Contacts of the helix formed by residues 216 - 251 (chain D) in PDB entry 4KNF
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 TYR 216 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ALA 3.3 25.6 - - - +
207D GLY* 2.8 15.4 + - - +
210D MET* 3.6 31.0 - - + +
211D GLY 5.3 5.2 - - - -
214D GLY 5.7 2.2 - - - -
215D VAL* 1.3 73.2 - - - +
217D ALA* 1.3 64.9 + - - +
218D SER 3.2 3.7 + - - -
219D ASN* 3.2 23.2 + - - +
220D LEU* 3.1 21.3 + - - +
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Residues in contact with ALA 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D TRP* 4.5 17.7 - - + -
87D GLY 5.7 0.9 - - - +
89D THR* 5.0 8.7 - - + +
215D VAL* 2.8 23.4 + - + +
216D TYR* 1.3 70.2 - - - +
218D SER* 1.3 61.7 + - - +
220D LEU* 3.5 4.8 - - - +
221D ASN* 2.7 37.4 + - - +
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Residues in contact with SER 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D VAL* 3.7 25.6 - - - +
83D TRP* 4.5 7.0 - - - -
216D TYR 3.3 1.0 - - - -
217D ALA* 1.3 75.4 - - - +
219D ASN* 1.3 66.2 + - - +
221D ASN* 3.5 1.4 + - - +
222D LEU* 3.0 41.0 + - - +
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Residues in contact with ASN 219 (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* 4.4 16.6 - - + -
216D TYR* 3.2 39.9 + - + +
218D SER* 1.3 78.9 + - - +
220D LEU* 1.3 62.3 + - - +
222D LEU* 3.8 10.6 - - - +
223D ILE* 2.6 41.5 + - + +
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Residues in contact with LEU 220 (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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89D THR* 4.1 20.9 - - + +
142D GLU* 3.7 7.0 - - - +
203D GLY 3.3 27.3 + - - +
204D TYR* 3.9 0.4 - - - -
207D GLY* 4.2 6.0 - - - -
208D TYR* 3.6 38.6 - - + +
215D VAL* 4.7 9.4 - - + -
216D TYR 3.1 9.8 + - - +
217D ALA* 3.5 9.4 - - - +
219D ASN* 1.3 80.5 - - - +
221D ASN* 1.3 58.5 + - - +
223D ILE* 3.1 3.1 + - - +
224D TYR* 2.9 67.9 + - + +
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Residues in contact with ASN 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D VAL* 3.9 20.4 - - + -
33D PHE* 3.9 8.9 - - + -
83D TRP* 3.9 12.9 - - - -
89D THR* 3.0 30.5 + - - -
90D PRO* 3.7 12.6 - - - +
94D ARG* 3.4 22.6 + - - +
217D ALA 2.7 28.8 + - - +
218D SER 4.0 0.9 - - - +
220D LEU* 1.3 81.5 - - - +
222D LEU* 1.3 53.6 + - - +
224D TYR* 4.4 3.4 - - - -
225D ASN* 2.8 41.9 + - - +
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Residues in contact with LEU 222 (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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28D THR* 4.2 18.8 - - + +
29D VAL* 3.6 41.3 - - + +
32D SER* 4.1 20.9 + - - +
218D SER* 3.0 26.5 + - - +
219D ASN* 3.8 11.4 - - - +
221D ASN* 1.3 74.8 - - - +
223D ILE* 1.3 61.2 + - + +
225D ASN* 3.8 2.3 - - - +
226D LEU* 2.9 28.9 + - - +
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Residues in contact with ILE 223 (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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199D ILE* 3.3 38.1 - - + +
202D ALA* 4.5 3.4 - - + +
203D GLY* 3.5 21.1 - - - +
206D ALA* 4.7 9.0 - - + -
219D ASN* 2.6 29.7 + - + +
220D LEU 3.6 3.1 - - - +
222D LEU* 1.3 75.7 - - + +
224D TYR* 1.3 62.1 + - - +
226D LEU* 3.2 6.6 + - + +
227D ALA* 2.7 28.8 + - - +
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Residues in contact with TYR 224 (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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94D ARG* 3.4 44.2 - - + +
98D TRP* 3.7 27.4 - + + -
142D GLU* 2.3 38.0 + - - -
200D TYR* 3.7 30.7 - + - -
203D GLY* 4.8 2.2 - - - -
204D TYR* 3.9 17.1 - - - +
220D LEU* 2.9 48.5 + - + +
221D ASN* 4.7 2.7 - - - -
223D ILE* 1.3 75.9 - - - +
225D ASN* 1.3 55.8 + - - +
227D ALA* 3.0 6.3 + - - +
228D ASP* 2.7 37.1 + - - +
301D RET 4.0 6.1 - - + +
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Residues in contact with ASN 225 (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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29D VAL* 4.3 2.8 + - - +
32D SER* 2.6 30.3 + - - +
33D PHE* 3.3 34.5 - - - +
36D VAL* 3.6 18.2 - - + +
76D TYR* 3.4 13.8 + - - +
94D ARG* 2.5 35.2 + - - -
221D ASN* 2.8 28.5 + - - +
222D LEU 3.8 2.0 - - - +
224D TYR* 1.3 70.2 - - - +
226D LEU* 1.3 62.8 + - - +
228D ASP* 3.6 1.4 + - - +
229D PHE* 3.1 22.5 + - - +
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Residues in contact with LEU 226 (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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36D VAL* 5.6 0.7 - - - -
199D ILE* 3.8 32.8 - - + -
222D LEU 2.9 19.0 + - - +
223D ILE* 3.6 6.7 - - + +
224D TYR 3.1 0.2 - - - -
225D ASN* 1.3 74.1 - - - +
227D ALA* 1.3 67.3 + - - +
229D PHE* 3.4 11.2 + - + +
230D VAL* 3.0 31.9 + - + +
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Residues in contact with ALA 227 (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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199D ILE* 3.8 26.9 - - + -
200D TYR* 3.4 36.1 - - + -
223D ILE 2.7 20.9 + - - +
224D TYR* 3.4 4.5 - - - +
226D LEU* 1.3 73.9 - - - +
228D ASP* 1.3 53.2 + - - +
230D VAL 3.1 1.2 + - - -
231D ASN* 2.8 41.7 + - - +
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Residues in contact with ASP 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D VAL* 4.9 1.6 - - + -
40D MET* 4.8 3.3 - - - +
76D TYR* 2.6 42.6 + - + +
94D ARG* 3.1 13.7 + - - -
97D ASN* 4.4 2.7 + - - -
98D TRP* 3.1 25.2 + - - -
200D TYR* 2.8 19.3 + - - -
224D TYR 2.7 15.3 + - - +
225D ASN 3.9 0.9 - - - +
227D ALA* 1.3 71.6 - - - +
229D PHE* 1.3 62.5 + - - +
232D LYS* 2.9 49.3 + - + +
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Residues in contact with PHE 229 (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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35D LEU* 5.3 3.1 - - + -
36D VAL* 3.9 26.5 - - + +
39D GLY* 4.8 10.3 - - - -
225D ASN 3.1 13.7 + - - +
226D LEU* 3.4 17.7 - - + +
228D ASP* 1.3 75.1 - - - +
230D VAL* 1.3 66.3 + - + +
233D ILE* 3.1 55.8 + - + +
234D LEU* 3.4 30.9 + - + -
100E LEU* 6.0 4.5 - - + -
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Residues in contact with VAL 230 (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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192D ILE* 4.8 7.7 - - + +
196D GLY* 4.8 7.9 - - - -
199D ILE* 4.2 18.4 - - + -
226D LEU* 3.0 37.8 + - + +
227D ALA 3.7 2.7 - - - +
229D PHE* 1.3 82.6 - - + +
231D ASN* 1.3 70.0 + - - +
234D LEU* 3.0 49.9 + - + +
235D PHE* 3.3 5.7 + - - +
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Residues in contact with ASN 231 (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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105D LEU* 4.0 14.6 - - - +
192D ILE* 3.7 8.8 - - - +
196D GLY* 3.1 38.2 + - - -
197D TRP* 3.3 24.8 - - + +
200D TYR* 3.1 31.3 - - + +
227D ALA* 2.8 30.4 + - - +
230D VAL* 1.3 82.7 - - - +
232D LYS* 1.3 61.2 + - + +
235D PHE* 3.2 23.4 - - - +
301D RET 4.5 4.3 - - + -
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Residues in contact with LYS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D MET* 3.7 27.8 - - + -
47D PHE* 4.2 1.7 - - - -
65D SER* 5.0 1.9 + - - +
68D ILE* 3.6 19.9 - - + +
69D THR* 3.9 11.3 - - + +
72D ALA* 4.1 9.4 - - + -
97D ASN* 4.5 3.8 - - - +
98D TRP* 3.8 4.6 - - - -
101D THR* 3.1 33.1 + - - -
105D LEU* 5.7 0.4 - - + -
228D ASP* 2.9 33.6 + - + +
231D ASN* 1.3 80.6 - - - +
233D ILE* 1.3 64.3 + - - +
235D PHE* 5.9 0.2 - - - -
236D GLY* 3.6 13.7 + - - -
301D RET 1.3 72.5 - - + +
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Residues in contact with ILE 233 (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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36D VAL 5.0 0.7 - - - +
39D GLY* 3.7 27.4 - - - +
40D MET* 4.0 17.0 - - - +
43D ALA* 3.9 24.0 - - + -
47D PHE* 3.7 6.1 - - + -
69D THR* 4.5 1.1 - - + -
229D PHE* 3.1 49.7 + - + +
232D LYS* 1.3 76.7 - - - +
234D LEU* 1.3 73.0 + - + +
236D GLY* 3.1 5.0 + - - -
237D LEU* 2.8 40.2 + - + +
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Residues in contact with LEU 234 (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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192D ILE* 5.6 0.9 - - - -
229D PHE* 3.4 31.2 + - + +
230D VAL* 3.0 42.2 + - + +
233D ILE* 1.3 77.4 - - + +
235D PHE* 1.3 60.8 + - - +
237D LEU* 3.3 24.7 + - + +
238D ILE* 3.1 29.4 + - + +
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Residues in contact with PHE 235 (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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65D SER* 5.8 0.7 - - - -
105D LEU* 3.1 38.4 - - + -
108D GLU* 4.1 15.3 - - + -
109D PHE* 3.6 21.1 - + - -
112D ILE* 5.0 1.1 - - + -
188D ALA* 3.9 19.5 - - + -
189D MET* 4.1 3.8 - - + -
192D ILE* 3.7 42.3 - - + +
230D VAL 3.3 7.1 + - - -
231D ASN 3.2 22.9 + - - +
232D LYS 5.9 0.2 - - - -
233D ILE 3.3 0.4 - - - -
234D LEU* 1.3 73.4 - - - +
236D GLY* 1.3 68.1 + - - +
238D ILE* 3.0 20.6 + - + +
239D ILE* 3.2 36.6 + - + +
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Residues in contact with GLY 236 (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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47D PHE* 3.4 25.0 - - - -
65D SER* 3.2 26.3 + - - -
232D LYS 3.6 7.6 + - - -
233D ILE 3.1 3.0 + - - -
235D PHE* 1.3 81.5 - - - +
237D LEU* 1.3 61.1 + - - +
239D ILE* 3.4 5.9 + - - +
240D TRP* 3.0 18.5 + - - +
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Residues in contact with LEU 237 (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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46D PHE* 3.7 37.7 - - + -
47D PHE* 3.8 5.1 - - + -
233D ILE* 2.8 28.0 + - + +
234D LEU* 3.5 31.0 - - + +
235D PHE 3.2 0.4 - - - -
236D GLY* 1.3 69.8 - - - +
238D ILE* 1.3 65.2 + - + +
240D TRP* 3.3 13.3 + - + +
241D ASN* 3.0 23.3 + - - +
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Residues in contact with ILE 238 (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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188D ALA* 3.5 31.2 - - + +
191D MET* 4.7 18.4 - - - -
192D ILE* 5.3 7.9 - - + -
234D LEU* 3.1 17.8 + - + +
235D PHE* 3.0 17.1 + - + +
237D LEU* 1.3 75.0 - - + +
239D ILE* 1.3 68.2 + - + +
241D ASN* 3.0 17.0 + - - +
242D VAL* 3.1 19.4 + - + +
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Residues in contact with ILE 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D TRP* 4.7 13.9 - - + -
61D SER* 4.1 20.6 - - - +
62D LEU* 4.9 6.5 - - + -
65D SER* 5.4 1.6 - - - +
108D GLU* 3.8 25.4 - - - +
112D ILE* 4.2 19.3 - - + -
185D ALA* 4.2 20.0 - - + -
188D ALA* 4.6 0.7 - - + -
235D PHE* 3.2 38.8 + - + +
236D GLY* 3.7 7.9 - - - +
238D ILE* 1.3 81.5 - - + +
240D TRP* 1.3 64.6 + - - +
242D VAL* 3.1 6.1 + - + +
243D ALA* 2.9 21.0 + - - +
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Residues in contact with TRP 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D PHE* 3.5 31.6 - + + -
47D PHE* 4.9 4.9 - + + -
50D GLU* 3.2 46.3 + - + +
54D VAL* 4.8 1.3 - - + -
62D LEU* 4.0 21.1 - - + +
236D GLY 3.0 14.5 + - - +
237D LEU* 3.4 19.7 - - + +
239D ILE* 1.3 78.6 - - - +
241D ASN* 1.3 82.7 + - + +
243D ALA* 3.4 5.3 + - - +
244D VAL* 2.9 55.7 + - + +
60E THR* 3.6 23.6 - - + -
111E LEU* 6.0 5.6 - - + -
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Residues in contact with ASN 241 (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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237D LEU 3.0 12.3 + - - +
238D ILE* 3.0 12.4 + - - +
240D TRP* 1.3 92.0 - - + +
242D VAL* 1.3 67.1 + - + +
244D VAL* 4.0 4.3 - - - +
245D LYS* 3.1 61.8 + - - +
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Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D TRP* 3.6 21.3 - - + -
181D ALA* 3.5 30.5 - - + +
184D SER* 3.7 25.4 - - - +
185D ALA* 4.3 11.9 - - + +
238D ILE* 3.1 18.9 + - + +
239D ILE* 3.6 9.2 - - - +
241D ASN* 1.3 79.3 - - + +
243D ALA* 1.3 63.1 + - - +
245D LYS* 3.4 8.6 + - - +
246D GLU* 3.0 22.2 + - - +
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Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D VAL* 3.6 14.6 - - + -
58D TRP* 3.3 46.2 - - + -
62D LEU* 4.3 6.7 - - + -
239D ILE 2.9 15.4 + - - +
240D TRP 3.8 2.2 - - - +
242D VAL* 1.3 77.9 - - - +
244D VAL* 1.3 56.1 + - - +
246D GLU* 3.9 0.9 - - - +
247D SER* 2.7 37.1 + - - -
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Residues in contact with VAL 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLN* 4.0 31.7 - - + +
54D VAL* 4.1 4.3 - - + -
240D TRP* 2.9 59.0 + - + +
241D ASN* 4.0 6.7 - - - +
243D ALA* 1.3 74.4 - - - +
245D LYS* 1.3 68.7 + - + +
247D SER* 3.5 2.1 + - - -
248D SER* 3.1 26.7 + - - +
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Residues in contact with LYS 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D ASN* 3.1 51.9 + - - +
242D VAL* 3.8 7.4 - - - +
244D VAL* 1.3 80.3 - - + +
246D GLU* 1.3 60.3 + - - +
248D SER* 3.0 19.2 + - - -
249D ASN* 3.1 25.1 + - - +
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Residues in contact with GLU 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D SER* 4.2 5.0 + - - -
57D LYS* 2.7 34.0 + - - +
58D TRP* 3.3 24.7 + - - +
179D SER* 4.7 4.0 + - - +
180D PRO* 5.4 6.2 - - + +
181D ALA* 3.6 28.3 - - + -
242D VAL 3.0 17.4 + - - +
245D LYS* 1.3 77.3 - - - +
247D SER* 1.3 63.1 + - - +
249D ASN* 3.4 7.1 + - + +
250D ALA* 2.9 37.8 + - + +
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Residues in contact with SER 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLN 4.1 5.4 - - - -
54D VAL* 3.4 8.8 - - - -
55D SER* 2.9 37.3 + - - -
58D TRP* 3.6 9.5 - - - -
243D ALA 2.7 23.5 + - - -
244D VAL 4.0 2.7 - - - -
245D LYS 3.3 0.2 - - - -
246D GLU* 1.3 79.9 - - - +
248D SER* 1.3 57.9 + - - +
250D ALA* 4.0 3.1 - - - +
251D LYS* 3.2 31.3 + - - +
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Residues in contact with SER 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D VAL* 3.1 14.4 + - - +
245D LYS* 3.0 15.8 + - - -
247D SER* 1.3 77.0 - - - +
249D ASN* 1.3 67.2 + - - +
251D LYS* 3.6 13.0 - - - +
252D LEU* 3.4 22.9 - - - +
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Residues in contact with ASN 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D PRO* 6.2 1.8 - - - +
245D LYS* 3.1 32.5 + - - +
246D GLU* 3.7 7.0 - - + +
248D SER* 1.3 77.4 + - - +
250D ALA* 1.3 61.9 + - - +
251D LYS 3.0 4.3 - - - -
252D LEU* 3.1 34.2 + - + +
253D LEU* 4.6 3.5 + - - +
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D GLU* 2.9 32.7 + - - +
247D SER* 4.0 4.3 - - - +
249D ASN* 1.3 74.4 - - - +
251D LYS* 1.3 59.1 + - - +
252D LEU 3.3 0.4 + - - -
253D LEU* 3.8 26.8 + - + +
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Residues in contact with LYS 251 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247D SER 3.2 20.8 + - - +
248D SER* 3.6 12.1 - - - +
249D ASN 3.0 1.0 - - - -
250D ALA* 1.3 75.1 - - - +
252D LEU* 1.3 62.9 + - + +
253D LEU 3.0 15.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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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