Contacts of the helix formed by residues 159 - 185 (chain C) in PDB entry 5JRE
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 ASN 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C TRP* 3.9 19.5 - - + -
113C PHE* 3.5 14.8 - - - -
157C LEU* 4.8 0.2 - - - +
158C LYS* 1.3 76.0 - - - +
160C PHE* 1.3 66.1 + - - +
161C ASP* 3.0 31.6 + - - +
162C LEU* 3.0 23.2 + - + +
163C ARG* 3.0 23.3 + - - +
12D TYR* 3.1 7.4 + - - +
16D GLU* 3.5 15.6 + - - +
19D LYS* 5.0 9.5 - - - +
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Residues in contact with PHE 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C LYS 3.5 3.6 + - - -
159C ASN* 1.3 74.3 - - - +
161C ASP* 1.3 75.8 + - - +
163C ARG* 3.2 34.8 + - + +
164C ARG* 3.1 56.6 + - + +
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Residues in contact with ASP 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C PHE* 3.8 21.2 - - + -
159C ASN* 3.0 11.8 + - - +
160C PHE* 1.3 85.5 - - - +
162C LEU* 1.3 62.5 + - - +
164C ARG* 3.1 31.2 + - - +
165C LYS* 3.2 30.8 + - - +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TRP* 5.0 3.1 - - + -
112C LEU* 3.9 18.4 - - + +
113C PHE* 3.6 52.3 - - + +
116C GLY* 5.9 0.2 - - - -
157C LEU* 3.7 33.0 - - + +
159C ASN* 3.0 29.3 + - + +
161C ASP* 1.3 76.3 - - - +
163C ARG* 1.3 61.4 + - - +
165C LYS* 3.2 20.7 + - + +
166C LEU 3.3 8.7 + - - -
12D TYR* 3.7 29.8 - - + +
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Residues in contact with ARG 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C LEU* 3.7 31.4 - - + +
158C LYS* 3.1 22.5 + - - +
159C ASN 3.0 24.9 + - - +
160C PHE* 3.2 40.7 + - - +
162C LEU* 1.3 77.8 - - - +
164C ARG* 1.3 63.7 + - + +
166C LEU* 3.2 22.6 + - + +
167C ASP* 3.3 14.3 + - - +
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Residues in contact with ARG 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C PHE* 3.1 44.0 + - + +
161C ASP* 3.1 36.2 + - - +
162C LEU 3.2 0.2 - - - -
163C ARG* 1.3 82.7 - - + +
165C LYS* 1.3 60.7 - - + +
167C ASP* 3.2 14.5 + - - +
168C TYR* 3.0 21.3 + - - +
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Residues in contact with LYS 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLN* 3.8 6.2 - - - +
113C PHE* 3.7 47.3 - - - +
116C GLY* 3.6 28.0 - - - +
117C ASP* 3.0 24.1 + - - +
152C LEU* 5.6 1.3 - - + -
161C ASP* 3.2 16.8 + - - +
162C LEU* 3.2 18.6 + - + +
164C ARG* 1.3 76.6 - - + +
166C LEU* 1.3 57.0 + - - +
168C TYR* 3.2 12.3 - - + +
169C VAL* 2.9 32.3 + - - +
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Residues in contact with LEU 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C TYR* 3.6 27.8 - - + +
152C LEU* 3.7 22.8 - - + +
153C LEU* 3.6 49.1 - - + +
157C LEU* 4.0 12.3 - - + +
162C LEU 3.3 8.0 + - - +
163C ARG* 3.2 12.7 + - - +
165C LYS* 1.3 79.2 - - - +
167C ASP* 1.3 74.0 + - - +
169C VAL* 3.2 10.3 + - - +
170C SER 3.1 17.7 + - - -
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163C ARG* 3.3 12.8 + - - +
164C ARG* 3.2 16.6 + - + +
166C LEU* 1.3 85.8 - - - +
168C TYR* 1.3 65.7 + - - +
170C SER* 2.8 24.9 + - - +
171C ASN* 3.0 20.0 + - - +
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Residues in contact with TYR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C GLY 3.8 23.6 - - - -
117C ASP* 4.3 15.7 + - - -
119C ALA* 4.5 4.7 - - + -
120C GLY* 3.1 38.3 + - - -
164C ARG 3.0 13.7 + - - +
165C LYS* 3.2 12.3 - - + +
167C ASP* 1.3 76.0 - - - +
169C VAL* 1.3 65.1 + - - +
171C ASN* 3.2 12.3 + - + +
172C ILE* 2.9 40.8 + - + +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C GLY* 4.5 10.1 - - - +
119C ALA* 3.9 28.5 - - + -
145C LEU* 4.1 9.2 - - + +
148C LEU* 4.7 9.9 - - + -
149C TYR* 4.0 30.1 - - + +
152C LEU* 4.2 20.6 - - + -
165C LYS 2.9 19.1 + - - +
166C LEU* 3.2 8.2 + - - +
168C TYR* 1.3 74.2 - - + +
170C SER* 1.3 58.4 + - - +
172C ILE* 3.1 4.0 + - - +
173C ILE* 3.0 35.1 + - + +
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Residues in contact with SER 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C TYR* 3.5 35.0 + - - -
166C LEU 3.1 5.2 + - - -
167C ASP* 2.8 25.6 + - - +
169C VAL* 1.3 75.6 - - - +
171C ASN* 1.3 66.2 + - - +
173C ILE* 3.4 9.3 + - - +
174C ASN* 3.2 28.8 + - - +
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Residues in contact with ASN 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C ASP* 3.0 23.7 + - - +
168C TYR* 3.2 12.5 + - + +
170C SER* 1.3 78.7 + - - +
172C ILE* 1.3 65.5 - - + +
174C ASN* 3.3 15.1 + - - +
175C LYS* 3.1 26.8 + - + +
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Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ALA* 3.5 35.9 - - + +
120C GLY* 4.2 8.7 - - - -
123C LEU* 3.8 30.7 - - + +
145C LEU* 3.7 18.6 - - + -
168C TYR* 2.9 43.2 + - + +
169C VAL 3.1 7.6 + - - +
171C ASN* 1.3 78.3 - - + +
173C ILE* 1.3 63.3 + - - +
175C LYS* 3.2 11.8 + - + +
176C LEU* 3.0 21.0 + - + +
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Residues in contact with ILE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LYS* 4.6 7.2 - - + +
145C LEU* 3.7 46.7 - - + +
146C GLU* 3.9 26.5 - - + +
149C TYR* 4.0 18.8 - - + -
169C VAL* 3.0 20.3 + - + +
170C SER* 3.6 9.0 - - - +
172C ILE* 1.3 76.2 - - - +
174C ASN* 1.3 59.4 + - - +
176C LEU* 3.2 7.9 + - - +
177C ILE* 2.9 46.5 + - + +
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Residues in contact with ASN 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C SER* 3.2 16.3 + - - +
171C ASN* 3.5 18.0 + - - +
173C ILE* 1.3 81.3 - - - +
175C LYS* 1.3 61.9 + - + +
177C ILE* 3.4 15.4 + - - +
178C GLU* 3.0 28.0 + - + +
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LYS* 5.6 6.7 - - - +
178A GLU* 2.2 37.7 + - - -
123C LEU* 4.3 24.5 - - + -
171C ASN* 3.1 17.6 + - + +
172C ILE* 3.5 11.7 - - + +
174C ASN* 1.3 77.6 - - + +
176C LEU* 1.3 63.3 + - - +
178C GLU* 3.4 5.1 + - - +
179C PHE* 3.0 38.3 + - + -
178F GLU* 5.9 1.6 + - - -
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 3.9 18.3 - - + +
126C SER* 3.9 24.2 - - - +
130C LEU* 4.6 8.3 - - + -
138C ALA* 3.9 21.5 - - + +
141C ALA* 3.9 9.4 - - + -
142C LYS* 3.5 37.0 - - + +
145C LEU* 4.0 19.1 - - + -
172C ILE 3.0 11.1 + - - +
173C ILE* 3.2 9.8 + - - +
175C LYS* 1.3 73.0 - - - +
177C ILE* 1.3 66.2 + - - +
179C PHE* 3.1 7.7 + - + +
180C ILE* 2.9 31.3 + - + +
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Residues in contact with ILE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C LYS* 3.5 31.6 - - + -
146C GLU* 4.8 2.0 - - - +
173C ILE* 2.9 37.0 + - + +
174C ASN* 3.7 14.4 - - - +
176C LEU* 1.3 74.1 - - - +
178C GLU* 1.3 72.3 + - - +
180C ILE* 3.2 10.5 + - - +
181C ILE* 2.9 39.9 + - + +
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Residues in contact with GLU 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TRP* 4.0 26.7 - - + -
174C ASN* 3.0 19.8 + - + +
175C LYS* 3.9 6.3 - - - +
176C LEU 3.2 0.4 - - - -
177C ILE* 1.3 84.7 - - - +
179C PHE* 1.3 60.6 + - - +
181C ILE* 3.1 36.5 + - - +
182C TRP* 3.0 23.2 + - - +
182F TRP* 5.3 8.7 + - - +
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Residues in contact with PHE 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE* 6.2 0.2 - - + -
178A GLU* 3.6 43.3 - - + -
181A ILE* 4.2 21.1 - - + -
182A TRP* 4.3 18.6 - + - -
123C LEU* 3.7 25.1 - - + -
127C SER* 3.6 22.0 - - - -
130C LEU* 3.6 29.6 - - + -
175C LYS* 3.0 32.9 + - + -
176C LEU* 3.1 8.3 + - + +
178C GLU* 1.3 75.5 - - - +
180C ILE* 1.3 58.0 + - - +
182C TRP* 3.4 5.7 + - - +
183C LYS* 3.0 33.8 + - - +
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Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C LEU* 5.3 1.3 - - + -
135C ILE* 4.7 5.4 - - + -
138C ALA* 3.7 43.3 - - + +
139C LYS* 4.0 29.8 - - + +
142C LYS* 4.1 22.2 - - + -
176C LEU* 2.9 24.4 + - + +
177C ILE* 3.5 7.6 - - - +
179C PHE* 1.3 75.0 - - - +
181C ILE* 1.3 67.1 + - + +
183C LYS* 3.4 2.6 + - - +
184C SER* 2.9 40.9 + - - +
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Residues in contact with ILE 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C ILE* 2.9 24.5 + - + +
178C GLU* 3.1 43.7 - - - +
180C ILE* 1.3 80.3 - - + +
182C TRP* 1.3 66.6 + - + +
184C SER* 4.3 3.0 - - - -
185C LYS* 3.6 21.7 + - - +
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Residues in contact with TRP 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ILE* 3.5 19.9 + - + -
182A TRP* 2.6 64.2 + + + -
184A SER 5.1 5.9 - - - -
178C GLU 3.0 6.6 + - - +
179C PHE* 3.7 7.9 - - - +
181C ILE* 1.3 82.3 - - + +
183C LYS* 1.3 71.8 + - + +
184C SER 3.4 0.5 + - - -
185C LYS* 3.5 24.8 + - - +
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Residues in contact with LYS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ILE* 4.2 36.9 + - + +
184A SER* 4.8 18.7 + - - -
130C LEU* 3.9 44.8 + - + +
131C ILE* 4.8 7.6 + - - +
133C GLY* 5.4 4.8 - - - -
135C ILE* 3.1 27.3 - - + +
179C PHE 3.0 16.9 + - - +
180C ILE* 4.4 1.6 - - - +
182C TRP* 1.3 82.8 - - + +
184C SER* 1.3 61.5 + - - +
185C LYS 3.5 0.4 + - - -
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Residues in contact with SER 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ILE* 3.6 24.7 - - - +
139C LYS* 4.2 10.2 + - - -
180C ILE* 2.9 24.5 + - - +
181C ILE* 4.3 3.8 - - - -
182C TRP 3.3 0.2 - - - -
183C LYS* 1.3 79.5 - - - +
185C LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ILE* 3.6 11.9 + - - +
182C TRP* 3.5 25.3 + - - +
183C LYS 3.5 2.0 - - - -
184C SER* 1.3 85.7 - - - +
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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