Contacts of the helix formed by residues 220 - 252 (chain A) in PDB entry 6VW1
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 GLY 220 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 5.1 0.4 - - - -
218A SER* 3.3 4.7 + - - -
219A ARG* 1.3 74.5 - - - +
221A GLN* 1.3 66.7 + - - +
222A LEU 3.0 2.0 - - - -
223A ILE* 3.0 27.1 + - - +
224A GLU* 3.0 13.5 + - - +
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Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 3.5 28.0 - - + -
218A SER* 3.3 30.6 + - - +
219A ARG 3.5 0.2 - - - -
220A GLY* 1.3 76.8 - - - +
222A LEU* 1.3 55.5 + - - +
224A GLU* 3.4 31.1 + - - +
225A ASP* 2.9 55.5 + - - +
578A ASN* 5.0 2.8 - - - +
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Residues in contact with LEU 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 3.7 31.2 - - + +
207A TYR* 3.7 53.4 - - + -
217A TYR* 3.3 24.0 + - + +
218A SER 3.9 0.6 + - - +
219A ARG* 3.7 12.5 + - - +
220A GLY 3.0 0.6 - - - -
221A GLN* 1.3 79.2 - - - +
223A ILE* 1.3 56.4 + - - +
225A ASP* 3.3 0.9 + - - +
226A VAL* 2.9 50.2 + - + +
461A TRP* 4.0 13.2 - - + -
513A ILE* 4.5 4.5 - - + -
517A THR* 4.6 7.2 - - + -
566A TRP* 6.5 0.2 - - + -
579A MET* 5.7 3.6 - - - -
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 3.5 46.9 - - - +
219A ARG 4.3 0.4 - - - +
220A GLY* 3.0 14.3 + - - +
222A LEU* 1.3 74.7 - - - +
224A GLU* 1.3 64.5 + - - +
226A VAL* 3.4 1.6 + - - -
227A GLU* 3.0 55.9 + - + +
458A LYS* 5.3 4.0 - - + +
461A TRP* 3.8 27.1 - - + -
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Residues in contact with GLU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLY 3.0 11.8 + - - +
221A GLN* 3.7 35.6 + - - +
223A ILE* 1.3 77.4 - - - +
225A ASP* 1.3 60.9 + - - +
227A GLU* 3.9 7.4 - - - +
228A HIS* 2.9 34.6 + - + +
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Residues in contact with ASP 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A TYR* 2.5 29.0 + - - +
221A GLN* 2.9 35.5 + - - +
222A LEU 3.9 1.6 - - - +
224A GLU* 1.3 77.3 - - - +
226A VAL* 1.3 66.3 + - - +
228A HIS* 3.3 5.5 + - - +
229A THR* 2.9 32.8 + - + +
578A ASN* 2.8 33.6 + - - +
579A MET* 4.7 12.8 - - + -
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LEU* 2.9 36.7 + - + +
223A ILE* 3.9 4.7 - - - +
225A ASP* 1.3 75.4 - - + +
227A GLU* 1.3 57.3 + - + +
229A THR* 2.9 7.2 + - - -
230A PHE* 2.9 26.0 + - - +
454A TYR* 3.5 32.3 - - + -
461A TRP* 5.0 4.5 - - + -
513A ILE* 4.1 23.6 - - + -
516A TYR* 3.2 30.1 + - + -
517A THR* 5.0 1.3 - - + -
579A MET* 4.8 7.0 - - - -
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Residues in contact with GLU 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 ILE* 3.0 34.4 + - + +
224A GLU* 3.9 5.5 - - - +
226A VAL* 1.3 74.6 - - + +
228A HIS* 1.3 66.2 + - - +
230A PHE* 3.3 5.9 + - - +
231A GLU* 3.0 30.9 + - + +
454A TYR* 3.2 25.0 + - + +
458A LYS* 3.2 29.8 - - - +
461A TRP* 6.4 0.2 - - + -
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Residues in contact with HIS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLU* 2.9 23.9 + - + +
225A ASP* 3.8 6.0 - - - +
227A GLU* 1.3 76.3 - - - +
229A THR* 1.3 70.4 + - + +
231A GLU* 3.7 16.4 - - + +
232A GLU* 3.5 34.9 + - + +
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ASP* 2.9 19.1 + - + +
226A VAL* 2.9 6.9 + - - -
228A HIS* 1.3 84.7 - - - +
230A PHE* 1.3 63.0 + - - +
231A GLU 3.2 1.8 - - - -
232A GLU* 3.1 6.2 + - - +
233A ILE* 3.0 24.8 + - - +
516A TYR* 2.4 34.4 + - - -
520A LEU* 4.2 12.6 - - + -
579A MET* 4.5 16.7 - - + +
581A VAL* 3.6 29.0 - - + +
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Residues in contact with PHE 230 (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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226A VAL 2.9 17.6 + - - +
227A GLU* 3.8 6.5 - - - +
229A THR* 1.3 73.0 - - - +
231A GLU* 1.3 68.8 + - - +
233A ILE* 3.1 14.9 + - + +
234A LYS* 3.0 59.5 + - + +
237A TYR* 5.7 3.1 - + + -
450A LEU* 4.9 1.1 - - + -
451A PRO* 3.6 39.9 - - + -
454A TYR* 3.8 27.1 - + + -
484A ILE* 3.8 31.0 - - + -
516A TYR* 3.0 22.5 + + + +
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Residues in contact with GLU 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 GLU* 3.0 21.2 + - + +
228A HIS* 3.7 10.3 - - + +
229A THR 3.2 0.4 - - - -
230A PHE* 1.3 79.4 - - + +
232A GLU* 1.3 61.4 + - + +
234A LYS* 3.3 49.8 - - - +
235A PRO* 3.8 4.3 - - - +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A HIS* 3.5 35.3 + - + +
229A THR* 3.1 7.9 + - - +
231A GLU* 1.3 75.0 - - + +
233A ILE* 1.3 64.1 + - - +
235A PRO* 3.2 12.9 - - - +
236A LEU 5.2 0.2 + - - -
581A VAL* 4.5 16.8 - - + +
585A LEU* 4.0 28.9 - - + +
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Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR 3.0 10.2 + - - +
230A PHE* 3.1 17.0 + - + +
232A GLU* 1.3 76.5 - - - +
234A LYS* 1.3 66.1 + - - +
235A PRO 3.1 1.4 - - - -
236A LEU* 3.3 18.0 + - + +
237A TYR* 3.4 17.0 + - + +
447A VAL* 5.7 4.5 - - + +
450A LEU* 3.9 35.9 - - + -
451A PRO* 5.9 0.2 - - + -
516A TYR* 3.6 31.6 - - + +
520A LEU* 4.3 3.1 - - + -
581A VAL* 3.5 26.7 - - + -
584A LEU* 4.5 5.2 - - + -
585A LEU* 4.8 10.8 - - + -
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Residues in contact with LYS 234 (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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230A PHE* 3.0 46.7 + - + +
231A GLU* 3.3 44.0 - - - +
233A ILE* 1.3 76.2 - - - +
235A PRO* 1.3 60.4 - - + +
237A TYR* 3.3 8.6 + - + +
238A GLU* 2.9 47.4 + - + +
483A GLU 5.1 3.0 + - - -
484A ILE* 4.6 16.0 + - - +
606A TRP* 5.6 4.6 - - - -
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Residues in contact with PRO 235 (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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231A GLU 3.8 5.8 - - - +
232A GLU* 3.2 17.9 - - - +
233A ILE 3.5 0.9 - - - +
234A LYS* 1.3 93.4 - - + +
236A LEU* 1.3 62.5 + - - +
238A GLU* 3.1 11.4 + - + +
239A HIS* 3.0 32.3 + - + -
592A PHE* 3.9 17.7 - - + -
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Residues in contact with LEU 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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232A GLU 5.2 0.4 + - - +
233A ILE* 3.3 12.6 + - + +
235A PRO* 1.3 79.2 - - - +
237A TYR* 1.3 58.3 + - - +
239A HIS* 3.3 2.1 + - - +
240A LEU* 3.0 28.7 + - + +
443A ALA* 6.3 0.4 - - + -
447A VAL* 4.5 21.5 - - + -
584A LEU* 5.5 3.4 - - + -
585A LEU* 4.0 27.1 - - + -
588A PHE* 3.9 32.1 - - + +
591A LEU* 5.2 4.3 - - + -
592A PHE* 3.5 46.3 - - + +
595A LEU* 4.2 11.2 - - + -
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Residues in contact with TYR 237 (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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230A PHE* 5.7 3.1 - + + -
233A ILE* 3.4 15.8 + - + +
234A LYS* 3.3 10.9 + - + +
235A PRO 3.3 0.6 - - - -
236A LEU* 1.3 78.8 - - - +
238A GLU* 1.3 59.4 + - + +
240A LEU* 3.4 5.9 + - + -
241A HIS* 2.8 31.9 + + + +
275A TRP* 3.3 42.4 - + - -
447A VAL* 3.8 25.4 - - + +
448A GLY* 4.4 5.3 + - - -
451A PRO* 3.5 39.0 - - + -
484A ILE 4.4 2.0 - - - -
485A VAL* 2.5 38.0 + - - +
606A TRP* 3.9 23.6 - + - -
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LYS* 2.9 36.9 + - + +
235A PRO* 3.1 13.5 + - + +
237A TYR* 1.3 77.2 - - + +
239A HIS* 1.3 57.0 + - + +
241A HIS* 3.3 8.0 + - - +
242A ALA* 2.9 28.2 + - - +
604A VAL* 3.9 23.0 - - + +
605A GLY* 4.5 12.8 + - - +
606A TRP* 3.9 25.8 - - + -
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Residues in contact with HIS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A PRO* 3.0 28.8 + - + +
236A LEU 3.9 2.9 - - - +
238A GLU* 1.3 74.8 - - + +
240A LEU* 1.3 65.6 + - - +
242A ALA 3.2 0.5 + - - -
243A TYR* 3.0 12.1 + - - +
592A PHE* 3.8 21.7 - + + -
595A LEU* 4.0 16.8 - - + +
596A LYS* 3.5 35.5 - - + +
599A ASN* 2.9 38.9 + - + +
604A VAL* 3.8 29.9 - - + +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.0 18.3 + - + +
237A TYR* 3.8 6.3 - - + +
239A HIS* 1.3 76.4 - - - +
241A HIS* 1.3 58.1 + - - +
243A TYR* 3.4 5.5 + - + +
244A VAL* 2.9 45.0 + - + +
275A TRP* 4.2 21.5 - - + -
440A LEU* 3.6 31.6 - - + -
443A ALA* 4.1 22.7 - - + +
444A LEU* 4.5 3.8 - - + +
447A VAL* 3.5 28.0 - - + -
448A GLY* 4.5 3.1 - - - +
595A LEU* 4.0 18.0 - - + +
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Residues in contact with HIS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A TYR* 2.8 39.0 + - + +
238A GLU* 3.4 8.2 + - - +
239A HIS 3.2 0.2 - - - -
240A LEU* 1.3 77.0 - - - +
242A ALA* 1.3 59.9 + - - +
244A VAL* 3.4 1.7 + - - +
245A ARG* 2.9 54.8 + - - +
260A GLY 4.1 7.6 - - - -
262A LEU* 3.4 31.8 - - + +
275A TRP* 4.1 12.5 - + + -
485A VAL 4.2 3.4 - - - -
486A GLY* 2.9 26.6 + - - -
605A GLY 4.6 0.6 + - - -
606A TRP* 3.5 30.2 - + + -
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLU 2.9 15.3 + - - +
239A HIS 3.2 0.2 + - - -
241A HIS* 1.3 76.9 + - - +
243A TYR* 1.3 63.0 + - - +
245A ARG* 3.2 15.7 + - - +
246A ALA* 3.0 23.6 + - - +
599A ASN* 3.6 23.5 - - - +
602A SER* 5.1 4.4 - - - -
603A PHE 3.4 24.9 - - - +
604A VAL* 4.2 8.7 - - + -
605A GLY 5.2 0.4 - - - +
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Residues in contact with TYR 243 (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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239A HIS 3.0 15.6 + - - +
240A LEU* 3.7 8.1 - - + +
242A ALA* 1.3 77.0 - - - +
244A VAL* 1.3 71.4 + - + +
246A ALA* 3.3 7.3 + - + +
247A LYS* 3.0 56.1 + - + +
282A THR* 2.8 32.0 + - - -
284A PRO* 3.4 18.2 - - - +
440A LEU* 4.2 24.9 - - + -
594A TRP* 3.8 28.0 - + - -
595A LEU* 4.8 8.3 - - + -
598A GLN* 4.3 22.0 - - + -
599A ASN* 3.8 15.1 + - - +
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 2.9 29.0 + - + +
241A HIS 3.9 2.7 - - - +
243A TYR* 1.3 81.4 - - + +
245A ARG* 1.3 59.0 + - - +
247A LYS* 3.7 4.9 - - - +
248A LEU* 2.8 39.7 + - + +
262A LEU* 4.2 11.2 - - + -
275A TRP* 4.1 14.6 - - + -
278A LEU* 3.7 27.6 - - + -
282A THR* 4.3 11.4 - - + -
444A LEU* 3.9 26.0 - - + -
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Residues in contact with ARG 245 (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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241A HIS* 2.9 30.7 + - + +
242A ALA* 3.4 10.9 + - - +
243A TYR 3.2 0.4 - - - -
244A VAL* 1.3 77.6 - - - +
246A ALA* 1.3 59.0 + - - +
248A LEU* 3.3 2.6 + - - +
249A MET* 2.9 34.8 + - - +
256A ILE* 4.3 5.6 - - + +
257A SER 3.9 9.2 - - - +
258A PRO* 3.1 37.9 + - - -
259A ILE* 3.7 4.0 + - - -
260A GLY 3.3 24.8 + - - +
262A LEU* 3.6 26.2 - - + -
603A PHE* 2.7 31.5 + - - +
605A GLY 2.3 33.1 + - - -
606A TRP* 3.6 8.1 - - - +
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ALA 3.0 13.0 + - - +
243A TYR* 3.7 9.6 - - + +
245A ARG* 1.3 77.8 - - - +
247A LYS* 1.3 63.8 + - + +
249A MET* 2.9 25.6 + - - +
250A ASN* 3.1 18.2 + - - +
599A ASN* 6.0 0.4 - - - +
602A SER* 4.9 13.0 - - - +
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Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR* 3.0 58.6 + - + +
244A VAL 3.8 0.7 - - - +
246A ALA* 1.3 76.9 - - + +
248A LEU* 1.3 62.1 + - - +
250A ASN* 3.3 26.7 + - + +
251A ALA* 3.4 10.9 + - - +
281A LEU 3.4 28.3 + - - +
282A THR* 3.7 18.8 - - + -
283A VAL* 3.4 20.8 + - - +
284A PRO 4.8 3.6 + - - -
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A VAL* 2.8 36.1 + - + +
245A ARG* 3.8 2.9 - - - +
247A LYS* 1.3 74.8 - - - +
249A MET* 1.3 61.0 + - - +
251A ALA* 2.8 3.6 + - - +
252A TYR* 2.8 42.5 + - + -
256A ILE* 3.7 20.2 - - + +
262A LEU* 4.3 21.3 - - + -
263A PRO* 5.9 0.2 - - + -
266A LEU* 4.0 22.4 - - + +
267A LEU* 5.0 2.2 - - + -
278A LEU* 4.1 25.4 - - + -
281A LEU* 4.2 23.1 - - + -
282A THR* 5.1 2.2 - - + -
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Residues in contact with MET 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ARG* 2.9 22.9 + - - +
246A ALA* 3.2 16.2 - - - +
248A LEU* 1.3 77.6 - - - +
250A ASN* 1.3 64.8 + - - +
251A ALA 3.3 0.5 + - - -
252A TYR 3.6 3.8 - - - -
253A PRO* 3.5 23.7 - - - +
256A ILE* 3.8 37.4 - - + +
257A SER 4.5 0.2 - - - +
258A PRO* 3.6 44.4 - - + -
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Residues in contact with ASN 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ALA* 3.1 14.2 + - - +
247A LYS* 3.5 23.0 - - + +
248A LEU 3.2 0.4 - - - -
249A MET* 1.3 77.8 - - - +
251A ALA* 1.3 59.6 + - - +
253A PRO* 4.0 10.7 - - - +
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 5.2 3.4 - - + +
247A LYS 3.4 8.6 + - - +
248A LEU* 2.8 13.2 + - - +
250A ASN* 1.3 82.1 - - - +
252A TYR* 1.3 81.2 + - + +
253A PRO* 3.4 7.9 - - - +
281A LEU* 3.8 30.7 - - + -
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Residues in contact with TYR 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER 3.8 2.1 + - - -
156A LEU* 3.3 42.7 - - + +
157A ASP 4.5 0.2 - - - -
158A TYR* 4.1 22.2 - - + -
161A ARG* 3.5 21.8 + - - -
248A LEU* 2.8 32.2 + - + +
249A MET* 3.6 6.2 - - - +
251A ALA* 1.3 90.4 - - + +
253A PRO* 1.3 67.6 - - - +
254A SER 3.5 0.3 + - - -
255A TYR* 3.3 30.0 + + + +
256A ILE* 4.0 13.8 + - + +
266A LEU* 3.6 42.7 + - + +
281A LEU* 4.5 5.0 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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