Contacts of the helix formed by residues 178 - 207 (chain A) in PDB entry 3N3B
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 LEU 178 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.4 43.7 + - + +
44A ALA* 3.8 11.7 - - + +
45A TRP* 4.0 24.2 - - + +
48A LEU* 3.8 19.7 - - + -
56A THR* 4.9 6.5 - - + -
112A LEU* 4.2 15.5 - - + -
169A PRO* 5.0 2.0 - - + +
172A PHE* 3.7 31.0 - - + -
176A GLY 4.3 0.2 + - - -
177A LYS* 1.3 74.9 - - + +
179A THR* 1.3 64.5 + - - +
180A ASN 3.4 2.9 - - - -
181A THR* 3.5 13.6 + - + +
182A ALA* 3.2 20.6 + - - +
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASP* 3.6 3.2 + - - -
173A SER* 4.9 11.0 - - - +
176A GLY* 4.0 30.1 - - - +
177A LYS 4.0 1.6 - - - +
178A LEU* 1.3 76.7 - - - +
180A ASN* 1.3 70.1 + - - +
182A ALA* 3.4 8.9 + - - +
183A ASP* 3.0 34.2 + - - +
186A ARG* 4.1 3.2 + - - -
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Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.4 17.4 - - + +
37A PRO* 3.3 41.8 + - - +
38A LEU* 4.2 3.1 - - - -
40A ASN* 3.4 25.8 + - - +
41A ASP* 2.8 26.4 + - - +
179A THR* 1.3 83.3 + - - +
181A THR* 1.3 63.2 + - - +
183A ASP* 3.3 13.3 + - - +
184A LEU* 3.1 18.0 + - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.0 13.6 - - - +
41A ASP* 2.8 27.8 + - - -
56A THR* 6.1 0.2 - - + -
60A PHE* 4.2 18.4 - - + -
108A ILE* 4.0 32.0 - - + +
112A LEU* 3.8 19.0 - - + +
169A PRO* 5.0 4.7 - - + -
178A LEU* 3.8 18.0 - - + +
179A THR 3.4 0.2 - - - -
180A ASN* 1.3 72.7 - - - +
182A ALA* 1.3 57.5 + - - +
184A LEU* 3.3 4.5 + - - +
185A ILE* 3.0 33.6 + - + +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 3.5 34.5 - - + +
170A MET* 3.8 4.2 - - + +
173A SER* 3.8 17.0 - - - +
178A LEU 3.2 13.4 + - - +
179A THR 3.5 9.6 - - - +
180A ASN 3.2 0.2 - - - -
181A THR* 1.3 74.8 - - - +
183A ASP* 1.3 59.1 + - - +
185A ILE* 3.3 2.1 + - - +
186A ARG* 2.9 42.4 + - - +
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 4.8 7.4 - - + -
179A THR* 3.0 19.4 + - - +
180A ASN* 3.3 19.7 + - - +
182A ALA* 1.3 74.6 - - - +
184A LEU* 1.3 61.6 + - - +
186A ARG* 2.7 37.4 + - - +
187A LEU* 3.3 27.4 + - + +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 4.3 7.9 - - + -
33A PRO* 4.0 24.2 - - + -
36A VAL* 4.1 14.3 - - + +
38A LEU* 3.8 34.1 - - + -
104A SER* 3.5 29.2 - - - +
108A ILE* 4.3 17.3 - - + -
180A ASN 3.1 11.5 + - - +
181A THR* 3.5 9.6 - - - +
182A ALA 3.3 0.2 - - - -
183A ASP* 1.3 74.3 - - - +
185A ILE* 1.3 66.2 + - + +
187A LEU* 3.2 22.2 + - - +
188A ILE* 3.3 20.3 + - + +
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Residues in contact with ILE 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.6 29.2 - - + -
105A TYR* 4.1 6.5 - - + -
108A ILE* 4.6 2.5 - - + -
166A PHE* 3.6 29.8 - - + -
169A PRO* 3.8 29.6 - - + -
170A MET* 4.1 3.6 - - + -
181A THR* 3.0 22.2 + - + +
182A ALA 3.7 4.9 - - - +
183A ASP 3.3 0.2 - - - -
184A LEU* 1.3 81.5 - - + +
186A ARG* 1.3 58.8 + - - +
188A ILE* 3.1 25.2 + - + +
189A ILE* 2.8 37.9 + - + +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A MET* 4.0 19.0 - - + +
173A SER* 3.5 28.9 + - - -
179A THR* 4.1 3.8 + - - +
182A ALA* 2.9 20.2 + - - +
183A ASP* 2.7 41.7 + - - +
184A LEU 3.3 0.4 - - - -
185A ILE* 1.3 75.6 - - - +
187A LEU* 1.3 57.4 + - - +
189A ILE* 3.8 11.0 - - + +
190A ARG* 2.9 28.9 + - - +
285A ALA* 2.8 35.8 + - - +
286A LEU* 4.3 11.4 - - - +
288A PRO* 5.4 10.5 - - - +
85D ASN 4.6 2.6 - - - +
87D GLY* 5.8 2.7 - - - -
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.6 41.3 + - + +
35A LYS* 6.5 0.2 - - + -
36A VAL* 3.9 27.4 - - + -
183A ASP* 3.3 16.2 + - + +
184A LEU* 3.2 8.9 + - - +
185A ILE 3.2 0.4 - - - -
186A ARG* 1.3 74.3 - - - +
188A ILE* 1.3 62.8 + - - +
190A ARG* 3.6 39.1 + - - +
191A ASP* 3.3 27.2 + - - +
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.6 17.0 - - + -
67A ASP* 4.9 0.2 - - - +
101A HIS* 3.8 31.6 - - + +
104A SER* 3.7 21.5 - - - +
105A TYR* 3.8 22.0 - - + +
166A PHE* 3.8 21.8 - - + -
184A LEU* 3.6 11.9 - - + +
185A ILE* 3.1 30.2 + - + +
187A LEU* 1.3 74.5 - - - +
189A ILE* 1.3 59.6 + - - +
191A ASP* 3.1 5.2 + - - +
192A GLU* 3.0 31.6 + - + +
320A MN 4.7 2.0 - - - +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 3.6 12.9 + - + +
166A PHE* 4.0 33.7 - - + -
170A MET* 4.3 19.5 - - + -
185A ILE* 2.8 37.9 + - + +
186A ARG* 3.8 12.1 - - + +
188A ILE* 1.3 76.8 - - - +
190A ARG* 1.3 56.9 + - - +
192A GLU* 3.2 6.5 + - - +
193A ALA* 3.0 29.1 + - - +
286A LEU* 5.1 6.5 - - + -
85D ASN* 3.4 40.3 - - + +
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.7 25.9 - - - +
29A ASN* 3.2 52.4 + - - +
30A PHE 5.3 0.2 + - - -
31A TRP* 4.4 4.6 - - - +
186A ARG 2.9 18.5 + - - +
187A LEU* 3.6 34.5 + - - +
188A ILE 3.3 0.2 - - - -
189A ILE* 1.3 76.1 - - - +
191A ASP* 1.3 63.6 + - - +
193A ALA* 3.7 5.2 + - - +
194A VAL* 3.6 22.0 + - - +
85D ASN 3.8 12.5 + - - +
86D PHE* 4.1 16.3 - - + +
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Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.6 13.2 - - - +
29A ASN* 4.4 19.6 - - - +
31A TRP* 2.8 26.8 + - - -
97A MET* 3.4 14.0 - - - +
101A HIS* 3.0 27.7 + - + +
187A LEU 3.3 8.3 + - - +
188A ILE 3.1 8.4 + - - +
190A ARG* 1.3 81.3 + - - +
192A GLU* 1.3 56.9 + - - +
194A VAL* 3.2 5.0 + - - +
195A HIS* 3.0 42.2 + - - +
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 3.1 1.0 - - - +
101A HIS* 3.1 9.0 - - - -
158A GLU* 3.0 37.1 - - + +
159A SER* 4.1 6.8 + - - -
162A PHE* 5.9 0.7 - - + -
163A TYR* 5.3 4.3 - - - +
166A PHE* 5.1 7.4 - - + -
188A ILE* 3.0 26.9 + - + +
189A ILE* 3.2 7.2 + - - +
191A ASP* 1.3 73.6 - - - +
193A ALA* 1.3 60.6 + - - +
195A HIS* 3.2 8.9 + - - +
196A GLY* 3.0 26.7 + - - -
320A MN 2.2 35.6 + - - +
321A MN 2.2 29.3 + - - -
322A PEO 5.0 0.9 - - - -
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE 3.0 16.8 + - - +
190A ARG* 3.8 7.4 - - - +
192A GLU* 1.3 78.4 - - - +
194A VAL* 1.3 59.4 + - - +
196A GLY* 4.4 0.3 - - - -
197A TYR* 3.4 21.3 + - - +
264A ASN* 5.1 1.4 + - - +
322A PEO 4.0 16.5 + - - +
83D ASN* 4.3 5.3 + - - +
85D ASN* 3.6 27.8 - - + +
86D PHE* 4.1 21.4 - - + -
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 3.9 27.8 - - + -
25A ARG* 4.1 24.0 - - + -
26A LEU* 3.8 24.0 - - + -
29A ASN* 5.6 1.1 - - - +
190A ARG 3.6 15.0 - - - +
191A ASP 3.2 7.0 + - - +
193A ALA* 1.3 75.9 - - - +
195A HIS* 1.3 58.1 + - - +
197A TYR* 3.3 8.3 + - + +
198A TYR* 2.9 29.5 + - - +
86D PHE* 3.8 23.3 - - + -
134D FMN 5.3 6.1 - - + -
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Residues in contact with HIS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.7 23.5 - - + +
93A ASN* 5.1 0.6 + - - -
94A ILE* 3.6 49.9 - - + +
97A MET* 4.7 6.7 - - + +
98A GLU* 3.4 5.6 + - - -
101A HIS* 4.4 10.1 - + - -
191A ASP* 3.0 30.1 + - + +
192A GLU* 3.2 21.6 + - - +
194A VAL* 1.3 76.1 - - - +
196A GLY* 1.3 56.1 + - - +
198A TYR* 3.9 3.0 - - - +
199A ILE* 3.0 46.7 + - + +
321A MN 2.4 31.4 + - - +
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Residues in contact with GLY 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 3.8 13.4 - - - +
159A SER* 3.6 23.1 - - - -
192A GLU 3.0 11.6 + - - -
193A ALA 4.4 0.2 - - - -
195A HIS* 1.3 73.7 - - - +
197A TYR* 1.3 60.0 + - - +
199A ILE* 5.0 0.9 - - - -
200A GLY* 3.0 27.4 + - - -
264A ASN* 3.5 15.3 - - - +
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Residues in contact with TYR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 2.8 30.6 + - + -
22A VAL* 4.5 12.6 - - + -
193A ALA 3.4 19.6 + - - +
194A VAL* 3.3 8.5 + - + +
195A HIS 3.3 0.2 - - - -
196A GLY* 1.3 76.9 - - - +
198A TYR* 1.3 60.1 + + - +
200A GLY* 3.7 0.5 - - - -
201A TYR* 2.8 40.2 + - + +
264A ASN* 3.9 19.5 + - - +
11D SER* 2.8 37.4 + - - -
13D ASN* 3.9 11.0 - - - -
49D TYR* 3.5 4.0 + - - -
111D LEU* 5.1 0.9 - - + -
134D FMN 3.5 59.0 - + + -
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Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS* 4.0 17.7 - - + -
19A ASP* 2.6 32.5 + - - -
22A VAL* 3.4 31.6 - - + -
26A LEU* 6.2 0.2 - - + -
87A GLU* 3.3 34.4 - - + +
90A VAL* 3.6 27.0 - - + +
91A LEU* 5.1 5.8 - - + -
94A ILE* 4.3 13.2 - - + -
194A VAL 2.9 17.7 + - - +
195A HIS* 3.9 4.0 - - - +
197A TYR* 1.3 78.6 - + - +
199A ILE* 1.3 65.0 + - + +
201A TYR* 3.1 11.1 + + - +
202A LYS* 2.9 50.0 + - + +
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Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 4.0 19.7 - - + -
91A LEU* 5.1 2.9 - - + -
94A ILE* 5.0 16.6 - - + -
151A LYS* 3.7 45.8 - - + +
154A SER* 3.5 25.4 - - - +
155A VAL* 3.8 7.9 - - + -
195A HIS* 3.0 31.6 + - + +
196A GLY* 5.3 0.9 - - - -
198A TYR* 1.3 82.7 - - + +
200A GLY* 1.3 57.1 + - - +
202A LYS* 3.4 5.9 + - - +
203A TYR* 2.9 27.4 + - - +
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Residues in contact with GLY 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 3.8 8.2 - - - +
196A GLY 3.0 17.9 + - - -
199A ILE* 1.3 75.6 - - - +
201A TYR* 1.3 62.1 + - - +
203A TYR* 3.3 9.6 - - - +
204A GLN* 3.2 27.9 + - - +
264A ASN 3.2 25.4 - - - +
265A LEU* 4.2 1.6 - - - -
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Residues in contact with TYR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 2.7 38.9 + - - -
18A LYS* 3.8 23.8 - - + -
197A TYR* 2.8 26.0 + - + +
198A TYR* 3.1 11.2 + + - +
200A GLY* 1.3 73.9 - - - +
202A LYS* 1.3 74.3 + - + +
204A GLN* 3.3 14.4 + - + +
205A LYS* 3.1 53.4 + - + +
264A ASN 4.0 0.4 + - - -
10D SER* 3.5 36.6 + - - -
11D SER* 3.8 26.5 - - - -
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 3.9 13.7 + - - +
19A ASP* 2.9 36.0 + - - -
83A LEU* 4.4 19.3 - - + +
84A THR* 4.1 4.4 + - - +
87A GLU* 3.2 33.8 + - - +
151A LYS* 3.9 16.2 - - - -
198A TYR* 2.9 43.2 + - + +
199A ILE* 3.8 6.1 - - - +
201A TYR* 1.3 89.4 - - + +
203A TYR* 1.3 63.5 + - - +
205A LYS* 3.8 3.8 - - + +
206A ASN* 2.8 34.2 + - - +
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 3.6 44.0 - - + +
151A LYS* 3.7 15.6 - - + +
152A ILE* 3.6 36.2 - - + +
199A ILE 2.9 15.0 + - - +
200A GLY* 3.3 10.8 - - - +
201A TYR 3.2 0.2 - - - -
202A LYS* 1.3 76.9 - - - +
204A GLN* 1.3 60.0 + - + +
206A ASN 3.3 2.1 + - - -
207A MET* 3.0 52.7 + - + +
218A LEU* 3.9 8.4 + - + +
265A LEU* 3.7 38.4 - - + -
267A TYR* 2.7 35.6 + + - -
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A GLY 3.2 10.2 + - - +
201A TYR* 3.7 11.6 - - + +
203A TYR* 1.3 76.0 - - + +
205A LYS* 1.3 63.3 + - + +
207A MET* 3.3 22.6 + - + +
208A GLU* 3.5 15.6 + - - +
263A MET 4.5 0.4 + - - -
264A ASN 2.9 27.5 + - - -
265A LEU 3.3 27.2 - - - +
266A GLY* 3.4 6.5 - - - +
11D SER* 4.2 5.6 + - - +
16D ARG* 3.1 37.3 + - - +
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP* 3.9 17.3 + - - +
83A LEU* 4.0 24.0 - - + +
201A TYR* 3.1 50.9 + - + +
202A LYS* 3.8 6.1 - - + +
203A TYR 3.3 0.2 - - - -
204A GLN* 1.3 76.3 - - + +
206A ASN* 1.3 60.7 + - - +
208A GLU* 3.4 43.7 + - - +
209A LYS* 4.3 6.2 + - - +
10D SER* 5.9 1.1 - - - +
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Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASP* 4.4 7.0 + - - +
83A LEU* 3.4 34.9 - - - +
87A GLU* 5.5 0.8 + - - -
147A PRO* 6.4 2.2 - - - -
148A LEU* 3.5 26.8 - - + +
151A LYS* 3.8 21.6 - - - +
202A LYS* 2.8 26.7 + - - +
203A TYR 3.3 0.2 + - - -
205A LYS* 1.3 72.7 - - - +
207A MET* 1.3 60.5 + - - +
208A GLU 3.1 5.9 + - - -
209A LYS* 3.4 29.2 + - - +
210A ILE* 4.1 10.6 - - - +
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Residues in contact with MET 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A LEU* 3.9 11.7 - - - -
203A TYR* 3.0 53.4 + - + +
204A GLN* 3.4 13.9 - - - +
205A LYS 3.2 0.4 - - - -
206A ASN* 1.3 75.1 - - - +
208A GLU* 1.3 55.5 + - - +
209A LYS 3.3 0.4 - - - -
210A ILE* 3.3 25.7 - - - +
215A ARG* 2.8 72.8 + - + +
218A LEU* 4.1 5.4 - - + -
267A TYR* 3.9 20.9 - - + +
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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