Contacts of the helix formed by residues 187 - 220 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 6.1 0.7 - - - +
69C GLY* 6.0 4.2 - - - -
73D VAL* 4.2 9.7 - - - +
151D TRP* 3.6 17.5 - - - -
181D LEU 5.7 0.4 - - - +
185D ALA* 3.1 10.4 + - + +
186D VAL* 1.3 76.5 - - - +
188D ASN* 1.3 87.3 + - - +
189D ALA* 3.4 6.7 - - + +
190D THR* 3.0 17.6 + - - +
191D LEU 3.2 8.0 + - - -
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Residues in contact with ASN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A THR* 5.0 0.6 + - - -
71D PRO 5.2 0.2 - - - -
72D HIS* 3.3 28.7 + - - +
73D VAL* 2.9 49.3 + - + +
187D ASP* 1.3 89.3 + - - +
189D ALA* 1.3 66.1 + - - +
190D THR 2.7 2.1 + - - -
191D LEU* 2.7 15.9 + - - +
192D ASN* 2.8 29.9 + - - +
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Residues in contact with ALA 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MET 4.6 2.0 - - - +
68A HIS* 6.2 2.7 - - - +
41C SER* 5.3 4.0 - - - +
44C VAL* 5.1 9.4 - - + -
181D LEU 4.1 9.0 - - - +
182D GLY 4.2 11.2 - - - +
187D ASP* 3.4 4.6 - - + +
188D ASN* 1.3 80.9 - - - +
190D THR* 1.3 61.9 + - - +
192D ASN* 3.9 7.1 - - - +
193D ARG* 2.9 44.9 + - - +
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Residues in contact with THR 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D TRP* 5.4 0.7 - - - -
159D ALA* 5.8 0.9 - - + -
163D THR* 4.8 0.7 - - + -
180D LEU 3.9 13.2 - - - +
181D LEU* 3.0 31.4 + - + -
186D VAL* 3.7 12.6 - - + -
187D ASP* 3.0 27.7 + - - +
188D ASN 2.7 4.0 + - - -
189D ALA* 1.3 72.6 - - - +
191D LEU* 1.3 66.9 + - - +
193D ARG* 2.9 25.4 - - - +
194D PHE* 3.0 40.9 + - + -
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Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TYR* 3.6 18.8 - - - +
71D PRO* 4.4 3.1 - - + -
72D HIS* 3.7 15.7 - - - +
73D VAL* 3.4 33.7 - - + +
76D ALA* 4.1 8.3 - - + -
148D VAL* 4.3 6.1 - - + -
149D LEU* 3.8 20.6 - - + +
151D TRP* 3.8 39.0 - - + -
187D ASP 3.2 4.1 + - - +
188D ASN* 2.7 13.1 + - - +
190D THR* 1.3 74.9 - - - +
192D ASN* 1.3 65.3 + - - +
194D PHE* 2.9 18.5 + - - +
195D PHE* 3.0 11.1 + - - +
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Residues in contact with ASN 192 (chain D).
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 3.0 26.5 + - - +
67A MET* 3.0 24.1 + - - +
68A HIS* 3.7 7.6 - - - +
69A TYR 3.2 21.3 + - - +
70A THR* 3.7 12.1 + - - -
71D PRO* 3.8 18.0 + - - +
188D ASN* 2.8 28.3 + - - +
189D ALA* 3.9 7.0 - - - +
191D LEU* 1.3 75.9 - - - +
193D ARG* 1.3 62.3 + - - +
195D PHE* 3.2 16.2 + - - +
196D SER 3.3 9.0 + - - -
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Residues in contact with ARG 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A MET* 3.8 32.7 + - + +
68A HIS* 4.4 15.5 - - - -
38C MET* 3.0 72.8 + - - +
39C ASN 4.9 1.2 + - - -
2D SMA 6.4 0.4 - - - -
179D TRP 3.2 5.3 + - - -
180D LEU 3.1 20.5 + - - -
182D GLY* 3.2 19.7 + - - +
189D ALA* 2.9 27.4 + - - +
190D THR* 2.9 22.6 - - - +
192D ASN* 1.3 79.3 - - - +
194D PHE* 1.3 70.9 + - + +
196D SER* 3.4 2.9 + - - -
197D LEU* 3.1 29.0 + - + +
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Residues in contact with PHE 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SMA 3.7 24.0 - - + -
144D PHE* 3.6 35.4 - + - -
145D MET* 3.7 25.1 - - + +
148D VAL* 3.7 27.8 - - + -
149D LEU* 4.5 8.5 - - + -
159D ALA* 4.5 4.9 - - + -
163D THR* 4.4 11.4 - - + -
180D LEU* 4.5 5.8 - - + -
190D THR* 3.0 41.5 + - + +
191D LEU* 2.9 11.5 + - - +
193D ARG* 1.3 84.1 - - + +
195D PHE* 1.3 56.4 + - - +
197D LEU* 3.8 3.1 - - + +
198D HIS* 2.6 39.7 + - - +
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Residues in contact with PHE 195 (chain D).
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 5.2 3.4 - - - -
195A PHE* 2.9 44.2 - + - -
199A TYR* 5.4 1.3 - + - -
66D ALA* 4.4 20.9 - - + -
69D TYR* 3.7 32.8 - + - -
71D PRO* 3.7 29.8 - - + -
149D LEU* 4.0 17.9 - - + +
191D LEU 3.0 8.9 + - - +
192D ASN* 3.2 9.6 + - - +
194D PHE* 1.3 76.9 - - - +
196D SER* 1.3 68.5 + - - +
197D LEU 3.0 0.2 + - - -
198D HIS* 3.1 3.9 + + + +
199D TYR* 3.0 37.0 + + + +
502D HEM 4.1 17.5 - - + -
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Residues in contact with SER 196 (chain D).
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* 2.8 27.4 + - - +
66A ALA* 3.3 15.6 - - - +
67A MET* 3.7 22.0 - - - -
199A TYR* 2.6 40.4 + - - -
192D ASN 3.3 2.4 + - - -
193D ARG 3.7 8.3 - - - -
194D PHE 3.3 0.4 - - - -
195D PHE* 1.3 82.9 - - - +
197D LEU* 1.3 58.9 + - - +
200D LEU* 3.2 13.5 + - - +
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Residues in contact with LEU 197 (chain D).
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* 4.8 2.2 - - + -
67A MET* 3.4 26.9 - - + -
38C MET* 5.1 7.6 - - + -
2D SMA 4.3 23.1 - - + -
145D MET* 3.8 17.3 - - + -
193D ARG* 3.1 22.7 + - + +
194D PHE* 3.8 2.0 - - + +
195D PHE 3.1 0.6 - - - -
196D SER* 1.3 75.5 - - - +
198D HIS* 1.3 65.6 + - - +
199D TYR 3.0 1.7 + - - -
200D LEU* 3.7 21.5 - - + +
201D LEU* 3.0 33.7 + - + +
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Residues in contact with HIS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D THR* 3.4 24.2 + - + +
145D MET* 4.2 14.9 - - + -
146D GLY* 3.5 13.2 + - - -
149D LEU* 3.4 21.3 - - + -
194D PHE 2.6 21.5 + - - +
195D PHE* 3.7 4.5 - + + +
197D LEU* 1.3 71.8 - - - +
199D TYR* 1.3 58.5 + - - +
202D PRO* 2.9 27.9 - - - +
502D HEM 2.0 95.9 + + + -
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Residues in contact with TYR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A PHE* 5.9 0.2 - + - -
196A SER* 2.6 42.0 + - - -
199A TYR* 3.3 52.5 - + + -
200A LEU* 3.3 14.3 - - - +
63D ILE* 3.7 7.7 - - + +
66D ALA* 4.1 8.1 - - + -
195D PHE* 3.0 24.1 + + + +
196D SER 3.7 0.2 - - - +
198D HIS* 1.3 78.4 - - - +
200D LEU* 1.3 58.6 + - - +
202D PRO* 3.0 20.8 - - - +
203D PHE* 3.5 35.8 - + - -
502D HEM 3.4 42.7 - - + +
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Residues in contact with LEU 200 (chain D).
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* 3.3 43.5 - - + -
199A TYR* 3.7 8.6 + - - +
203A PHE* 3.9 20.4 - - + -
196D SER 3.2 13.9 + - - +
197D LEU* 3.2 17.2 + - + +
199D TYR* 1.3 77.6 - - - +
201D LEU* 1.3 71.1 + - + +
203D PHE* 3.1 20.1 + - + +
204D VAL* 3.5 21.0 + - + -
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Residues in contact with LEU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SMA 6.1 1.3 - - + -
138D ALA* 3.9 13.2 - - + +
141D ALA* 3.8 12.8 - - + -
142D THR* 3.3 28.3 - - + +
145D MET* 3.7 24.9 - - + -
197D LEU* 3.0 22.3 + - + +
198D HIS 4.6 0.2 - - - +
200D LEU* 1.3 76.2 - - + +
202D PRO* 1.3 61.6 - - + +
204D VAL* 2.7 44.4 + - + +
205D ILE* 2.8 15.0 + - + +
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Residues in contact with PRO 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.4 5.9 - - + +
59D ILE* 4.3 13.3 - - + +
142D THR* 4.0 6.9 - - + +
198D HIS 2.9 28.9 - - - +
199D TYR 3.0 13.2 - - - +
201D LEU* 1.3 82.4 - - + +
203D PHE* 1.3 57.1 + - + +
205D ILE* 3.2 14.4 - - + +
206D ALA* 2.8 27.0 + - - +
502D HEM 3.7 51.4 - - + -
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Residues in contact with PHE 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.9 22.2 - - + -
203A PHE* 3.3 59.2 - + + -
59D ILE* 4.6 25.8 - - + -
63D ILE* 4.9 1.3 - - + -
199D TYR* 3.5 36.6 - + - -
200D LEU* 3.1 13.6 + - + +
201D LEU 3.1 0.6 - - - -
202D PRO* 1.3 73.4 - - - +
204D VAL* 1.3 63.7 + - + +
206D ALA* 3.2 9.5 - - + +
207D ALA* 2.8 28.6 + - - +
502D HEM 5.5 3.4 - - + -
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ALA* 5.9 2.9 - - + -
200D LEU* 3.6 25.8 - - + +
201D LEU* 2.7 34.8 + - + +
203D PHE* 1.3 72.6 - - + +
205D ILE* 1.3 62.8 + - - +
207D ALA* 3.1 10.8 + - + +
208D LEU* 2.9 34.9 + - + +
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Residues in contact with ILE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.1 13.0 - - + -
104D PHE* 5.2 0.9 - - + -
135D ILE* 4.4 9.0 - - + -
138D ALA* 3.9 16.4 - - + -
139D MET* 3.9 35.7 - - + +
142D THR* 4.0 11.7 - - - +
201D LEU 2.8 17.7 + - - +
202D PRO* 3.2 10.5 - - + +
204D VAL* 1.3 75.8 - - - +
206D ALA* 1.3 56.9 + - - +
208D LEU* 2.7 33.0 + - - +
209D VAL* 2.7 30.5 + - + +
501D HEM 4.2 11.2 - - + -
502D HEM 4.2 16.6 - - + -
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 3.8 20.4 - - + -
59D ILE* 4.9 7.4 - - + -
202D PRO 2.8 13.8 + - - +
203D PHE* 3.2 16.8 - - + +
205D ILE* 1.3 76.6 - - - +
207D ALA* 1.3 64.2 + - - +
209D VAL* 3.2 4.8 + - - +
210D ALA* 3.1 19.8 + - - +
504D ANJ 4.3 17.5 - - + +
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Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D PHE 2.8 11.8 + - - +
204D VAL* 3.2 14.1 - - + +
206D ALA* 1.3 76.1 - - - +
208D LEU* 1.3 67.5 + - + +
210D ALA* 3.0 23.8 - - - +
211D ILE* 3.4 9.0 + - + +
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Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D VAL* 4.0 11.0 - - + +
134D LEU* 3.9 35.7 - - + +
135D ILE* 3.8 23.6 - - + +
138D ALA* 5.1 4.5 - - + -
204D VAL* 2.9 28.2 + - + +
205D ILE* 2.7 15.5 + - - +
207D ALA* 1.3 72.6 - - + +
209D VAL* 1.3 51.7 + - - +
211D ILE* 2.8 23.1 + - + +
212D HIS* 2.7 34.4 + - - +
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.0 10.8 - - + -
135D ILE* 4.0 4.9 - - + +
205D ILE* 2.7 32.5 + - + +
206D ALA* 3.3 8.3 - - - +
208D LEU* 1.3 71.3 - - - +
210D ALA* 1.3 65.6 + - - +
212D HIS* 3.2 9.2 - - + +
213D ILE* 2.9 27.3 + - + +
501D HEM 3.5 52.7 - - + -
504D ANJ 3.7 21.8 - - + +
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ALA 3.1 10.1 + - - +
207D ALA* 3.0 15.8 + - - +
209D VAL* 1.3 74.6 - - - +
211D ILE* 1.3 53.7 + - + +
213D ILE* 2.8 12.4 + - - +
214D TRP* 2.7 32.3 + - - +
504D ANJ 4.6 14.5 + - + -
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Residues in contact with ILE 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.9 28.9 - - + -
25A ILE* 4.7 16.6 - - + -
131D VAL* 4.3 17.9 - - + -
207D ALA 3.9 11.2 - - - +
208D LEU* 2.8 25.6 + - + +
210D ALA* 1.3 74.5 - - + +
212D HIS* 1.3 55.9 + - - +
214D TRP* 2.9 17.4 + - + -
215D ALA* 2.7 35.1 + - + +
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Residues in contact with HIS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D THR* 3.6 32.3 + - + +
131D VAL* 3.9 13.8 - - + +
132D GLY* 4.0 7.2 + - - -
135D ILE* 4.1 4.7 - - + -
208D LEU 2.7 15.3 + - - +
209D VAL* 3.2 16.2 - - + +
211D ILE* 1.3 72.3 - - - +
213D ILE* 1.3 64.4 + - - +
215D ALA* 3.2 5.6 + - - +
216D PHE* 3.1 22.7 + + - +
501D HEM 2.0 100.6 + + + -
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Residues in contact with ILE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D THR* 5.7 1.8 - - + -
209D VAL* 2.9 14.8 + - + +
210D ALA* 2.8 13.7 + - - +
212D HIS* 1.3 71.0 - - + +
214D TRP* 1.3 65.5 + - - +
216D PHE* 3.1 24.5 + - + -
217D HIS* 2.9 56.5 + - + +
501D HEM 5.3 1.6 - - + -
504D ANJ 3.0 71.1 - - + +
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Residues in contact with TRP 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.6 14.8 - - + -
24A PRO* 4.0 25.0 - - + +
25A ILE* 3.5 45.8 - - + -
28A LEU* 3.8 31.0 - - + -
210D ALA 2.7 15.8 + - - +
211D ILE* 3.3 23.3 - - + +
213D ILE* 1.3 74.4 - - - +
215D ALA* 1.3 60.3 + - - +
217D HIS* 3.3 8.4 + - + +
218D SER* 2.9 29.0 + - - -
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Residues in contact with ALA 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG 4.2 1.7 - - - +
23A LEU* 3.8 22.4 - - + -
127D VAL* 4.7 10.8 - - + -
128D THR* 3.9 25.1 + - - +
131D VAL* 5.7 0.4 - - + -
211D ILE* 2.7 19.9 + - + +
212D HIS* 3.5 5.6 - - - +
214D TRP* 1.3 71.0 - - - +
216D PHE* 1.3 57.7 + - - +
217D HIS 2.9 4.7 - - - -
218D SER* 3.0 19.9 + - - -
219D THR* 3.4 15.6 + - - +
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Residues in contact with PHE 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D THR* 4.0 7.0 - - + +
212D HIS* 3.1 28.4 + + - +
213D ILE* 3.1 35.4 - - + -
215D ALA* 1.3 77.0 - - - +
217D HIS* 1.3 71.1 + + - +
219D THR* 4.0 4.3 - - - -
220D GLY* 3.2 26.9 + - - -
221D ASN* 3.3 27.1 + - - -
501D HEM 3.3 73.4 - + + +
504D ANJ 3.4 26.5 - - - -
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Residues in contact with HIS 217 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLY 5.2 4.7 + - - -
4D ILE* 5.8 0.9 - - - +
31D ASP 4.6 2.4 + - - -
32D THR* 3.2 45.8 + - + +
35D ILE* 3.8 41.6 - - + +
213D ILE* 2.9 47.5 + - + +
214D TRP* 3.4 11.7 - - + +
216D PHE* 1.3 96.5 - + - +
218D SER* 1.3 60.6 + - - +
219D THR 3.5 0.3 + - - -
220D GLY* 3.8 5.9 + - - -
504D ANJ 4.1 9.5 + - - -
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Residues in contact with SER 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER 4.8 5.5 - - - +
22A ARG 3.3 25.1 + - - +
23A LEU* 4.4 0.3 - - - +
24A PRO* 4.1 12.5 - - - +
3D GLY* 4.7 11.7 + - - +
214D TRP* 2.9 30.3 + - - -
215D ALA* 3.0 6.4 + - - -
217D HIS* 1.3 78.4 - - - +
219D THR* 1.3 61.1 + - - +
220D GLY 3.6 0.2 - - - -
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Residues in contact with THR 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER 4.8 2.2 - - - +
22A ARG* 3.9 20.9 - - + +
3D GLY 5.7 0.4 - - - -
4D ILE* 5.1 2.5 - - - -
124D PRO* 4.3 37.2 - - + +
125D ARG* 4.1 13.6 + - - +
128D THR* 4.9 3.2 + - - +
215D ALA 3.4 13.8 + - - +
216D PHE* 3.8 2.9 + - - -
217D HIS 3.3 0.2 - - - -
218D SER* 1.3 82.9 - - - +
220D GLY* 1.3 71.9 + - - +
228D GLU* 4.3 0.7 - - - +
231D ARG* 3.5 22.2 + - - +
501D HEM 3.9 9.2 + - - -
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Residues in contact with GLY 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 4.4 18.5 - - - +
35D ILE* 4.8 7.9 - - - -
36D PRO 6.0 0.9 - - - -
125D ARG* 3.6 6.3 + - - -
216D PHE 3.2 14.2 + - - +
217D HIS 3.8 6.9 + - - -
218D SER 3.6 1.0 - - - -
219D THR* 1.3 96.0 + - - +
221D ASN* 1.3 66.5 + - - -
231D ARG* 4.8 2.0 - - - -
501D HEM 3.6 4.2 - - - +
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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