Contacts of the helix formed by residues 206 - 238 (chain A) in PDB entry 5AM8
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 THR 206 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER* 3.0 3.8 - - - -
205A PRO* 1.3 88.0 - - + +
207A PHE* 1.3 63.8 + - - +
208A GLU 3.3 2.9 + - - -
209A ASP* 3.3 24.3 + - - +
210A ASP* 2.9 50.3 + - - +
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ARG* 4.2 31.6 - - + +
202A TYR* 3.5 55.2 - + + -
204A SER* 3.2 23.4 + - - +
205A PRO 3.5 2.0 + - - -
206A THR* 1.3 76.5 - - - +
208A GLU* 1.3 64.6 + - + +
210A ASP* 3.1 11.3 + - + +
211A LEU* 3.0 62.6 + - + +
447A TRP* 4.4 6.5 - + - -
499A ILE* 4.0 18.8 - - + -
503A VAL* 4.4 4.9 - - + -
552A TRP* 6.3 1.8 - + - -
565A LEU* 5.4 4.9 - - + -
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ARG* 3.3 38.5 + - - -
206A THR 3.4 0.6 - - - -
207A PHE* 1.3 76.6 - - + +
209A ASP* 1.3 67.1 + - - +
211A LEU* 3.4 8.7 + - - +
212A GLU* 3.1 23.3 + - - +
440A TYR* 4.4 2.3 + - - -
447A TRP* 3.8 32.0 - - + +
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Residues in contact with ASP 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 3.3 23.5 + - - +
208A GLU* 1.3 79.7 - - - +
210A ASP* 1.3 59.4 + - - +
212A GLU* 3.3 6.6 + - - +
213A HIS* 2.9 49.6 + - + +
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Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A SER* 4.7 5.4 - - - -
206A THR* 2.9 51.6 + - - +
207A PHE* 3.5 9.8 + - + +
209A ASP* 1.3 76.8 - - - +
211A LEU* 1.3 63.5 + - + +
213A HIS* 3.5 9.4 + - - +
214A LEU* 3.1 29.8 + - + +
565A LEU* 6.3 2.9 - - + -
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PHE* 3.0 61.0 + - + +
208A GLU* 3.7 9.9 - - - +
209A ASP 3.3 0.2 - - - -
210A ASP* 1.3 73.9 - - + +
212A GLU* 1.3 60.8 + - - +
214A LEU* 3.2 13.1 + - + +
215A TYR* 2.8 29.1 + - - +
440A TYR* 3.8 18.1 + - + -
447A TRP* 4.0 12.8 - - + -
499A ILE* 3.9 17.0 - - + -
502A PHE* 3.9 28.2 - - + -
503A VAL* 4.2 11.2 - - + -
565A LEU* 4.9 3.1 - - + -
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Residues in contact with GLU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU 3.1 15.3 + - - +
209A ASP* 3.3 8.0 + - - +
211A LEU* 1.3 77.7 - - - +
213A HIS* 1.3 59.5 + - + +
215A TYR* 3.3 6.2 + - - +
216A GLN* 3.0 56.1 + - - +
440A TYR* 2.8 38.7 + - - +
470A TYR* 4.2 8.7 + - - -
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Residues in contact with HIS 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 2.9 37.2 + - + +
210A ASP* 3.8 10.8 + - - +
212A GLU* 1.3 76.1 - - + +
214A LEU* 1.3 66.1 + - + +
216A GLN* 3.5 26.7 + - - +
217A GLN* 3.5 26.3 + - - +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASP* 3.1 21.4 + - + +
211A LEU* 3.2 10.5 + - + +
213A HIS* 1.3 75.5 - - - +
215A TYR* 1.3 63.8 + - - +
217A GLN* 3.0 23.3 + - - +
218A LEU* 3.2 21.8 + - + +
502A PHE* 4.3 20.6 - - + -
506A VAL* 4.4 12.1 - - + -
565A LEU* 3.9 52.3 - - + +
566A ASP* 4.4 0.7 - - - -
567A ALA* 4.0 25.5 - - + +
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Residues in contact with TYR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU 2.8 15.2 + - - +
212A GLU* 3.3 7.8 + - - +
214A LEU* 1.3 73.6 - - - +
216A GLN* 1.3 58.4 + - - +
218A LEU* 3.0 10.6 + - + -
219A GLU* 2.8 66.4 + - + +
222A TYR* 4.1 12.2 - - + +
436A LEU* 4.1 6.7 - - + -
437A PRO* 3.3 49.0 - - + +
440A TYR* 3.6 32.8 - + + -
470A TYR* 3.8 33.9 + + - -
502A PHE* 4.0 15.5 - + + -
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Residues in contact with GLN 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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212A GLU* 3.0 43.3 + - - +
213A HIS* 3.6 30.1 + - - +
214A LEU 3.2 0.4 - - - -
215A TYR* 1.3 77.3 - - - +
217A GLN* 1.3 63.0 + - + +
219A GLU* 4.1 7.6 - - - +
220A PRO* 3.4 18.0 - - - +
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Residues in contact with GLN 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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213A HIS* 3.5 16.9 + - - +
214A LEU* 3.0 18.8 + - - +
216A GLN* 1.3 78.2 - - + +
218A LEU* 1.3 62.3 + - - +
220A PRO* 3.7 9.3 - - - +
221A LEU* 4.3 3.5 - - - +
566A ASP* 5.3 3.5 + - - +
567A ALA* 4.3 24.7 + - + +
568A GLN* 4.2 16.8 + - - +
571A LEU* 4.1 23.3 - - + +
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Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A LEU* 3.3 17.9 - - + +
215A TYR* 3.0 11.5 + - + +
217A GLN* 1.3 77.6 - - - +
219A GLU* 1.3 65.7 + - - +
220A PRO 3.3 1.3 - - - -
221A LEU* 2.9 25.4 + - + +
222A TYR* 3.3 5.9 + - - +
436A LEU* 4.1 24.7 - - + +
502A PHE* 3.9 32.1 - - + -
506A VAL* 4.1 15.0 - - + -
567A ALA* 4.2 19.5 - - + -
570A LEU* 3.8 32.8 - - + -
571A LEU* 4.6 5.2 - - + -
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Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 2.8 49.2 + - + +
216A GLN* 4.1 7.7 - - - +
218A LEU* 1.3 76.8 - - - +
220A PRO* 1.3 65.4 - - + +
222A TYR* 3.0 6.1 + - + +
223A LEU* 2.8 54.9 + - + +
469A LYS 5.0 7.8 - - - +
470A TYR* 5.5 2.8 - - - +
594A TRP* 5.4 2.8 - - - -
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Residues in contact with PRO 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLN 3.4 17.3 - - - +
217A GLN* 3.7 8.3 - - - +
218A LEU 3.4 4.5 - - - -
219A GLU* 1.3 91.6 - - + +
221A LEU* 1.3 66.7 + - + +
223A LEU* 4.2 13.0 - - + -
224A ASN* 3.0 36.1 + - - +
578A THR* 6.3 0.2 - - - -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN 4.3 6.1 - - - +
218A LEU* 2.9 15.8 + - + +
220A PRO* 1.3 82.3 - - + +
222A TYR* 1.3 61.7 + - - +
224A ASN* 3.4 4.3 + - - +
225A LEU* 3.1 22.2 + - - +
433A ILE* 4.0 34.9 - - + +
570A LEU* 4.1 7.6 - - + -
571A LEU* 3.5 36.1 - - + -
574A PHE* 4.5 7.6 - - + -
578A THR* 3.7 40.4 - - + +
581A LEU* 5.4 2.3 - - - +
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Residues in contact with TYR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A TYR* 4.1 13.2 - - + +
218A LEU 3.3 4.7 + - - +
219A GLU* 3.0 9.9 + - + +
221A LEU* 1.3 76.9 - - - +
223A LEU* 1.3 64.2 + - + +
225A LEU* 3.2 3.2 + - + +
226A HIS* 2.8 44.3 + + + +
261A TRP* 3.2 41.5 - + - -
433A ILE* 3.7 30.2 - - + +
434A ALA* 3.8 12.5 + - - -
436A LEU* 5.8 1.3 - - + -
437A PRO* 3.7 23.6 - - + -
470A TYR 3.4 19.5 - - - -
471A GLN* 2.5 37.6 + - - +
473A ILE* 5.1 0.2 - - - +
594A TRP* 4.1 9.0 - + - -
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A GLU* 2.8 48.3 + - + +
220A PRO* 3.9 11.7 - - + +
221A LEU 3.4 0.2 - - - -
222A TYR* 1.3 73.9 - - + +
224A ASN* 1.3 59.8 + - - +
226A HIS* 3.6 5.3 + - - +
227A ALA* 3.1 28.6 + - - +
592A LEU* 3.9 24.7 - - + +
593A GLY* 4.3 15.2 + - - +
594A TRP* 3.7 34.8 - - + -
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Residues in contact with ASN 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A PRO* 3.0 29.9 + - - +
221A LEU* 3.9 4.5 - - - +
223A LEU* 1.3 77.0 - - - +
225A LEU* 1.3 64.9 + - - +
228A PHE* 3.0 15.6 + - - +
578A THR* 5.4 5.6 - - + +
581A LEU* 4.3 14.4 - - + -
582A GLN* 3.5 33.0 + - - +
585A ASN* 2.9 40.3 + - - +
592A LEU* 3.6 26.9 - - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU 3.1 16.5 + - - +
222A TYR* 3.7 5.8 - - + +
224A ASN* 1.3 74.2 - - - +
226A HIS* 1.3 57.2 + - - +
228A PHE* 3.3 4.4 + - + +
229A VAL* 2.9 37.4 + - + +
261A TRP* 4.0 13.5 - - + -
426A LEU* 3.9 27.4 - - + -
429A ALA* 3.5 35.9 - - + +
430A LEU* 4.2 12.6 - - + -
433A ILE* 4.0 9.2 - - + -
434A ALA* 3.8 26.2 - - + +
581A LEU* 4.3 15.9 - - + +
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Residues in contact with HIS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 2.8 29.7 + + + +
223A LEU* 3.6 7.0 + - - +
225A LEU* 1.3 76.9 - - - +
227A ALA* 1.3 61.9 + - - +
229A VAL* 3.3 2.3 + - - +
230A ARG* 2.8 54.0 + - - +
246A GLY 4.4 1.6 - - - -
248A ILE* 3.6 26.7 - - + +
261A TRP* 3.9 16.1 - + + -
471A GLN 3.3 20.4 - - - -
472A GLY 3.0 23.3 + - - -
593A GLY 4.9 1.0 + - - -
594A TRP* 3.4 30.6 - + - -
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Residues in contact with ALA 227 (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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223A LEU 3.1 15.7 + - - +
224A ASN 3.9 1.1 - - - +
225A LEU 3.4 0.2 - - - -
226A HIS* 1.3 83.4 + - - +
228A PHE* 1.3 62.2 + - - +
230A ARG* 3.4 24.1 + - - +
231A ARG* 3.0 23.0 + - - +
585A ASN* 3.8 10.8 - - - +
590A GLU* 4.2 12.1 - - + +
591A VAL 4.2 2.9 - - - +
592A LEU* 3.7 22.2 - - + -
593A GLY 5.4 0.2 - - - +
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Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN 3.0 18.6 + - - +
225A LEU* 3.5 3.8 - - + +
227A ALA* 1.3 77.7 - - - +
229A VAL* 1.3 72.1 + - + +
231A ARG* 3.4 11.2 + - + +
232A ALA* 3.3 17.9 + - + +
235A ARG* 6.3 0.9 - - - -
268A VAL* 3.7 36.1 - - + -
270A PRO* 4.9 1.6 - - + -
426A LEU* 4.0 18.6 - - + -
580A TRP* 3.8 28.9 - + - -
581A LEU* 3.5 24.0 - - + -
584A GLN* 4.2 20.0 - - + -
585A ASN* 3.4 10.7 + - - +
588A ASN* 6.0 3.8 - - - -
590A GLU* 5.4 0.2 - - - -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 2.9 25.0 + - + +
226A HIS 3.8 3.1 - - - +
228A PHE* 1.3 80.4 - - + +
230A ARG* 1.3 66.9 + - - +
232A ALA* 3.1 9.3 + - - +
233A LEU* 3.0 26.6 + - + +
248A ILE* 4.8 0.7 - - + -
253A LEU* 3.6 20.4 - - + -
261A TRP* 3.7 20.9 - - + -
264A ILE* 3.5 28.0 - - + -
268A VAL* 4.6 7.2 - - + -
430A LEU* 4.0 18.2 - - + -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 2.8 30.8 + - - +
227A ALA* 3.4 17.3 + - - +
229A VAL* 1.3 76.1 - - - +
231A ARG* 1.3 62.2 + - - +
233A LEU* 3.2 6.8 + - - +
234A HIS* 2.9 23.4 + - - +
242A ILE* 3.7 16.1 - - + +
243A ASN 3.4 17.7 - - - -
244A LEU* 3.0 27.9 + - + +
246A GLY 2.8 36.7 + - - +
247A PRO 5.3 0.2 - - - -
248A ILE* 3.8 24.9 - - + +
590A GLU* 5.2 3.4 + - - -
591A VAL 2.7 30.1 + - - +
593A GLY 2.8 24.4 + - - +
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Residues in contact with ARG 231 (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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227A ALA 3.0 8.0 + - - +
228A PHE* 3.4 14.6 - - + +
229A VAL 3.3 0.2 - - - -
230A ARG* 1.3 75.4 - - - +
232A ALA* 1.3 63.1 + - - +
234A HIS* 3.2 13.8 + - - +
235A ARG* 3.1 59.7 + - - +
244A LEU* 3.6 40.8 - - - +
588A ASN* 3.8 24.0 + - - +
589A GLY 5.3 1.0 + - - -
590A GLU* 2.6 47.7 + - - +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE* 3.3 8.2 + - + +
229A VAL 3.1 7.0 + - - +
231A ARG* 1.3 77.7 - - - +
233A LEU* 1.3 62.8 + - + +
235A ARG* 3.2 17.6 + - - +
236A ARG* 3.0 22.5 + - - +
267A MET* 4.3 15.4 - - + +
268A VAL* 3.4 34.3 - - + -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A VAL* 3.0 21.7 + - + +
230A ARG* 3.7 7.6 - - - +
231A ARG 3.2 0.2 - - - -
232A ALA* 1.3 77.5 - - - +
234A HIS* 1.3 56.3 + - - +
236A ARG* 4.4 1.1 - - - -
237A TYR* 2.8 54.5 + - + +
242A ILE* 3.6 16.1 - - + +
248A ILE* 3.6 33.7 - - + -
252A LEU* 3.8 23.3 - - + +
253A LEU* 4.0 17.7 - - + -
264A ILE* 4.9 5.4 - - + -
267A MET* 3.4 25.6 - - + -
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ARG 2.9 13.4 + - - +
231A ARG* 3.2 16.9 + - - +
233A LEU* 1.3 74.4 - - - +
235A ARG* 1.3 63.6 + - - +
238A GLY* 2.8 31.2 + - - +
239A ASP* 2.8 40.6 + - + -
242A ILE* 3.4 34.7 - - + +
244A LEU* 3.7 37.7 - - + +
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Residues in contact with ARG 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PHE* 6.3 1.2 - - - -
231A ARG* 3.1 46.7 + - - +
232A ALA* 3.4 15.7 - - - +
234A HIS* 1.3 85.3 - - - +
236A ARG* 1.3 61.4 + - - +
238A GLY* 4.5 1.0 + - - -
588A ASN* 3.9 17.2 + - - +
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Residues in contact with ARG 236 (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 ARG* 4.0 22.6 - - - +
232A ALA 3.0 15.1 + - - +
233A LEU 3.7 3.8 - - - +
234A HIS 3.2 0.2 - - - -
235A ARG* 1.3 78.6 - - - +
237A TYR* 1.3 89.0 + - + +
238A GLY 3.7 0.2 - - - -
266A ASP 5.8 0.2 + - - -
267A MET* 3.5 45.9 + - + +
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Residues in contact with TYR 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG* 3.6 46.3 - - - +
153A TYR* 4.1 32.8 - + + -
156A LEU* 3.8 11.1 - - - +
233A LEU* 2.8 50.6 + - + +
236A ARG* 1.3 91.5 - - + +
238A GLY* 1.3 62.5 + - - +
240A ARG* 5.0 0.7 + - - +
241A TYR* 3.6 34.4 - + + -
242A ILE* 4.4 4.5 - - + -
252A LEU* 4.1 26.3 + - + +
267A MET* 4.7 1.8 - - + -
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Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A HIS* 2.8 22.7 + - - -
235A ARG 4.5 1.0 + - - -
236A ARG 3.7 1.0 - - - -
237A TYR* 1.3 80.0 - - - +
239A ASP* 1.3 64.2 + - - -
240A ARG* 3.2 4.5 + - - -
241A TYR 3.3 2.8 + - - -
242A ILE* 3.1 24.3 + - - +
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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