Contacts of the helix formed by residues 187 - 220 (chain A) in PDB entry 2QJK
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 ASP 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.3 8.8 - - - +
151A TRP* 3.6 15.8 - - - -
181A LEU 5.7 0.2 - - - +
185A ALA* 3.1 10.6 + - + +
186A VAL* 1.3 75.7 - - - +
188A ASN* 1.3 87.4 + - - +
189A ALA* 3.3 6.3 - - + +
190A THR* 3.0 18.7 + - - +
191A LEU 3.1 7.6 + - - -
44F VAL* 6.0 2.3 - - - +
69F GLY* 6.1 3.3 - - - -
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Residues in contact with ASN 188 (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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72A HIS* 3.3 28.0 - - - +
73A VAL* 2.8 51.9 + - + +
187A ASP* 1.3 86.7 + - - +
189A ALA* 1.3 68.1 + - - +
190A THR 2.6 1.9 + - - -
191A LEU* 2.7 15.0 + - - +
192A ASN* 2.8 28.8 + - - +
70D THR* 5.0 0.8 + - - -
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Residues in contact with ALA 189 (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 LEU 4.1 9.4 - - - +
182A GLY 4.2 10.8 - - - +
187A ASP* 4.5 4.6 - - + +
188A ASN* 1.3 80.3 - - - +
190A THR* 1.3 61.0 + - - +
192A ASN* 3.8 7.6 + - - +
193A ARG* 2.9 46.5 + - - +
67D MET 4.5 2.6 - - - +
68D HIS* 6.1 3.6 - - + +
41F SER* 5.4 6.7 - - - +
44F VAL* 5.6 3.6 - - + -
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Residues in contact with THR 190 (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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151A TRP* 5.4 0.4 - - - -
159A ALA* 5.8 0.7 - - + -
163A THR* 4.8 0.7 - - + -
180A LEU 3.9 12.6 - - - +
181A LEU* 3.0 30.3 + - + -
186A VAL* 3.7 12.7 - - + -
187A ASP 3.0 27.8 + - - -
188A ASN 2.6 4.6 + - - -
189A ALA* 1.3 71.9 - - - +
191A LEU* 1.3 68.0 + - - -
193A ARG* 2.9 26.2 - - - +
194A PHE* 3.0 41.6 + - + -
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Residues in contact with LEU 191 (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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69A TYR* 3.6 19.1 - - - +
71A PRO* 4.4 3.6 - - + -
72A HIS* 3.8 15.5 - - - +
73A VAL* 3.4 31.6 - - + +
76A ALA* 4.1 8.5 - - + -
148A VAL* 4.3 5.6 - - + -
149A LEU* 3.8 20.4 - - + +
151A TRP* 3.8 42.3 - - + -
187A ASP 3.1 4.1 + - - +
188A ASN* 2.7 13.9 + - - +
190A THR* 1.3 73.8 - - - +
192A ASN* 1.3 65.4 + - - +
194A PHE* 2.9 18.7 + - + +
195A PHE* 3.0 10.4 + - - +
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Residues in contact with ASN 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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71A PRO* 3.8 17.0 + - - +
188A ASN* 2.8 28.7 + - - +
189A ALA* 3.9 6.7 - - - +
191A LEU* 1.3 75.1 - - - +
193A ARG* 1.3 61.7 + - - +
195A PHE* 3.3 16.7 + - - +
196A SER 3.3 8.3 + - - -
66D ALA 2.9 28.6 + - - +
67D MET* 3.0 23.6 + - - +
68D HIS* 3.6 10.3 - - - +
69D TYR 3.2 21.1 + - - +
70D THR* 3.7 9.9 + - - -
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Residues in contact with ARG 193 (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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179A TRP 3.3 4.6 + - - -
180A LEU 3.2 20.2 + - - -
182A GLY* 3.3 18.8 - - - -
189A ALA* 2.9 27.4 + - - +
190A THR* 2.9 21.9 + - - +
192A ASN* 1.3 75.6 - - - +
194A PHE* 1.3 75.0 + - + +
196A SER* 3.5 2.6 + - - -
197A LEU* 3.1 29.2 + - + +
67D MET* 3.7 33.1 + - + +
68D HIS* 4.2 15.3 - - - -
38F MET* 2.9 74.8 + - + +
39F ASN 4.8 1.2 + - - -
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Residues in contact with PHE 194 (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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1A SMA 4.1 20.2 - - + -
144A PHE* 3.6 35.4 - + - -
145A MET* 3.7 28.2 - - + +
148A VAL* 3.7 28.9 - - + -
149A LEU* 4.5 8.5 - - + -
159A ALA* 4.6 5.2 - - + -
163A THR* 4.4 9.6 - - + -
180A LEU* 4.5 7.9 - - + -
190A THR* 3.0 40.1 + - + -
191A LEU* 2.9 10.7 + - - +
193A ARG* 1.3 84.1 - - + +
195A PHE* 1.3 57.9 + - - +
197A LEU* 3.1 4.0 + - + +
198A HIS* 2.6 39.4 + - - +
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Residues in contact with PHE 195 (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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66A ALA* 4.5 21.5 - - + -
69A TYR* 3.6 33.9 - + - -
71A PRO* 3.7 30.7 - - + -
149A LEU* 4.0 18.5 - - + +
191A LEU 3.0 8.2 + - - +
192A ASN 3.4 10.3 - - - +
193A ARG 3.2 0.2 - - - -
194A PHE* 1.3 76.7 - - - +
196A SER* 1.3 67.0 + - - +
197A LEU 3.1 0.3 + - - -
198A HIS* 3.1 4.4 + - + +
199A TYR* 3.0 34.0 + + - +
502A HEM 3.9 21.5 - - + -
66D ALA 5.2 3.1 - - - -
71D PRO* 5.8 0.2 - - + -
195D PHE* 2.9 42.0 - + - -
199D TYR* 5.7 0.2 - + - -
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Residues in contact with SER 196 (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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192A ASN 3.3 2.4 + - - -
193A ARG 3.7 3.4 - - - -
194A PHE 3.3 0.2 - - - -
195A PHE* 1.3 83.8 - - - +
197A LEU* 1.3 57.2 + - - +
199A TYR* 3.5 0.7 - - - +
200A LEU* 3.2 11.8 + - - +
63D ILE* 2.8 32.9 + - - +
66D ALA* 3.3 20.9 - - - +
67D MET* 3.7 24.9 - - - -
199D TYR* 2.6 33.4 + - - -
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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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1A SMA 3.8 27.6 - - + -
145A MET* 3.7 19.1 - - + -
193A ARG* 3.1 21.7 + - + +
194A PHE* 4.9 3.1 - - + -
195A PHE 3.1 0.6 - - - -
196A SER* 1.3 76.5 - - - +
198A HIS* 1.3 67.4 + - - +
199A TYR 3.0 1.8 - - - -
200A LEU* 4.2 21.3 - - + -
201A LEU* 3.0 33.5 + - + +
63D ILE* 4.7 2.7 - - + -
67D MET* 3.4 26.0 - - + -
38F MET* 5.0 9.4 - - + -
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Residues in contact with HIS 198 (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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142A THR* 3.3 30.1 + - + +
145A MET* 4.1 13.8 - - + -
146A GLY* 3.5 10.0 + - - -
149A LEU* 3.5 18.4 - - + -
194A PHE 2.6 21.1 + - - +
195A PHE* 3.7 4.3 - + + +
197A LEU* 1.3 72.1 - - - +
199A TYR* 1.3 57.1 + - - +
202A PRO* 2.9 28.5 - - - +
502A HEM 2.0 98.1 + + + -
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Residues in contact with TYR 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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63A ILE* 3.8 11.7 - - + +
66A ALA* 4.6 3.8 - - + -
195A PHE* 3.0 23.9 + + - +
196A SER 3.5 9.9 - - - +
198A HIS* 1.3 76.2 - - - +
200A LEU* 1.3 60.0 + - - +
202A PRO* 3.0 21.0 - - - +
203A PHE* 3.6 35.8 - + - -
502A HEM 3.2 39.5 - - + +
195D PHE* 5.5 0.9 - + - -
196D SER* 2.6 42.3 + - - -
199D TYR* 3.3 47.1 - + + -
200D LEU* 3.7 10.3 - - - +
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Residues in contact with LEU 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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196A SER 3.2 6.7 + - - +
197A LEU* 3.3 17.7 + - + +
199A TYR* 1.3 79.0 - - - +
201A LEU* 1.3 69.8 + - + +
203A PHE* 3.1 17.8 + - + +
204A VAL* 3.5 21.2 + - + -
63D ILE* 3.2 43.1 - - + -
199D TYR* 3.3 16.4 - - - +
203D PHE* 3.9 20.0 - - + -
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Residues in contact with LEU 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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1A SMA 6.2 0.9 - - + -
138A ALA* 4.0 11.9 - - + +
141A ALA* 3.6 27.4 - - + -
142A THR* 3.3 22.4 - - - +
145A MET* 3.7 17.9 - - + -
197A LEU* 3.0 22.2 + - + +
200A LEU* 1.3 75.4 - - + +
202A PRO* 1.3 63.3 - - + +
204A VAL* 2.7 44.5 + - + +
205A ILE* 2.8 14.9 + - + +
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Residues in contact with PRO 202 (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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55A LEU* 4.4 4.7 - - + +
59A ILE* 4.3 14.7 - - + +
142A THR* 4.1 5.2 - - + +
198A HIS 2.9 28.0 - - - +
199A TYR 3.0 13.2 - - - +
201A LEU* 1.3 82.2 - - + +
203A PHE* 1.3 56.8 + - + +
205A ILE* 3.2 15.0 - - + +
206A ALA* 2.8 28.4 + - - +
502A HEM 3.6 52.9 - - + -
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Residues in contact with PHE 203 (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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59A ILE* 4.6 25.6 - - + -
63A ILE* 4.9 1.1 - - + -
199A TYR* 3.6 34.3 - + - -
200A LEU* 3.1 13.8 + - + +
201A LEU 3.0 0.8 - - - -
202A PRO* 1.3 74.6 - - + +
204A VAL* 1.3 67.8 + - + +
206A ALA* 3.2 10.5 + - + +
207A ALA* 2.9 22.7 + - - +
502A HEM 5.4 2.9 - - + -
200D LEU* 3.9 25.1 - - + -
203D PHE* 3.3 59.5 - + + -
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Residues in contact with VAL 204 (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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138A ALA* 5.9 3.1 - - + -
200A LEU* 3.6 25.8 - - + +
201A LEU* 2.7 33.5 + - + +
203A PHE* 1.3 72.5 - - + +
205A ILE* 1.3 64.4 + - - +
207A ALA* 3.1 10.8 + - + +
208A LEU* 2.9 34.5 + - + +
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Residues in contact with ILE 205 (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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55A LEU* 4.1 12.8 - - + -
104A PHE* 5.2 0.9 - - + -
135A ILE* 4.4 9.0 - - + -
138A ALA* 3.9 15.7 - - + -
139A MET* 3.9 34.8 - - + +
142A THR* 4.0 12.1 - - - +
201A LEU 2.8 18.4 + - - +
202A PRO* 3.2 8.7 - - + +
204A VAL* 1.3 76.6 - - - +
206A ALA* 1.3 56.4 + - - +
208A LEU* 2.7 33.0 + - - +
209A VAL* 2.7 29.7 + - + +
501A HEM 4.2 11.9 - - + -
502A HEM 4.0 19.5 - - + -
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Residues in contact with ALA 206 (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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55A LEU* 3.7 21.3 - - + -
59A ILE* 4.9 7.0 - - + -
202A PRO 2.8 16.6 + - - +
203A PHE* 3.2 16.8 - - + +
205A ILE* 1.3 71.8 - - - +
207A ALA* 1.3 63.4 + - - +
209A VAL* 3.2 5.1 + - - +
210A ALA* 3.1 19.6 + - - +
504A ANJ 4.5 13.9 - - + +
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Residues in contact with ALA 207 (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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203A PHE 2.9 12.5 + - - +
204A VAL* 3.2 14.1 - - + +
206A ALA* 1.3 75.7 - - - +
208A LEU* 1.3 66.6 + - + +
210A ALA* 2.9 23.5 - - - +
211A ILE* 3.4 9.8 + - - +
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Residues in contact with LEU 208 (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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131A VAL* 4.0 11.8 - - + +
134A LEU* 3.9 35.7 - - + +
135A ILE* 3.8 23.1 - - + +
138A ALA* 5.2 4.7 - - + -
204A VAL* 2.9 26.9 + - + +
205A ILE* 2.7 16.2 + - - +
207A ALA* 1.3 73.7 - - + +
209A VAL* 1.3 52.1 + - - +
211A ILE* 2.8 22.1 + - + +
212A HIS* 2.7 34.8 + - - +
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Residues in contact with VAL 209 (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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52A ALA* 6.1 0.2 - - - -
55A LEU* 4.0 11.0 - - + -
135A ILE* 4.0 4.5 - - + +
205A ILE* 2.7 32.8 + - + +
206A ALA* 3.3 8.1 - - - +
208A LEU* 1.3 71.7 - - - +
210A ALA* 1.3 65.4 + - - +
212A HIS* 3.2 10.1 - - + +
213A ILE* 3.0 25.6 + - + +
501A HEM 3.6 51.8 - - + -
504A ANJ 3.5 23.3 - - + +
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Residues in contact with ALA 210 (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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206A ALA 3.1 10.5 + - - +
207A ALA* 2.9 16.7 + - - +
209A VAL* 1.3 74.8 - - - +
211A ILE* 1.3 52.6 + - + +
213A ILE* 2.7 28.4 + - - +
214A TRP* 2.8 17.5 + - - +
504A ANJ 4.3 14.8 + - + +
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Residues in contact with ILE 211 (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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131A VAL* 4.2 18.4 - - + -
207A ALA* 3.9 11.7 - - + +
208A LEU* 2.8 24.5 + - + +
210A ALA* 1.3 79.5 - - + +
212A HIS* 1.3 52.7 + - - +
214A TRP* 2.9 17.9 + - + -
215A ALA* 2.6 35.7 + - + +
23D LEU* 3.8 28.9 - - + -
25D ILE* 4.5 17.9 - - + -
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Residues in contact with HIS 212 (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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128A THR* 3.6 30.2 + - + +
131A VAL* 3.9 14.3 - - + +
132A GLY* 4.0 7.2 + - - -
135A ILE* 4.1 4.9 - - + -
208A LEU 2.7 14.9 + - - +
209A VAL* 3.2 16.6 - - - +
211A ILE* 1.3 72.8 - - - +
213A ILE* 1.3 64.3 + - + +
215A ALA* 3.1 5.4 + - - +
216A PHE* 3.1 23.1 + + - +
501A HEM 2.0 101.5 + + + -
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Residues in contact with ILE 213 (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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32A THR* 5.7 3.1 - - + -
209A VAL* 3.0 13.6 + - + +
210A ALA* 2.7 13.9 + - - +
212A HIS* 1.3 69.9 - - + +
214A TRP* 1.3 67.0 - - - +
216A PHE* 3.2 24.5 + - + -
217A HIS* 2.9 50.7 + - + +
501A HEM 5.2 2.2 - - + -
504A ANJ 2.9 72.7 - - + +
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Residues in contact with TRP 214 (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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210A ALA 2.8 15.2 + - - +
211A ILE* 3.3 24.7 - - + +
213A ILE* 1.3 74.4 - - - +
215A ALA* 1.3 60.6 + - - +
217A HIS* 3.3 7.8 + - + +
218A SER* 2.9 30.0 + - - -
23D LEU* 3.6 13.7 - - + -
24D PRO* 3.9 25.2 - - + +
25D ILE* 3.4 46.0 - - + -
28D LEU* 3.8 31.0 - - + -
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Residues in contact with ALA 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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127A VAL* 4.7 7.2 - - + -
128A THR* 3.9 24.8 + - - +
131A VAL* 5.7 0.4 - - + -
211A ILE* 2.6 20.4 + - + +
212A HIS* 3.5 5.2 - - - +
214A TRP* 1.3 70.0 - - - +
216A PHE* 1.3 58.9 + - - +
217A HIS 2.9 4.9 - - - -
218A SER* 3.0 19.8 + - - -
219A THR* 3.5 15.8 + - - +
22D ARG 4.0 3.0 - - - +
23D LEU* 3.7 24.4 - - + +
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Residues in contact with PHE 216 (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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35A ILE* 5.2 0.2 - - - +
128A THR* 3.9 7.8 + - + +
212A HIS* 3.1 28.0 + + - +
213A ILE* 3.2 34.8 - - + -
215A ALA* 1.3 76.8 - - - +
217A HIS* 1.3 76.7 + + - +
218A SER 3.3 0.2 - - - -
219A THR* 4.0 8.1 - - - -
220A GLY* 3.2 27.2 + - - -
221A ASN* 3.8 23.7 - - - +
501A HEM 3.4 70.2 - + + +
504A ANJ 3.3 24.7 - + - -
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Residues in contact with HIS 217 (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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3A GLY 4.9 5.7 + - - -
4A ILE* 6.0 0.2 - - - +
31A ASP 4.3 4.0 + - - -
32A THR* 3.2 44.5 + - + +
35A ILE* 3.8 42.6 - - + +
213A ILE* 2.9 41.1 + - + +
214A TRP* 3.4 11.2 - - + +
216A PHE* 1.3 98.5 - + - +
218A SER* 1.3 60.2 + - - +
219A THR 3.3 1.2 + - - -
220A GLY* 3.8 4.9 + - - -
504A ANJ 4.4 7.3 + - - -
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLY* 4.5 10.9 + - - +
214A TRP* 2.9 30.4 + - - -
215A ALA* 3.0 5.5 + - - -
217A HIS* 1.3 78.0 - - - +
219A THR* 1.3 60.1 + - - +
220A GLY 3.6 0.2 - - - -
21D SER 4.7 6.1 - - - +
22D ARG 3.2 24.9 + - - +
23D LEU* 4.4 0.3 - - - +
24D PRO* 4.0 12.1 - - - +
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Residues in contact with THR 219 (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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3A GLY 5.1 4.3 - - - +
124A PRO* 4.3 33.9 - - + +
125A ARG* 3.9 14.6 + - - +
128A THR* 4.8 3.0 + - - +
215A ALA 3.5 14.1 + - - +
216A PHE* 3.8 6.9 + - - -
218A SER* 1.3 82.0 - - - +
220A GLY* 1.3 71.5 + - - +
228A GLU* 4.3 2.3 - - - +
231A ARG* 3.5 21.5 + - - +
501A HEM 4.0 3.1 + - - -
21D SER 4.6 2.9 - - - +
22D ARG* 3.9 23.8 - - + +
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Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLY 5.1 0.2 - - - +
4A ILE* 4.3 20.8 - - - +
35A ILE* 4.8 7.4 - - - -
36A PRO 6.0 0.9 - - - -
125A ARG* 2.4 28.2 + - - -
216A PHE 3.2 13.5 + - - +
217A HIS 3.8 6.5 + - - -
218A SER 3.6 1.0 - - - -
219A THR* 1.3 83.1 + - - +
221A ASN* 1.3 57.5 + - - -
228A GLU* 5.7 0.2 - - - -
231A ARG* 4.9 1.8 - - - -
501A HEM 3.6 1.0 - - - +
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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