Contacts of the helix formed by residues 137 - 169 (chain R) in PDB entry 5VAI
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 PRO 137 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135R SER* 3.4 6.1 - - - +
136R SER* 1.3 89.0 - - - +
138R GLU* 1.3 54.2 + - + +
139R GLU* 2.8 12.3 + - + -
140R ARG* 2.9 49.9 + - - +
141R LEU* 4.1 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 138 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P ASP* 4.8 3.3 - - - +
19P TYR* 2.7 46.5 + - + -
136R SER* 3.1 30.1 + - - +
137R PRO* 1.3 81.1 - - + +
139R GLU* 1.3 62.7 + - - +
140R ARG 3.2 0.2 - - - -
141R LEU* 2.9 15.9 + - - +
142R LEU* 2.4 38.3 + - + +
381R PHE* 4.2 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P TYR* 4.0 4.5 - - - -
23P GLN* 3.9 18.7 + - - -
135R SER 5.2 0.9 - - - +
136R SER* 3.0 22.6 + - - +
137R PRO* 2.8 2.1 + - + +
138R GLU* 1.3 99.9 - - - +
140R ARG* 1.3 58.5 + - + +
142R LEU* 3.1 32.6 - - - +
143R SER* 2.1 50.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137R PRO* 2.9 41.9 + - - +
139R GLU* 1.3 75.9 - - + +
141R LEU* 1.3 68.6 + - - +
144R LEU* 3.1 42.4 - - + +
145R TYR 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 5.3 0.2 - - - -
137R PRO 4.1 0.6 + - - +
138R GLU* 2.9 13.0 + - - +
140R ARG* 1.3 85.7 - - - +
142R LEU* 1.3 57.7 + - - +
145R TYR* 3.1 29.6 + - - +
381R PHE* 3.7 34.3 - - + -
382R VAL* 4.4 26.7 - - + -
385R PHE* 3.2 43.3 - - + -
386R THR* 4.9 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P PHE* 4.6 13.1 - - + -
16P VAL* 3.3 49.8 - - + -
19P TYR* 3.5 27.1 - - + -
23P GLN* 5.7 0.4 - - - +
138R GLU* 2.4 34.2 + - + +
139R GLU* 2.9 37.4 + - - +
141R LEU* 1.3 69.1 - - - +
143R SER* 1.3 67.7 + - - +
145R TYR* 3.7 8.5 + - - +
146R ILE* 4.3 10.9 + - - +
381R PHE* 6.0 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139R GLU* 2.1 51.4 + - - +
142R LEU* 1.3 73.1 - - - +
144R LEU* 1.3 69.8 + - - -
145R TYR 3.4 0.7 + - - -
146R ILE* 3.6 13.9 + - - +
147R ILE* 4.0 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140R ARG* 3.1 38.1 + - + +
143R SER* 1.3 84.7 - - - +
145R TYR* 1.3 52.6 + - - +
147R ILE* 3.0 27.4 + - + +
148R TYR* 2.5 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P GLU* 4.8 9.2 + - + -
12P PHE* 4.2 13.7 - + + -
141R LEU 3.1 22.8 + - - +
142R LEU 4.1 4.7 - - - +
143R SER 3.3 2.0 - - - -
144R LEU* 1.3 77.2 - - - +
146R ILE* 1.3 58.8 + - + +
148R TYR* 2.9 27.9 + + - +
149R THR* 2.4 69.3 + - + +
152R TYR* 5.4 1.6 - - + +
194R VAL* 6.1 0.7 - - + -
385R PHE* 3.2 29.4 - + + -
388R LEU* 3.7 20.3 - - + +
389R SER* 3.8 17.8 - - - -
392R SER* 3.3 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P VAL* 5.2 14.4 - - + -
142R LEU 4.3 11.9 + - - +
143R SER* 3.6 8.8 + - - +
144R LEU 3.2 0.6 - - - -
145R TYR* 1.3 80.1 - - + +
147R ILE* 1.3 67.2 + - + +
149R THR* 3.0 12.5 + - - -
150R VAL* 3.0 23.0 + - + +
197R LYS* 6.3 1.3 - - - +
198R ASP* 3.2 37.0 - - - +
201R LEU* 6.4 2.2 - - + -
202R LYS* 5.8 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 147 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143R SER 4.0 4.8 + - - +
144R LEU* 3.0 31.4 + - + +
146R ILE* 1.3 80.0 - - + +
148R TYR* 1.3 60.9 + - - +
150R VAL* 2.8 37.4 + - + +
151R GLY 3.9 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144R LEU* 2.5 23.0 + - + +
145R TYR* 3.2 29.6 - + - +
147R ILE* 1.3 76.2 - - - +
149R THR* 1.3 56.0 + - - +
151R GLY* 2.9 23.0 + - - -
152R TYR* 3.7 2.0 + - + -
385R PHE* 6.2 0.2 - + - -
389R SER* 4.0 25.3 + - - -
393R PHE* 3.5 35.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 149 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R TYR* 2.4 68.0 + - + +
146R ILE* 3.3 12.6 - - + -
148R TYR* 1.3 67.1 - - - +
150R VAL* 1.3 59.9 + - - +
151R GLY 3.1 0.4 - - - -
152R TYR* 2.8 51.7 + - + +
153R ALA* 3.0 6.4 + - - +
194R VAL* 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146R ILE* 3.0 17.0 + - + +
147R ILE* 2.8 29.0 + - + +
149R THR* 1.3 76.5 - - - +
151R GLY* 1.3 61.4 + - - +
153R ALA* 2.9 25.4 + - + +
154R LEU* 3.7 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147R ILE 3.9 0.8 + - - -
148R TYR 2.9 11.5 + - - -
150R VAL* 1.3 79.3 - - - +
152R TYR* 1.3 56.1 + - - +
154R LEU* 2.9 36.4 + - - +
155R SER 3.8 1.2 + - - -
393R PHE* 4.4 9.9 - - - -
396R LEU* 5.7 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 152 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R TYR* 5.5 1.3 - - + +
148R TYR 3.7 2.8 + - - -
149R THR* 2.8 37.1 + - + +
151R GLY* 1.3 75.2 - - - +
153R ALA* 1.3 66.8 + - - +
155R SER* 2.9 28.1 + - - +
156R PHE* 3.8 1.6 + - - +
187R PHE* 4.2 8.1 + - - +
190R ARG* 4.5 10.9 + - - +
191R ALA* 4.0 39.4 + - + +
194R VAL* 4.8 14.8 - - + +
392R SER* 2.8 50.1 + - - -
393R PHE* 3.4 34.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149R THR 3.0 5.9 + - - +
150R VAL* 2.9 20.6 + - + +
152R TYR* 1.3 79.7 - - - +
154R LEU* 1.3 64.1 + - - +
156R PHE* 2.9 24.6 + - - +
157R SER* 3.5 6.2 + - - -
195R PHE* 5.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150R VAL 3.7 1.2 + - - -
151R GLY* 2.9 21.5 + - - +
153R ALA* 1.3 77.4 - - - +
155R SER* 1.3 61.9 + - - +
157R SER* 3.0 20.9 + - - -
158R ALA* 3.3 10.7 + - + +
396R LEU* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 155 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151R GLY 3.8 0.6 + - - -
152R TYR* 2.9 34.5 + - - -
154R LEU* 1.3 78.3 - - - +
156R PHE* 1.3 62.7 + - - +
158R ALA* 3.1 4.9 + - - +
159R LEU* 2.8 26.5 + - - +
187R PHE* 6.1 0.3 - - - +
191R ALA* 6.5 0.2 - - - -
392R SER 5.0 0.4 + - - -
393R PHE* 5.2 2.5 - - - -
395R GLY* 4.0 2.1 - - - -
396R LEU* 2.9 52.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 156 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152R TYR 3.8 1.0 + - - +
153R ALA* 2.9 15.7 + - - +
155R SER* 1.3 77.7 - - - +
157R SER* 1.3 67.9 + - - +
159R LEU* 3.0 8.0 + - + +
160R VAL* 2.8 44.7 + - + +
188R ILE* 3.3 43.3 - - + -
191R ALA* 3.9 27.3 - - + +
192R LEU* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 157 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153R ALA 3.7 7.1 + - - -
154R LEU* 3.0 14.6 + - - -
156R PHE* 1.3 82.8 - - - +
158R ALA* 1.3 64.4 + - - +
160R VAL* 3.0 8.2 + - - +
161R ILE* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154R LEU* 3.3 7.2 + - + +
155R SER 3.1 1.6 + - - -
157R SER* 1.3 77.6 - - - +
159R LEU* 1.3 52.2 + - - +
161R ILE* 3.0 9.3 + - - +
162R ALA* 2.6 38.1 + - - +
396R LEU* 3.5 28.7 - - + -
399R ALA* 6.0 0.4 - - - -
400R ILE* 4.3 15.0 - - + -
404R PHE* 5.8 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R SER* 2.8 18.2 + - - +
156R PHE* 3.5 11.2 - - + +
158R ALA* 1.3 76.2 - - - +
160R VAL* 1.3 64.3 + - - +
162R ALA* 3.0 7.0 + - + +
163R SER* 2.8 25.9 + - - -
184R PHE* 3.1 55.4 - - + +
187R PHE* 3.6 20.9 - - + -
188R ILE* 3.4 18.2 - - + +
395R GLY 4.6 6.7 - - - +
396R LEU* 4.9 2.3 - - - +
399R ALA* 3.5 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 160 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R PHE* 2.8 58.6 + - + +
157R SER* 3.4 8.3 - - - +
159R LEU* 1.3 71.7 - - - +
161R ILE* 1.3 62.2 + - + +
163R SER* 3.0 9.3 + - - -
164R ALA* 2.9 27.1 + - + +
188R ILE* 5.0 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 161 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157R SER* 3.0 21.0 + - - +
158R ALA* 3.7 7.6 - - - +
160R VAL* 1.3 79.3 - - + +
162R ALA* 1.3 58.5 + - - +
164R ALA* 3.0 11.2 + - + +
165R ILE* 2.7 38.2 + - + +
404R PHE* 5.1 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158R ALA 2.6 17.9 + - - +
159R LEU* 3.3 15.3 - - + +
161R ILE* 1.3 71.7 - - - +
163R SER* 1.3 62.6 + - - +
165R ILE* 3.0 10.5 + - - +
166R LEU* 2.9 35.0 + - + +
184R PHE* 5.4 0.9 - - + -
399R ALA* 4.5 14.6 - - + +
400R ILE* 6.2 1.1 - - + -
403R CYS* 6.2 0.2 - - + -
404R PHE* 4.4 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 163 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159R LEU 2.8 15.4 + - - -
160R VAL* 3.4 10.1 - - - -
162R ALA* 1.3 75.0 - - - +
164R ALA* 1.3 58.0 + - - +
166R LEU* 2.9 2.6 + - - +
167R LEU* 2.8 32.2 + - - +
181R LEU* 3.7 28.7 + - - +
184R PHE* 4.0 16.1 - - - +
188R ILE* 4.6 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160R VAL* 2.9 14.3 + - + +
161R ILE* 3.0 17.7 + - + +
163R SER* 1.3 76.9 - - - +
165R ILE* 1.3 51.4 + - - +
167R LEU* 3.7 4.1 - - - +
168R GLY* 2.7 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 165 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161R ILE* 2.7 23.0 + - + +
162R ALA* 3.3 11.2 - - - +
164R ALA* 1.3 72.5 - - - +
166R LEU* 1.3 71.8 + - + +
168R GLY* 2.9 12.5 + - - -
169R PHE* 3.9 20.3 + - + -
403R CYS 5.7 1.6 - - - +
404R PHE* 4.4 26.2 - - + +
409R VAL* 4.2 25.1 - - + -
413R PHE* 3.5 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R ALA* 2.9 21.7 + - + +
163R SER 2.9 6.3 + - - +
165R ILE* 1.3 85.8 - - + +
167R LEU* 1.3 61.7 + - - +
170R ARG* 4.5 5.9 + - - -
172R LEU* 3.7 41.3 + - + +
173R HIS 5.4 0.5 + - - -
177R ASN* 5.1 7.9 - - + -
181R LEU* 3.4 30.3 - - + -
184R PHE* 3.4 33.4 - - + -
403R CYS* 3.4 31.4 - - + +
404R PHE* 6.3 0.4 - - - -
409R VAL* 5.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163R SER 2.8 17.3 + - - +
164R ALA* 4.3 4.5 - - - +
166R LEU* 1.3 74.5 - - - +
168R GLY* 1.3 67.3 + - - +
169R PHE 3.2 1.4 + - - -
170R ARG* 3.3 20.7 + - + +
173R HIS* 5.3 13.2 - - + -
181R LEU* 4.6 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 168 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164R ALA 2.7 25.0 + - - -
165R ILE* 2.9 10.6 + - - -
167R LEU* 1.3 76.2 - - - +
169R PHE* 1.3 59.1 + - - -
170R ARG* 5.2 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 169 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165R ILE* 3.9 23.7 + - + -
166R LEU 4.5 0.2 + - - -
167R LEU 3.4 0.2 - - - -
168R GLY* 1.3 76.3 - - - +
170R ARG* 1.3 67.4 + - - +
171R HIS* 2.9 25.9 + - + +
172R LEU* 3.4 39.9 - - + -
409R VAL* 4.6 5.6 - - + -
412R GLU* 3.4 39.5 - - + +
413R PHE* 4.4 29.8 - + + -
416R SER* 5.0 14.1 - - - +
420R TRP* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
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