Contacts of the helix formed by residues 178 - 215 (chain A) in PDB entry 5IWS
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 178 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 3.6 26.9 - + + +
163A TYR* 3.8 25.4 - + + -
166A LEU* 3.6 28.7 - - + -
173A PHE* 3.1 24.9 + - + +
174A ASN* 4.3 0.2 - - - -
175A GLY 3.0 19.8 + - - +
177A ARG* 1.3 78.0 - - - +
179A VAL* 1.3 64.6 + - - +
180A PRO* 3.4 2.2 - - - -
181A PHE* 3.2 33.9 + + + +
182A VAL* 3.2 40.3 + - + +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 5.1 0.2 - - - +
86A ALA* 3.8 28.7 - - + -
156A LEU* 4.2 3.4 - - + +
157A TYR* 3.7 42.8 - - + +
160A TYR* 3.7 31.0 - - + +
161A TYR* 3.9 4.3 - - - +
175A GLY 4.0 3.1 - - - +
176A LYS 4.0 5.6 - - - +
178A PHE* 1.3 76.9 - - - +
180A PRO* 1.3 69.8 - - + +
182A VAL* 3.1 7.9 + - - +
183A VAL* 2.9 30.1 + - + +
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Residues in contact with PRO 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 4.7 18.6 - - + -
86A ALA* 6.5 0.2 - - - -
89A LEU* 3.8 20.6 - - + +
176A LYS 3.3 17.0 - - - +
177A ARG* 3.8 10.3 - - - +
178A PHE 3.5 3.1 - - - -
179A VAL* 1.3 90.4 - - + +
181A PHE* 1.3 60.5 + - - +
183A VAL* 3.3 5.6 + - + +
184A ILE* 3.1 31.0 + - + +
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Residues in contact with PHE 181 (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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173A PHE* 6.1 3.6 - - + -
177A ARG 4.9 3.1 + - - +
178A PHE* 3.2 39.3 + + + +
179A VAL 3.2 0.8 - - - -
180A PRO* 1.3 76.7 - - - +
182A VAL* 1.3 69.0 + - + +
184A ILE* 3.2 20.5 + - + +
185A VAL* 3.1 43.5 + - + +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 3.5 10.0 - - + +
160A TYR* 3.6 35.9 - - + -
178A PHE* 3.4 46.2 - - + +
179A VAL* 3.1 8.4 + - - +
181A PHE* 1.3 74.9 - - + +
183A VAL* 1.3 66.8 + - - +
185A VAL* 3.3 4.8 + - + +
186A TRP* 3.0 46.1 + - + +
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Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 3.8 32.8 - - + +
89A LEU* 3.8 16.6 - - + -
90A ALA* 3.5 37.9 - - + +
93A LEU* 5.0 0.7 - - + -
153A GLY* 5.1 2.0 - - - -
156A LEU* 3.7 17.4 - - + +
179A VAL* 2.9 23.0 + - + +
180A PRO* 3.5 8.7 - - + +
181A PHE 3.2 0.2 - - - -
182A VAL* 1.3 77.9 - - - +
184A ILE* 1.3 56.8 + - - +
187A SER* 2.8 37.8 + - - +
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Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.7 5.4 - - + -
93A LEU* 3.6 29.6 - - + -
97A ILE* 5.0 1.2 - - + +
180A PRO* 3.1 18.7 + - + +
181A PHE* 3.2 20.4 + - + +
183A VAL* 1.3 76.5 - - - +
185A VAL* 1.3 61.6 + - + +
187A SER* 4.2 1.0 - - - -
188A THR* 2.9 33.6 + - - +
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Residues in contact with VAL 185 (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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181A PHE* 3.1 41.7 + - + +
182A VAL* 3.7 8.7 - - + +
183A VAL 3.2 0.2 - - - -
184A ILE* 1.3 80.3 - - + +
186A TRP* 1.3 70.3 + - + +
188A THR* 3.3 7.6 + - - -
189A VAL* 3.1 32.7 + - + +
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Residues in contact with TRP 186 (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 LEU* 4.0 14.4 - - + -
156A LEU* 3.5 26.5 - - + +
160A TYR* 4.8 8.1 + - - -
182A VAL* 3.0 45.3 + - + +
185A VAL* 1.3 84.4 - - + +
187A SER* 1.3 57.2 + - - +
188A THR 3.2 0.2 - - - -
189A VAL* 3.7 30.4 - - + +
190A THR* 2.6 40.4 + - - -
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA* 3.3 30.8 - - - +
93A LEU* 4.0 21.8 - - - -
94A THR* 3.4 17.8 + - - -
97A ILE* 4.0 2.9 - - - +
152A LEU* 3.9 4.0 - - - +
183A VAL* 2.8 24.1 + - - +
184A ILE 4.2 1.8 - - - -
186A TRP* 1.3 74.7 - - - +
188A THR* 1.3 60.4 + - - +
190A THR* 3.8 3.0 - - - -
191A ALA* 2.8 31.4 + - - +
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Residues in contact with THR 188 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ILE* 3.4 26.7 - - + +
184A ILE* 2.9 20.6 + - - +
185A VAL* 3.4 10.4 - - - -
186A TRP 3.2 0.2 - - - -
187A SER* 1.3 74.5 - - - +
189A VAL* 1.3 61.2 + - + +
191A ALA* 3.3 1.6 + - - +
192A ILE* 2.9 53.7 + - + +
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Residues in contact with VAL 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.1 22.9 + - + +
186A TRP* 3.7 35.2 - - + +
188A THR* 1.3 77.4 - - + +
190A THR* 1.3 64.9 + - - +
192A ILE* 3.4 9.8 + - + +
193A VAL* 3.0 33.4 + - + +
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Residues in contact with THR 190 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 4.2 8.1 - - + +
148A ILE* 3.8 30.3 - - + -
152A LEU* 3.5 19.6 - - + +
186A TRP* 2.6 30.2 + - - -
187A SER* 3.8 7.4 - - - -
189A VAL* 1.3 73.6 - - - +
191A ALA* 1.3 57.7 + - - +
193A VAL* 3.3 7.2 + - + +
194A LEU* 2.8 47.5 + - + +
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Residues in contact with ALA 191 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 3.6 26.0 - - - +
97A ILE* 3.6 27.4 - - + -
98A THR* 3.9 6.1 + - - +
101A ILE* 4.3 0.7 - - - -
187A SER 2.8 21.9 + - - +
188A THR 3.9 0.2 - - - +
190A THR* 1.3 73.9 - - - +
192A ILE* 1.3 51.2 + - - +
194A LEU* 3.7 7.5 - - - +
195A SER* 2.7 42.4 + - - -
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Residues in contact with ILE 192 (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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97A ILE* 5.3 0.4 - - + -
101A ILE* 3.9 22.2 - - + -
188A THR* 2.9 40.1 + - + +
189A VAL* 3.7 9.2 - - + +
191A ALA* 1.3 76.6 - - - +
193A VAL* 1.3 65.8 + - + +
195A SER* 3.3 3.5 + - - -
196A LEU* 3.3 32.5 + - + +
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Residues in contact with VAL 193 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL* 3.0 27.3 + - + +
190A THR* 3.7 5.4 - - - +
192A ILE* 1.3 79.3 - - + +
194A LEU* 1.3 62.2 + - + +
196A LEU* 3.1 6.0 + - + -
197A LEU* 2.9 48.9 + - + +
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Residues in contact with LEU 194 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 3.6 28.5 - - + -
98A THR* 4.6 3.6 - - - +
139A LEU* 3.9 3.0 - - - +
141A MSE 3.6 33.9 - - - -
144A PHE* 5.1 2.5 - - + -
145A VAL* 4.6 4.5 - - + -
148A ILE* 4.1 23.3 - - + -
190A THR* 2.8 32.6 + - + +
191A ALA* 3.7 5.4 - - - +
193A VAL* 1.3 75.1 - - + +
195A SER* 1.3 58.4 + - - +
197A LEU* 5.1 1.8 - - + -
198A TRP* 2.9 53.5 + - + +
199A PRO* 3.2 2.1 - - - +
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Residues in contact with SER 195 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A THR* 3.2 15.4 + - - -
101A ILE* 3.3 27.4 - - - +
102A PHE* 3.4 39.6 - - - -
118A SER* 5.5 2.1 - - - -
119A VAL* 5.7 2.1 + - - +
139A LEU* 4.1 3.4 - - - -
191A ALA 2.7 27.1 + - - -
192A ILE 3.6 6.3 - - - -
193A VAL 3.3 0.4 - - - -
194A LEU* 1.3 72.7 - - - +
196A LEU* 1.3 61.7 + - - +
199A PRO* 3.4 10.1 - - - +
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Residues in contact with LEU 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 3.7 38.6 - - + +
120A LEU* 3.3 34.0 + - + +
192A ILE* 3.3 22.4 + - + +
193A VAL* 3.1 9.9 + - + +
194A LEU 3.1 0.4 - - - -
195A SER* 1.3 83.7 - - - +
197A LEU* 1.3 72.6 + - + +
198A TRP 3.7 0.4 - - - -
199A PRO* 4.1 4.9 - - - +
200A PHE 4.5 1.6 + - - -
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Residues in contact with LEU 197 (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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120A LEU* 5.2 10.1 - - + -
193A VAL* 2.9 44.7 + - + +
194A LEU* 5.1 2.2 - - + -
196A LEU* 1.3 92.1 - - + +
198A TRP* 1.3 66.7 + - - +
199A PRO 3.5 0.7 - - - -
200A PHE* 3.2 15.6 + - + +
201A ILE* 3.1 29.9 + - + +
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Residues in contact with TRP 198 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.3 16.2 - - + -
140A ASN 2.9 21.0 + - - -
141A MSE 3.3 39.1 - - + +
144A PHE* 3.4 49.4 - + + -
194A LEU* 2.9 36.2 + - + +
197A LEU* 1.3 75.7 - - - +
199A PRO* 1.3 55.0 - - + +
201A ILE* 2.9 33.8 + - + +
202A GLN* 2.5 60.4 + - + +
205A LEU* 4.5 12.3 - - + -
242A MSE 5.1 5.2 - - + -
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Residues in contact with PRO 199 (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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102A PHE* 4.0 8.5 - - + -
118A SER* 4.4 5.6 - - - -
120A LEU 6.0 0.2 - - - +
121A ALA* 3.5 14.5 - - + +
124A LEU* 3.8 29.8 - - + -
129A TYR* 3.5 15.0 - - + -
139A LEU* 3.9 10.5 - - + -
194A LEU 3.2 13.5 - - - +
195A SER 3.4 20.4 - - - +
196A LEU 4.1 3.6 - - - +
197A LEU 3.7 2.0 - - - -
198A TRP* 1.3 90.9 - - + +
200A PHE* 1.3 54.9 + - - +
202A GLN* 4.4 0.9 - - + -
203A SER* 3.0 29.6 + - - -
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Residues in contact with PHE 200 (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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120A LEU* 3.4 40.4 - - + +
121A ALA* 4.2 6.6 - - - +
196A LEU 4.5 1.8 + - - +
197A LEU* 3.2 18.4 + - + +
198A TRP 3.1 0.6 - - - -
199A PRO* 1.3 78.3 - - - +
201A ILE* 1.3 69.7 + - + +
203A SER* 3.6 5.0 + - - -
204A GLY* 3.5 15.1 + - - -
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Residues in contact with ILE 201 (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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144A PHE* 5.7 3.6 - - + -
197A LEU* 3.1 20.1 + - + +
198A TRP* 2.9 46.8 + - + +
200A PHE* 1.3 81.4 - - + +
202A GLN* 1.3 64.4 + - - +
204A GLY* 3.1 4.2 + - - -
205A LEU* 3.1 32.0 + - + +
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Residues in contact with GLN 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP 4.1 8.2 + - - +
129A TYR* 3.6 30.3 - - + +
140A ASN* 3.2 33.2 + - - +
198A TRP* 2.5 42.1 + - + +
201A ILE* 1.3 74.4 - - - +
203A SER* 1.3 55.4 + - - +
205A LEU* 3.4 15.9 + - - +
206A ASN* 2.9 62.1 + - - +
242A MSE 4.6 7.7 - - - +
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Residues in contact with SER 203 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 4.5 10.7 + - - +
129A TYR* 3.2 24.6 + - - -
199A PRO 3.0 17.6 + - - -
200A PHE* 3.8 8.1 - - - -
201A ILE 3.2 0.2 - - - -
202A GLN* 1.3 77.2 - - - +
204A GLY* 1.3 60.9 + - - +
206A ASN* 4.0 2.9 - - - +
207A GLU* 3.2 38.3 + - - +
210A ARG* 4.8 0.3 + - - -
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Residues in contact with GLY 204 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A PHE 3.5 6.3 + - - -
201A ILE 3.1 7.5 + - - -
203A SER* 1.3 77.9 - - - +
205A LEU* 1.3 61.1 + - - +
207A GLU* 3.4 9.8 + - - +
208A PHE* 2.8 30.7 + - - +
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Residues in contact with LEU 205 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 4.5 7.9 - - + -
201A ILE* 3.1 30.7 + - + +
202A GLN* 3.4 22.4 + - - +
204A GLY* 1.3 77.0 - - - +
206A ASN* 1.3 58.8 + - - +
208A PHE* 3.6 15.7 - - + +
209A GLY* 2.8 26.3 + - - -
242A MSE 3.7 31.4 - - + -
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Residues in contact with ASN 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP* 3.1 30.6 + - - +
129A TYR* 3.8 17.5 - - - +
202A GLN* 2.9 45.3 + - - +
203A SER* 4.0 4.0 - - - +
205A LEU* 1.3 77.8 - - - +
207A GLU* 1.3 58.1 + - - +
209A GLY* 3.3 1.9 + - - -
210A ARG* 3.0 51.7 + - - +
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Residues in contact with GLU 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 3.2 27.5 + - - +
204A GLY* 3.8 8.3 - - - +
205A LEU 3.4 0.2 - - - -
206A ASN* 1.3 74.4 - - - +
208A PHE* 1.3 60.8 + - - +
210A ARG* 3.3 28.0 + - - +
211A TRP* 3.0 26.2 + - - +
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Residues in contact with PHE 208 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY 2.8 22.5 + - - +
205A LEU* 3.6 16.4 - - + +
207A GLU* 1.3 72.0 - - - +
209A GLY* 1.3 64.9 + - - +
211A TRP* 3.1 30.6 + + + +
212A ILE* 3.1 53.8 + - + +
226A VAL* 5.7 6.1 - - + -
230A LEU* 4.1 27.4 - - + -
243A LEU* 5.4 1.6 - - + -
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Residues in contact with GLY 209 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU 2.8 20.5 + - - -
206A ASN* 3.3 2.7 + - - -
208A PHE* 1.3 75.6 - - - +
210A ARG* 1.3 60.4 + - - +
212A ILE* 3.3 7.3 + - - +
213A ALA* 3.3 19.4 + - - +
252A LEU* 3.4 29.3 - - - +
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Residues in contact with ARG 210 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP* 4.8 11.5 + - - -
203A SER 4.8 0.2 + - - -
206A ASN* 3.0 33.7 + - - +
207A GLU* 3.3 38.7 + - - +
208A PHE 3.3 0.2 - - - -
209A GLY* 1.3 76.1 - - - +
211A TRP* 1.3 60.2 + - - +
213A ALA* 3.8 6.3 + - - +
214A ALA* 3.3 24.3 + - - +
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Residues in contact with TRP 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU 3.0 14.3 + - - +
208A PHE* 3.1 36.9 + + + +
210A ARG* 1.3 77.2 - - - +
212A ILE* 1.3 64.9 + - + +
214A ALA* 4.0 3.8 - - + +
215A SER* 2.3 61.5 + - - -
226A VAL* 5.5 12.1 - - + -
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Residues in contact with ILE 212 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A PHE* 3.1 48.2 + - + +
209A GLY* 3.3 11.4 + - - +
211A TRP* 1.3 85.2 - - + +
213A ALA* 1.3 57.9 + - - +
215A SER* 3.6 3.0 - - - -
216A LYS* 2.9 37.9 + - + +
227A TYR* 5.3 6.3 - - + -
230A LEU* 5.9 0.2 - - + -
243A LEU* 3.6 28.3 - - + -
247A MSE 5.1 8.1 - - - -
252A LEU* 4.0 21.1 - - + +
306A PHE* 5.7 5.8 - - + -
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Residues in contact with ALA 213 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLY 3.3 13.4 + - - +
210A ARG* 4.3 6.1 - - - +
212A ILE* 1.3 81.0 - - - +
214A ALA* 1.3 62.4 + - - +
216A LYS* 3.8 12.1 + - - +
217A ASP* 5.1 2.6 - - - +
251A GLU 4.6 3.8 - - - +
252A LEU* 3.4 36.7 + - - +
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Residues in contact with ALA 214 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ARG 3.3 19.0 + - - +
211A TRP* 4.3 5.2 - - + +
213A ALA* 1.3 79.9 - - - +
215A SER* 1.3 58.8 + - - +
216A LYS 3.4 0.6 + - - -
217A ASP 5.0 0.7 + - - -
218A SER* 4.2 10.2 + - - -
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Residues in contact with SER 215 (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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211A TRP* 2.3 59.6 + - - -
212A ILE* 3.6 2.6 + - - -
214A ALA* 1.3 76.3 - - - +
216A LYS* 1.3 64.3 + - - +
217A ASP 3.4 2.2 + - - -
218A SER* 3.8 16.2 - - - -
219A ALA* 3.6 22.0 + - - +
223A ALA* 4.3 3.1 - - - +
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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) + - + + + + + -
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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