Contacts of the helix formed by residues 167 - 191 (chain F) in PDB entry 5D4D
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 167 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F SER 4.3 2.9 - - - +
166F LEU* 1.3 98.5 - - + +
168F LYS* 1.3 59.9 + - - +
169F GLU* 3.4 24.9 - - - +
170F HIS* 2.9 20.1 + - + +
171F LYS 2.8 24.9 + - - -
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Residues in contact with LYS 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D PHE* 5.5 7.2 - - - -
404D GLU 4.5 6.9 + - - -
405D ASP* 3.0 32.4 + - - +
406D ASP* 3.8 27.4 + - + +
442D ASN* 5.7 3.8 - - - +
166F LEU 3.7 0.8 + - - -
167F PRO* 1.3 72.3 - - - +
169F GLU* 1.3 62.2 + - - +
171F LYS* 3.2 8.3 + - - +
172F ARG* 3.0 28.9 + - - +
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Residues in contact with GLU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F PRO* 3.4 22.8 - - - +
168F LYS* 1.3 86.7 + - - +
170F HIS* 1.3 78.2 + - + +
172F ARG* 3.3 24.1 - - - +
173F TYR* 3.5 16.3 - - - -
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Residues in contact with HIS 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F LEU* 3.9 7.4 - - - +
119F ILE* 3.5 43.7 - - + +
166F LEU* 3.9 22.7 - - + -
167F PRO* 2.9 28.6 + - + +
169F GLU* 1.3 98.0 + - + +
171F LYS* 1.3 63.0 + - - +
172F ARG 3.1 1.6 - - - -
173F TYR* 3.1 28.8 + + - +
174F LEU 3.8 2.3 + - - -
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Residues in contact with LYS 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D ASP* 4.2 15.2 + - - +
407D VAL 2.6 30.9 + - - +
408D GLU* 3.7 24.0 + - - +
409D VAL 5.0 2.2 - - - -
410D SER* 6.2 0.4 - - - -
163F LEU 4.2 11.7 - - - +
164F LYS* 3.5 39.9 + - - +
166F LEU* 4.0 18.9 - - + +
167F PRO 2.8 13.1 + - - +
168F LYS* 3.2 7.2 + - - +
170F HIS* 1.3 73.1 - - - +
172F ARG* 1.3 65.7 + - - +
174F LEU* 2.9 27.1 + - + +
175F HIS* 3.0 32.6 + - + -
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Residues in contact with ARG 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D VAL* 6.2 1.8 - - - +
439D LEU* 3.6 33.6 - - + +
168F LYS 3.0 12.7 + - - +
169F GLU* 3.3 22.0 - - - +
171F LYS* 1.3 75.3 - - - +
173F TYR* 1.3 70.9 + - + +
175F HIS* 3.1 13.7 + - - +
176F ILE* 3.0 47.3 + - + +
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Residues in contact with TYR 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F GLU 6.2 0.2 - - - -
112F ALA* 3.4 32.3 - - + +
115F LYS* 3.7 49.8 + - + -
116F LEU* 4.0 9.8 - - + +
119F ILE* 4.2 12.3 - - + -
169F GLU 3.5 21.5 - - - -
170F HIS* 3.1 17.3 + + - +
172F ARG* 1.3 86.0 - - + +
174F LEU* 1.3 61.7 + - - +
176F ILE* 3.3 10.3 + - + -
177F ALA* 2.9 26.2 + - - +
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Residues in contact with LEU 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D SER* 4.3 17.5 - - - +
116F LEU* 3.7 18.1 - - + +
131F VAL* 4.2 15.9 - - + -
160F ASP* 4.8 5.4 - - - +
163F LEU* 3.6 54.7 - - + +
164F LYS* 4.2 15.7 - - + -
170F HIS 3.8 1.4 + - - -
171F LYS* 2.9 25.1 + - + +
173F TYR* 1.3 78.1 - - - +
175F HIS* 1.3 65.2 + - + +
177F ALA* 3.1 2.3 + - - +
178F ARG* 3.0 32.2 + - + +
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Residues in contact with HIS 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D ASP* 5.5 0.9 - - - -
407D VAL* 4.0 21.2 - - + +
409D VAL 3.1 22.0 + - - -
410D SER* 3.1 27.6 + - - -
411D THR* 4.5 4.4 + - - +
437D VAL* 3.4 34.1 - - + +
439D LEU* 4.3 18.8 - - + +
171F LYS* 3.0 46.3 + - + -
172F ARG* 3.1 10.9 + - - +
174F LEU* 1.3 76.8 - - + +
176F ILE* 1.3 64.5 + - - +
178F ARG* 3.3 3.6 + - - +
179F GLU* 3.0 24.9 + - - +
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Residues in contact with ILE 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D LEU* 4.6 15.0 - - + -
105F LYS 4.8 1.0 - - - +
108F GLU* 3.6 46.7 - - + +
109F GLY* 3.9 1.5 - - - +
112F ALA* 3.7 7.0 - - + -
172F ARG* 3.0 38.2 + - + +
173F TYR* 3.4 12.8 - - + +
175F HIS* 1.3 77.7 - - - +
177F ALA* 1.3 56.1 + - - +
179F GLU* 3.4 11.5 + - - +
180F GLY* 2.9 25.6 + - - -
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Residues in contact with ALA 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109F GLY* 4.2 12.5 - - - +
112F ALA* 4.0 2.2 - - + +
113F ILE* 3.8 27.4 - - + +
116F LEU* 4.5 4.0 - - + -
131F VAL* 3.6 23.7 - - + +
173F TYR 2.9 13.8 + - - +
174F LEU* 3.1 11.2 + - - +
176F ILE* 1.3 74.0 - - - +
178F ARG* 1.3 66.5 + - - +
180F GLY* 3.1 1.9 + - - -
181F GLU* 2.9 21.3 + - - +
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Residues in contact with ARG 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D SER* 3.5 24.6 + - - +
411D THR* 2.4 52.2 + - - +
412D GLY* 4.3 0.6 - - - -
413D ASP* 3.1 32.5 + - - +
131F VAL* 3.6 23.8 + - + +
134F LYS* 3.5 23.0 + - - +
135F ILE* 3.4 22.8 - - + +
160F ASP* 3.0 32.5 + - - -
164F LYS* 3.7 8.3 - - - +
174F LEU* 3.0 23.8 + - + +
175F HIS 3.6 7.2 - - - +
177F ALA* 1.3 75.7 - - - +
179F GLU* 1.3 62.9 + - - +
181F GLU 3.2 2.4 + - - -
182F ALA* 3.0 18.9 + - - +
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Residues in contact with GLU 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D THR* 4.8 13.6 - - + +
437D VAL 5.0 8.0 - - - +
105F LYS* 2.5 46.2 + - + -
175F HIS 3.0 17.1 + - - +
176F ILE* 3.9 10.9 - - - +
178F ARG* 1.3 77.3 - - - +
180F GLY* 1.3 56.9 + - - +
182F ALA* 3.5 8.2 + - + +
183F ALA* 2.9 29.2 + - + +
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Residues in contact with GLY 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F LYS* 3.5 26.2 + - - +
106F VAL* 3.9 7.7 - - - +
109F GLY* 4.2 7.4 - - - -
176F ILE 2.9 13.6 + - - -
177F ALA 3.1 4.2 + - - -
179F GLU* 1.3 74.0 - - - +
181F GLU* 1.3 58.9 + - - +
183F ALA* 3.3 2.8 + - - +
184F ARG* 2.9 29.0 + - - +
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Residues in contact with GLU 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F ARG* 3.9 13.3 - - + +
131F VAL* 3.9 21.5 - - + -
132F ARG* 3.1 50.8 + - + +
135F ILE* 3.9 17.7 - - + -
177F ALA 2.9 9.0 + - - +
178F ARG 3.6 7.2 - - - +
180F GLY* 1.3 75.8 - - - +
182F ALA* 1.3 63.2 + - - +
184F ARG* 3.2 25.1 + - - +
185F GLN* 3.0 33.7 + - - +
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Residues in contact with ALA 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411D THR* 5.4 6.3 - - + -
434D ARG* 5.8 3.8 - - - +
135F ILE* 4.1 21.6 - - + +
178F ARG 3.0 13.3 + - - +
179F GLU* 3.7 13.0 - - + +
181F GLU* 1.3 75.0 - - - +
183F ALA* 1.3 62.7 + - - +
185F GLN* 3.1 9.4 + - - +
186F HIS* 3.0 21.9 + - - +
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Residues in contact with ALA 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102F LEU* 3.7 31.8 - - + +
105F LYS* 3.6 27.6 - - + -
106F VAL* 3.9 3.1 - - + -
179F GLU* 2.9 19.2 + - + +
180F GLY 3.6 4.5 - - - +
181F GLU 3.3 0.2 - - - -
182F ALA* 1.3 75.8 - - - +
184F ARG* 1.3 64.2 + - - +
186F HIS* 3.2 3.9 + - - +
187F LEU* 2.9 25.1 + - - +
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Residues in contact with ARG 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560D GLN 2.8 24.4 + - - -
561D GLY 3.4 7.9 + - - -
562D ALA* 4.9 0.4 - - - +
106F VAL* 3.4 22.3 - - + +
132F ARG* 3.4 26.0 - - - +
180F GLY 2.9 14.7 + - - +
181F GLU* 3.3 20.8 + - - +
183F ALA* 1.3 76.1 - - - +
185F GLN* 1.3 91.6 + - - +
187F LEU* 3.3 3.4 + - - +
188F ILE* 3.0 40.5 + - + +
221F ILE* 3.9 16.6 - - - +
224F VAL* 4.2 13.7 - - + +
225F GLU* 3.4 32.6 + - - +
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Residues in contact with GLN 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561D GLY 3.7 5.2 + - - +
563D PRO* 3.5 35.6 - - + +
132F ARG* 4.7 0.6 - - - +
135F ILE* 4.7 6.0 - - + +
136F LEU* 3.5 29.8 - - + +
181F GLU* 3.0 28.4 + - - +
182F ALA* 3.3 10.1 - - - +
184F ARG* 1.3 107.9 - - - +
186F HIS* 1.3 58.3 + - - +
188F ILE* 3.4 2.1 + - - +
189F GLU* 3.0 41.3 + - - +
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Residues in contact with HIS 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F VAL* 4.4 20.6 - - + +
92F PRO* 5.0 8.9 + - + +
94F LEU* 4.3 19.4 - - + +
98F GLU* 6.4 1.3 - - - -
102F LEU* 3.7 21.7 - - + +
182F ALA 3.0 12.7 + - - +
183F ALA* 3.8 5.4 - - - +
185F GLN* 1.3 76.6 - - - +
187F LEU* 1.3 57.9 + - - +
189F GLU* 3.8 11.6 - - - +
190F ALA* 2.9 28.7 + - + +
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Residues in contact with LEU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F LEU* 3.6 17.9 - - + -
99F GLU* 4.6 13.0 - - + +
102F LEU* 3.7 16.0 - - + +
103F ALA* 4.1 29.2 - - + +
106F VAL* 4.5 4.7 - - + -
183F ALA 2.9 16.4 + - - +
184F ARG 3.3 4.7 + - - +
186F HIS* 1.3 72.5 - - - +
188F ILE* 1.3 65.3 + - - +
190F ALA* 3.1 3.0 + - - +
191F ASN* 3.0 49.7 + - - +
224F VAL* 3.8 31.4 - - + +
227F PHE* 5.4 1.6 - - + -
235F PHE* 4.7 14.8 - - + -
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Residues in contact with ILE 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D PRO* 3.6 30.5 - - + -
566D ILE* 3.8 17.7 - - + -
184F ARG* 3.0 47.0 + - + +
185F GLN* 3.7 3.6 - - - +
187F LEU* 1.3 75.4 - - - +
189F GLU* 1.3 64.1 + - - +
191F ASN 3.1 11.4 + - - -
192F LEU* 3.4 9.9 - - - +
220F LEU* 3.5 16.2 - - + +
221F ILE* 3.6 32.3 - - + -
224F VAL* 3.6 25.1 - - + -
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Residues in contact with GLU 189 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D PRO* 3.5 28.6 - - + +
564D GLU* 4.5 6.8 + - - +
565D ILE* 3.6 29.1 + - + +
88F ILE* 5.2 2.1 - - - +
91F VAL* 3.7 27.2 - - + +
185F GLN* 3.0 24.8 + - - +
186F HIS* 3.9 12.3 - - + +
188F ILE* 1.3 75.0 - - - +
190F ALA* 1.3 62.1 - - - +
191F ASN 3.5 0.2 + - - -
192F LEU* 3.6 25.7 + - + +
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Residues in contact with ALA 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F VAL* 3.7 13.1 - - + +
92F PRO 4.1 9.6 - - - +
93F LEU* 3.3 26.0 - - - +
94F LEU* 3.5 37.9 + - + +
186F HIS* 2.9 19.3 + - + +
187F LEU 3.6 4.3 - - - +
189F GLU* 1.3 78.9 - - - +
191F ASN* 1.3 60.4 + - - +
192F LEU 3.3 1.9 + - - -
193F ARG* 4.6 2.8 + - - +
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Residues in contact with ASN 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU* 4.4 4.9 - - - +
99F GLU* 5.1 1.4 + - - +
187F LEU* 3.0 40.8 + - - +
188F ILE 3.1 2.6 + - - -
190F ALA* 1.3 82.6 - - - +
192F LEU* 1.3 55.4 + - - +
193F ARG 3.1 5.4 - - - -
194F LEU* 3.1 26.3 + - + +
195F VAL 3.8 2.4 + - - -
220F LEU* 3.7 28.1 - - + +
235F PHE* 3.1 28.9 - - + +
236F SER 4.9 0.2 + - - -
6H T 2.8 37.7 + - - +
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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