Contacts of the helix formed by residues 280 - 313 (chain B) in PDB entry 5VBL
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 PRO 280 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B HIS 4.7 0.7 - - - +
279B TRP* 1.4 94.8 - - + +
281B CYS* 1.3 63.4 + - - +
282B ASP* 4.5 9.6 - - + +
283B PHE* 3.2 27.3 + - + +
284B ASP* 3.2 8.8 - - - +
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Residues in contact with CYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B CYS* 2.0 56.4 - - + -
21B TYR* 4.6 5.0 - - - -
279B TRP 3.6 2.5 + - - -
280B PRO* 1.3 71.8 - - - +
282B ASP* 1.3 65.9 + - - +
284B ASP* 3.4 19.3 + - - +
285B LEU* 3.5 12.3 + - - +
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B PRO* 3.3 6.4 - - + +
281B CYS* 1.3 78.9 + - - +
283B PHE* 1.4 61.5 + - - +
285B LEU* 3.5 13.5 + - - +
286B PHE* 3.4 18.5 + - - +
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Residues in contact with PHE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 3.7 33.0 - - + -
279B TRP* 4.1 26.5 - + + -
280B PRO* 3.2 26.6 + - + +
282B ASP* 1.4 75.8 - - - +
284B ASP* 1.4 62.9 + - - +
286B PHE* 3.3 23.3 + + + +
287B LEU* 3.2 45.9 + - + +
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Residues in contact with ASP 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 4.1 29.2 + - + +
271B TYR* 4.4 22.4 - - + +
274B GLY* 4.6 17.9 - - - +
275B SER* 4.9 1.8 + - - -
279B TRP* 4.0 13.4 - - - +
280B PRO 3.2 17.7 - - - +
281B CYS* 3.4 13.6 + - - +
283B PHE* 1.4 76.2 - - - +
285B LEU* 1.4 57.9 + - - +
287B LEU* 3.5 14.0 + - - +
288B MET* 3.2 33.9 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU 5.9 3.1 - - - +
281B CYS 3.5 9.6 + - - +
282B ASP* 3.6 15.5 - - - +
283B PHE 3.3 0.2 - - - -
284B ASP* 1.4 78.1 - - - +
286B PHE* 1.4 61.5 + - - +
288B MET* 3.5 10.8 + - + +
289B ASN* 3.0 46.1 + - - +
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Residues in contact with PHE 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASP 3.4 9.4 + - - +
283B PHE* 3.3 31.3 + + + +
285B LEU* 1.4 79.0 - - - +
287B LEU* 1.4 68.5 + - + +
289B ASN* 3.6 4.8 + - - +
290B ILE* 3.3 48.8 + - + +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A NLE 4.8 1.8 - - - -
267B VAL* 3.6 38.9 - - + +
270B LEU* 4.0 42.4 - - + +
271B TYR* 4.1 15.9 - - + +
283B PHE* 3.2 38.5 + - + +
284B ASP* 3.8 14.6 - - - +
285B LEU 3.4 0.4 - - - -
286B PHE* 1.4 81.6 - - + +
288B MET* 1.3 57.8 + - - +
290B ILE* 3.5 7.6 - - + +
291B PHE* 3.1 30.7 + - - +
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Residues in contact with MET 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 4.9 6.1 - - + +
15A NLE 5.0 0.9 - - - -
21B TYR* 4.0 31.2 - - + -
22B THR 5.4 6.1 - - - +
24B TRP* 3.5 55.2 - - + +
271B TYR* 3.3 33.7 - - + +
284B ASP 3.2 20.5 + - - +
285B LEU* 3.7 10.3 - - + +
286B PHE 3.4 0.2 - - - -
287B LEU* 1.3 77.4 - - - +
289B ASN* 1.3 58.5 + - - +
291B PHE* 4.6 0.2 - - - -
292B PRO* 3.4 20.1 - - - +
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Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 4.0 23.8 - - - +
27B SER* 5.2 0.7 + - - -
285B LEU* 3.0 37.9 + - - +
286B PHE* 4.2 4.6 - - - +
287B LEU 3.4 0.2 - - - -
288B MET* 1.3 76.5 - - - +
290B ILE* 1.3 59.3 + - - +
291B PHE 3.5 0.4 - - - -
292B PRO* 3.4 13.0 - - - +
293B TYR* 3.5 19.6 - - - -
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B VAL* 3.9 22.0 - - + -
286B PHE* 3.3 43.6 + - + +
287B LEU* 3.5 14.1 - - + +
289B ASN* 1.3 75.3 - - - +
291B PHE* 1.4 65.5 + - - +
292B PRO 3.6 0.4 - - - -
293B TYR* 3.4 15.4 + - + +
294B CYS* 3.1 29.7 + - - -
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Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A NLE 3.6 47.6 - - + -
16A PRO* 4.3 7.4 - - + -
17A 200 3.3 34.3 - + + -
24B TRP* 4.1 12.8 - + + -
264B TYR* 3.8 27.4 - + - -
267B VAL* 3.7 13.2 - - + -
268B LYS* 4.5 5.8 - - + -
287B LEU 3.1 19.1 + - - +
288B MET 3.9 4.7 - - - +
290B ILE* 1.4 72.9 - - - +
292B PRO* 1.4 72.1 - - + +
294B CYS* 3.0 18.3 + - + +
295B THR* 3.0 35.5 + - + -
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Residues in contact with PRO 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A 200 6.1 1.8 - - + -
24B TRP* 4.4 8.3 - - + -
25B LYS 5.9 1.3 - - - +
27B SER* 4.0 13.9 - - - +
31B ILE* 3.8 27.8 - - + +
35B TYR* 4.2 2.4 + - - -
89B THR* 5.7 1.6 - - + -
93B TYR* 3.9 23.1 - - - +
288B MET 3.4 17.7 - - - +
289B ASN* 3.4 14.6 - - - +
290B ILE 3.6 0.2 - - - -
291B PHE* 1.4 91.6 - - + +
293B TYR* 1.3 55.8 + - + +
295B THR* 2.8 19.6 + - - +
296B CYS* 3.2 15.9 + - - +
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.6 26.0 + - - -
30B LEU* 4.0 25.6 - - + +
31B ILE* 3.8 23.1 - - + -
289B ASN 3.5 24.7 - - - -
290B ILE* 3.6 15.9 - - + +
291B PHE 3.2 0.4 - - - -
292B PRO* 1.3 75.2 - - + +
294B CYS* 1.4 63.2 + - - +
295B THR 3.4 0.2 - - - -
296B CYS* 3.6 7.5 - - + +
297B ILE* 3.3 31.6 + - + +
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Residues in contact with CYS 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B CYS 4.3 0.5 - - - +
263B PRO* 3.7 22.7 - - - -
264B TYR* 3.8 24.0 + - - +
267B VAL* 3.8 24.5 - - + -
290B ILE* 3.1 30.9 + - - +
291B PHE* 3.0 15.1 + - + +
293B TYR* 1.4 77.0 - - - +
295B THR* 1.3 60.0 + - - +
297B ILE* 3.7 11.2 - - - +
298B SER* 3.3 21.1 + - - -
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A 200 3.8 23.2 - - + -
35B TYR* 3.5 12.3 + - - -
264B TYR* 3.6 15.3 - - + -
291B PHE* 3.0 47.8 + - + +
292B PRO* 2.8 22.9 + - - +
294B CYS* 1.3 72.9 - - - +
296B CYS* 1.4 58.5 + - - +
298B SER* 3.4 5.8 + - - -
299B TYR* 3.0 42.1 + - - +
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Residues in contact with CYS 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 4.3 13.2 - - + -
34B ILE* 3.7 45.1 - - - -
35B TYR* 3.7 23.1 - - + +
292B PRO 3.2 15.0 + - - +
293B TYR* 3.6 11.7 - - - +
294B CYS 3.4 0.2 - - - -
295B THR* 1.4 79.8 + - - +
297B ILE* 1.4 62.0 + - + +
299B TYR* 3.0 20.6 + - - +
300B VAL* 3.1 16.1 + - - +
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Residues in contact with ILE 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B LEU 3.9 4.5 - - - +
260B CYS* 3.4 48.6 - - - +
263B PRO* 3.6 20.6 - - + -
293B TYR* 3.3 18.4 + - + +
294B CYS* 3.7 6.5 - - - +
296B CYS* 1.4 81.6 - - + +
298B SER* 1.4 60.6 + - - +
300B VAL* 3.4 25.7 + - + +
301B ASN 3.6 5.0 + - - -
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Residues in contact with SER 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B CYS* 3.4 19.7 - - - -
261B LYS* 3.2 43.4 + - - +
264B TYR* 4.1 16.6 - - - +
294B CYS 3.3 19.3 + - - -
295B THR* 3.4 10.1 + - - -
297B ILE* 1.4 77.5 - - - +
299B TYR* 1.3 66.9 + - - +
301B ASN* 3.4 7.8 - - - +
302B SER* 4.8 0.9 + - - -
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A 200 3.1 43.9 + + - +
35B TYR* 3.6 39.5 - + + -
38B VAL* 3.4 16.3 - - + +
78B PHE* 3.5 33.4 - + + -
82B LEU* 3.8 17.3 - - + -
85B TRP* 5.5 2.9 - + - -
109B ILE* 3.6 27.9 - - + +
112B ASN* 6.2 0.4 - - - -
261B LYS* 6.4 0.2 - - - -
264B TYR* 5.7 6.6 - + - -
295B THR* 3.0 19.1 + - + -
296B CYS 3.0 9.7 + - - +
298B SER* 1.3 84.9 - - - +
300B VAL* 1.4 62.1 + - + +
301B ASN 3.2 2.0 - - - -
302B SER* 3.4 16.0 + - - -
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 3.8 17.5 - - + -
35B TYR* 6.2 0.2 - - + -
38B VAL* 3.8 22.2 - - + -
260B CYS* 5.7 0.9 - - - -
296B CYS* 3.1 16.1 + - - +
297B ILE* 3.4 20.8 + - + +
299B TYR* 1.4 71.3 - - - +
301B ASN* 1.4 58.4 + - - +
302B SER 3.0 10.9 + - - -
303B CYS* 3.0 23.9 + - - -
304B LEU* 3.2 29.6 + - + +
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Residues in contact with ASN 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASP* 5.3 3.2 + - - -
116B SER* 5.4 5.3 + - - -
253B LEU 5.2 0.2 - - - +
256B THR* 3.9 3.5 + - - +
257B PHE* 3.4 39.6 + - - +
260B CYS* 3.7 21.9 - - + +
261B LYS* 3.2 19.5 - - - +
297B ILE 3.6 4.2 + - - -
298B SER 3.4 17.3 - - - +
300B VAL* 1.4 74.5 - - - +
302B SER* 1.4 62.0 + - - +
304B LEU* 3.4 22.2 + - - +
305B ASN* 3.8 25.3 + - - +
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 4.6 0.2 - - - -
46B ASN* 3.0 24.0 + - - +
75B ASP* 3.0 32.9 + - - +
78B PHE* 3.3 25.8 - - - -
79B VAL* 3.9 22.2 - - - -
112B ASN* 4.0 6.9 + - - -
261B LYS* 5.5 1.6 + - - -
298B SER 5.3 0.5 + - - -
299B TYR* 3.4 11.6 + - - -
300B VAL 3.0 0.8 + - - -
301B ASN* 1.4 78.8 - - - +
303B CYS* 1.3 57.3 + - - +
304B LEU 3.7 0.2 + - - -
306B PRO* 4.2 3.3 - - - +
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Residues in contact with CYS 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.7 45.5 - - + +
41B LEU* 4.0 21.1 - - + +
42B GLY* 3.7 17.9 - - - +
46B ASN* 4.4 0.2 - - - +
300B VAL* 3.0 24.9 + - - -
302B SER* 1.3 75.7 - - - +
304B LEU* 1.3 60.9 + - - +
305B ASN 3.6 1.3 - - - -
306B PRO* 3.4 11.2 - - - +
307B PHE* 3.2 26.4 - - - -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B THR* 4.1 27.4 - - + -
260B CYS* 4.0 26.7 - - - -
300B VAL* 3.2 30.9 + - + +
301B ASN* 3.6 14.8 - - - +
302B SER 3.4 0.6 - - - -
303B CYS* 1.3 78.9 - - - +
305B ASN* 1.4 64.1 + - - +
307B PHE* 3.4 13.5 + - + +
308B LEU* 3.3 29.0 + - + +
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Residues in contact with ASN 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 5.2 2.2 + - - +
71B LEU* 3.5 23.0 - - - +
75B ASP* 3.0 25.9 + - - +
120B LEU* 5.8 0.8 - - - +
253B LEU* 3.3 24.1 - - + +
256B THR* 4.8 2.1 + - - -
301B ASN* 3.8 23.1 + - - +
304B LEU* 1.4 71.6 - - - +
306B PRO* 1.4 65.5 - - + +
308B LEU* 2.9 31.1 + - - +
309B TYR* 3.0 33.7 + - + +
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Residues in contact with PRO 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU 5.2 0.2 - - - +
45B GLY* 3.5 42.2 - - - +
46B ASN* 3.8 12.1 - - - +
48B LEU* 6.5 0.4 - - + -
49B VAL* 4.0 11.9 - - + -
302B SER 4.2 5.2 - - - +
303B CYS* 3.4 21.8 - - - +
305B ASN* 1.4 91.3 - - + +
307B PHE* 1.3 57.7 + - + +
309B TYR* 3.6 10.5 + - + -
310B ALA* 3.2 24.9 + - - +
316B PHE* 3.7 12.4 - - + -
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 3.7 44.9 - - + -
45B GLY* 6.6 0.2 - - - -
303B CYS* 3.2 28.3 - - - -
304B LEU* 3.4 12.0 + - + +
305B ASN 3.2 0.4 - - - -
306B PRO* 1.3 79.5 - - + +
308B LEU* 1.4 63.3 + - - +
310B ALA* 3.3 7.7 + - + +
311B PHE* 3.2 45.0 + + + -
----------------------------------------------------------
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B ILE* 5.8 0.8 - - - +
252B VAL* 3.9 34.4 - - + +
253B LEU* 4.2 13.0 - - + -
256B THR* 3.4 37.7 - - + +
304B LEU* 3.3 22.6 + - + +
305B ASN* 2.9 24.5 + - - +
307B PHE* 1.4 77.6 - - + +
309B TYR* 1.4 59.0 + - - +
311B PHE* 5.1 1.1 - - - -
312B PHE* 3.0 45.1 + - + +
----------------------------------------------------------
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Residues in contact with TYR 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 6.1 0.4 - - - -
49B VAL* 4.1 20.6 - - + -
68B ILE* 3.7 34.3 + - + +
71B LEU* 3.4 26.8 - - + +
249B ILE* 3.8 21.1 - - + -
253B LEU* 3.6 33.6 - - + +
305B ASN* 3.0 35.0 + - + -
306B PRO* 3.6 8.0 + - + +
307B PHE 3.3 0.2 - - - -
308B LEU* 1.4 76.0 - - - +
310B ALA* 1.3 57.6 + - - +
311B PHE 3.3 0.2 - - - -
313B ASP* 2.9 46.5 + - + +
316B PHE* 3.6 26.9 - + + -
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B PRO 3.2 14.3 + - - +
307B PHE* 3.3 15.2 + - + +
309B TYR* 1.3 77.8 - - - +
311B PHE* 1.3 65.0 + - + +
316B PHE* 3.9 13.4 - - + -
317B ARG* 3.3 31.0 + - + +
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 3.2 38.4 + + + +
308B LEU* 5.1 0.4 - - - -
310B ALA* 1.3 84.2 - - + +
312B PHE* 1.4 80.9 + - + +
317B ARG* 3.6 13.7 + - - +
----------------------------------------------------------
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Residues in contact with PHE 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ARG* 5.2 3.5 - - - +
248B SER* 5.1 11.6 - - - +
249B ILE* 4.0 17.6 - - + +
252B VAL* 3.8 44.0 - - + -
308B LEU* 3.0 32.1 + - + +
311B PHE* 1.4 95.0 - - + +
313B ASP* 1.3 61.0 + - - +
314B PRO* 3.4 13.9 - - - +
317B ARG* 3.5 7.9 + - - +
----------------------------------------------------------
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 2.9 32.0 + - - -
68B ILE* 5.1 2.9 - - - +
249B ILE* 3.4 21.8 - - + +
309B TYR* 2.9 44.5 + - + +
312B PHE* 1.3 74.8 - - - +
314B PRO* 1.4 63.4 - - - +
315B ARG* 3.0 19.4 + - - +
316B PHE* 2.8 33.7 + - + -
317B ARG* 3.4 17.4 + - - -
----------------------------------------------------------
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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