R PHE* 1.3 93.0 - - + +
204R VAL* 1.3 64.9 + - + +
206R LEU* 3.8 9.6 - - + +
207R LEU* 2.9 48.1 + - + +
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Residues in contact with VAL 204 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126R CYS* 3.4 28.3 - - - +
129R SER* 6.0 0.4 - - - -
130R ILE* 4.5 12.1 - - + -
200R VAL* 2.9 31.1 + - + +
201R PRO* 3.8 4.9 - - + +
202R PHE 3.2 0.2 - - - -
203R ILE* 1.3 79.5 - - + +
205R ILE* 1.3 57.7 + - - +
207R LEU* 3.9 4.8 - - - +
208R VAL* 2.9 47.5 + - + +
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Residues in contact with ILE 205 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ILE 4.4 3.4 - - - +
125R LEU* 3.9 14.1 - - + +
126R CYS* 3.7 39.3 - - + +
129R SER* 3.9 8.1 - - - +
201R PRO* 2.9 24.6 + - + +
202R PHE* 3.9 3.1 - - - +
204R VAL* 1.3 75.1 - - - +
206R LEU* 1.3 64.8 + - - +
208R VAL* 3.9 4.4 - - - +
209R TYR* 2.9 53.8 + - + -
378R TYR 5.6 1.1 - - - +
379R LEU* 3.6 13.2 - - + -
382R PHE* 4.5 24.0 - - + -
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Residues in contact with LEU 206 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202R PHE* 2.9 41.1 + - + +
203R ILE* 3.8 11.2 - - + +
205R ILE* 1.3 78.6 - - - +
207R LEU* 1.3 62.7 + - + +
209R TYR* 3.9 1.2 - - - +
210R ILE* 2.9 52.4 + - + +
379R LEU* 3.9 29.4 - - + +
383R ILE* 5.3 7.0 - - + -
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Residues in contact with LEU 207 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203R ILE* 2.9 41.6 + - + +
204R VAL* 4.0 4.9 - - - +
206R LEU* 1.3 81.3 - - + +
208R VAL* 1.3 60.0 + - + +
210R ILE* 3.3 16.6 + - + +
211R LYS* 2.9 40.2 + - - +
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Residues in contact with VAL 208 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129R SER* 3.1 42.0 - - - +
130R ILE* 5.1 5.4 - - + -
133R TYR* 3.8 23.3 - - + -
204R VAL* 2.9 35.6 + - + +
205R ILE 3.9 2.5 - - - +
207R LEU* 1.3 78.4 - - + +
209R TYR* 1.3 59.3 + - - +
211R LYS* 3.2 10.1 + - + +
212R ILE* 2.9 34.6 + - + +
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Residues in contact with TYR 209 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R LEU 4.9 0.7 + - - -
128R ILE* 4.9 1.0 - - - +
129R SER* 2.9 31.5 + - - -
132R ARG* 3.6 31.8 + - - -
205R ILE* 2.9 40.1 + - + +
206R LEU 4.1 0.2 - - - +
208R VAL* 1.3 76.2 - - - +
210R ILE* 1.3 58.8 + - - +
212R ILE* 3.7 10.3 - - + +
213R TYR* 2.9 28.8 + - - +
375R LEU* 3.2 38.6 - - + +
378R TYR* 3.6 31.0 - + + +
379R LEU* 3.7 29.4 - - + -
426R TYR* 4.1 7.9 + - - -
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Residues in contact with ILE 210 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206R LEU* 2.9 51.0 + - + +
207R LEU* 3.6 16.4 - - + +
208R VAL 3.2 0.2 - - - -
209R TYR* 1.3 76.9 - - + +
211R LYS* 1.3 62.8 + - + +
213R TYR* 3.3 7.5 + - + +
214R ILE* 2.9 45.1 + - + +
379R LEU* 5.6 2.2 - - + -
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Residues in contact with LYS 211 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133R TYR* 3.7 41.3 + - + +
207R LEU* 2.9 25.9 + - - +
208R VAL* 3.6 7.6 - - + +
210R ILE* 1.3 77.6 - - + +
212R ILE* 1.3 58.8 + - - +
214R ILE* 3.2 13.4 + - + +
215R VAL* 2.9 36.0 + - + +
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Residues in contact with ILE 212 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU* 4.3 9.2 - - + -
132R ARG* 3.7 33.0 - - + +
133R TYR* 3.8 16.2 - - + +
136R VAL* 3.9 22.4 - - + -
208R VAL* 2.9 28.0 + - + +
209R TYR* 3.7 16.8 - - + +
210R ILE 3.2 0.2 - - - -
211R LYS* 1.3 74.1 - - - +
213R TYR* 1.3 66.0 + - - +
215R VAL* 3.2 6.2 + - - +
216R LEU* 2.9 42.0 + - + +
375R LEU* 3.8 19.5 - - + -
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Residues in contact with TYR 213 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209R TYR 2.9 17.5 + - - +
210R ILE* 3.7 7.2 - - + +
212R ILE* 1.3 77.3 - - - +
214R ILE* 1.3 70.8 + - + +
216R LEU* 3.9 3.8 - - + -
217R ARG* 2.9 56.2 + - + +
220R ARG* 5.8 1.8 - - - -
372R THR* 3.4 41.8 + - + +
375R LEU* 4.3 17.7 - - + -
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Residues in contact with ILE 214 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210R ILE* 2.9 38.0 + - + +
211R LYS* 3.5 15.0 - - + +
213R TYR* 1.3 83.5 - - + +
215R VAL* 1.3 66.4 + - + +
217R ARG* 4.0 2.6 - - - +
218R ARG* 2.9 43.5 + - + +
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Residues in contact with VAL 215 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 5.9 1.3 - - + -
133R TYR* 6.2 1.6 - - + -
136R VAL* 4.6 32.5 - - + +
137R ALA* 5.7 6.1 - - + -
211R LYS* 2.9 23.3 + - + +
212R ILE* 3.2 6.7 + - - +
214R ILE* 1.3 80.2 - - + +
216R LEU* 1.3 66.5 + - + +
218R ARG* 3.8 23.5 - - - +
219R ARG* 2.9 49.6 + - + +
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Residues in contact with LEU 216 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ILE* 5.3 3.6 - - + -
348A LEU* 3.7 32.3 - - + -
353A LEU* 5.2 6.1 - - + -
136R VAL* 5.1 4.0 - - + -
212R ILE* 2.9 38.0 + - + +
213R TYR* 3.9 4.9 - - + +
215R VAL* 1.3 82.3 - - + +
217R ARG* 1.3 58.4 + - - +
219R ARG* 3.9 6.4 - - - +
220R ARG* 2.9 57.9 + - - +
367R LYS* 4.5 2.9 - - - +
371R ALA* 3.7 28.0 - - + -
375R LEU* 4.0 10.3 - - + -
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Residues in contact with ARG 217 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213R TYR* 2.9 52.7 + - + +
214R ILE* 4.0 2.9 - - - +
216R LEU* 1.3 73.0 - - - +
218R ARG* 1.3 61.0 + - - +
220R ARG* 4.2 20.8 - - - +
221R LYS* 2.8 76.5 + - - +
368R GLU* 3.0 37.5 - - - +
372R THR* 5.5 0.4 - - - -
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Residues in contact with ARG 218 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214R ILE* 2.9 32.4 + - + +
215R VAL* 3.8 27.3 + - - +
217R ARG* 1.3 75.0 - - - +
219R ARG* 1.3 69.1 + - + +
221R LYS* 3.3 8.4 + - - +
222R LEU* 3.1 44.1 + - + +
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Residues in contact with ARG 219 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASP* 4.4 6.7 + - - -
340A THR* 3.9 15.6 - - - +
341A ASP* 2.3 32.1 + - - -
344A ILE* 3.3 38.4 - - - +
215R VAL* 2.9 39.6 + - + +
216R LEU* 3.9 7.6 - - + +
218R ARG* 1.3 83.0 - - + +
220R ARG* 1.3 59.7 + - + +
222R LEU* 2.8 22.0 + - - +
223R VAL* 2.9 22.4 + - + +
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Residues in contact with ARG 220 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LYS* 5.1 8.0 - - - +
213R TYR* 5.8 1.4 - - - -
216R LEU* 2.9 50.1 + - - +
217R ARG* 4.2 21.6 - - - +
219R ARG* 1.3 71.5 - - + +
221R LYS* 1.3 60.4 + - - +
222R LEU 2.9 10.7 + - - -
223R VAL* 3.1 33.6 + - + +
224R ASN 4.5 0.7 + - - -
364R SER* 4.5 21.1 - - - +
367R LYS* 2.9 58.6 + - - +
368R GLU* 3.6 23.8 + - - +
371R ALA* 4.2 5.1 - - - +
372R THR* 4.3 6.5 + - - -
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Residues in contact with LYS 221 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217R ARG* 2.8 64.9 + - - +
218R ARG* 3.9 6.7 - - - +
220R ARG* 1.3 74.6 - - - +
222R LEU* 1.3 70.8 + - + +
224R ASN* 5.2 1.8 - - - +
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Residues in contact with LEU 222 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218R ARG* 3.2 31.9 - - + +
219R ARG* 2.8 9.0 + - - +
221R LYS* 1.3 90.2 - - + +
223R VAL* 1.3 61.2 + - - +
224R ASN* 3.3 19.6 + - - -
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Residues in contact with VAL 223 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASP* 5.2 12.8 - - - +
345A LYS* 5.7 5.8 - - - +
219R ARG* 2.9 27.9 + - + +
220R ARG* 3.1 28.7 + - + +
222R LEU* 1.3 76.2 - - - +
224R ASN* 1.3 73.5 + - - +
225R THR* 3.2 39.6 + - + +
364R SER* 4.5 5.4 - - - +
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Residues in contact with ASN 224 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220R ARG 4.5 1.4 + - - -
221R LYS 5.2 1.6 - - - +
222R LEU* 3.3 18.5 + - - +
223R VAL* 1.3 80.2 + - - +
225R THR* 1.3 62.4 + - - +
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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