Contacts of the helix formed by residues 259 - 291 (chain A) in PDB entry 2B9S
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 SER 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLU* 3.2 21.8 - - - -
175A GLN 4.6 2.5 - - - +
255A LEU* 3.3 34.5 - - - +
256A ALA* 2.8 23.8 + - - +
257A PRO 3.6 2.3 - - - +
258A SER* 1.3 83.2 + - - +
260A SER* 1.3 59.1 + - - +
261A VAL* 3.6 2.5 - - - +
262A LYS* 3.3 13.7 + - - +
263A GLY* 3.0 23.0 + - - -
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 3.6 33.0 - - - +
169A TRP* 5.3 5.5 - - - -
172A ARG* 5.7 0.3 - - - +
174A GLU* 2.7 27.0 + - - -
258A SER 3.9 0.6 + - - -
259A SER* 1.3 72.1 - - - +
261A VAL* 1.3 61.6 + - - +
263A GLY* 4.3 0.7 - - - +
264A GLN* 2.9 45.8 + - - +
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 3.5 25.9 + - + +
169A TRP* 3.7 38.6 - - + +
174A GLU* 4.9 0.6 + - - -
237A THR* 4.1 10.5 - - + -
255A LEU* 3.7 25.8 - - + -
259A SER* 3.6 12.8 - - - +
260A SER* 1.3 81.2 + - - +
262A LYS* 1.3 69.1 + - + +
264A GLN* 4.3 7.8 - - - +
265A SER* 3.4 22.9 + - - -
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A THR* 5.3 3.1 + - - -
254A MET* 3.9 25.8 - - - +
255A LEU* 3.3 27.6 - - - +
256A ALA 3.3 9.9 - - - +
257A PRO* 3.6 24.5 - - + +
259A SER* 3.3 17.6 + - - +
260A SER 3.2 0.2 - - - -
261A VAL* 1.3 82.1 - - + +
263A GLY* 1.3 60.6 + - - +
265A SER* 3.3 5.1 + - - -
266A ASP* 2.9 32.5 + - - +
8C C 4.9 0.2 - - - -
9C T 2.7 38.5 + - - +
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Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 3.7 10.5 - - - -
257A PRO 4.3 4.7 + - - -
259A SER 3.0 15.7 + - - -
260A SER* 3.8 1.8 - - - -
262A LYS* 1.3 77.3 - - - +
264A GLN* 1.3 55.1 + - - +
266A ASP* 3.2 7.3 - - - +
267A MET* 2.9 26.2 + - - +
250B LYS 4.9 2.9 - - - -
253B TRP* 3.6 24.8 + - - -
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Residues in contact with GLN 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 3.5 55.9 - - + +
36A LEU* 4.2 7.3 - - - +
38A ILE* 3.7 35.1 - - + +
39A ALA 5.2 1.0 + - - -
260A SER* 2.9 34.9 + - - +
261A VAL* 4.3 6.2 - - - +
263A GLY* 1.3 74.5 - - - +
265A SER* 1.3 65.3 + - - +
267A MET* 3.4 2.1 + - - +
268A VAL* 3.1 28.6 + - - +
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 4.7 4.2 - - - +
45A ARG* 4.6 13.5 - - - -
261A VAL 3.4 14.2 + - - -
262A LYS* 3.3 8.7 + - - +
263A GLY 3.4 0.4 - - - -
264A GLN* 1.3 79.4 - - - +
266A ASP* 1.3 58.8 + - - +
268A VAL* 3.6 9.0 + - - +
269A LYS* 3.0 28.6 + - - +
9C T 2.9 27.2 + - - -
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Residues in contact with ASP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS 2.9 18.6 + - - +
263A GLY* 3.2 10.6 - - - +
265A SER* 1.3 79.7 + - - +
267A MET* 1.3 58.4 + - - +
269A LYS* 2.8 36.4 + - - +
270A PHE* 3.1 32.7 + - - -
220B ILE 5.3 0.2 - - - +
250B LYS* 3.7 19.3 + - - +
251B PHE* 3.6 25.7 - - - -
253B TRP* 4.2 7.0 + - + -
9C T 5.9 0.3 - - - +
10C T 4.7 0.2 + - - -
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Residues in contact with MET 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 3.8 28.5 - - + -
31A TRP* 4.3 13.9 - - + +
38A ILE* 5.1 7.4 - - - -
263A GLY 2.9 15.4 + - - +
264A GLN 3.9 4.3 - - - +
265A SER 3.4 0.2 - - - -
266A ASP* 1.3 73.1 - - - +
268A VAL* 1.3 61.8 + - - +
270A PHE* 3.1 3.6 + - - +
271A GLU* 2.8 42.0 + - + +
226B ARG* 4.1 17.7 - - - +
253B TRP* 3.5 45.5 - - + +
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Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.8 32.3 - - + +
40A MET* 6.5 1.3 - - + -
264A GLN 3.1 20.8 + - - +
265A SER* 3.8 7.9 - - - +
267A MET* 1.3 76.8 - - + +
269A LYS* 1.3 58.3 + - - +
271A GLU* 3.2 10.2 + - + +
272A LYS* 3.0 38.9 + - + +
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER 3.0 17.7 + - - +
266A ASP* 2.8 29.7 + - - +
268A VAL* 1.3 77.5 - - - +
270A PHE* 1.3 83.3 + - - +
272A LYS* 3.4 16.3 + - - +
273A ALA* 3.3 19.2 + - - +
407A LYS* 4.2 11.4 - - - +
408A VAL* 5.3 1.6 - - - +
411A THR* 4.5 12.3 - - + +
220B ILE 5.4 0.6 + - - -
221B ASN* 3.0 24.7 + - - +
250B LYS* 6.0 1.0 - - - +
9C T 4.3 5.8 - - - +
10C T 2.9 39.1 + - - +
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ASP* 3.1 25.2 + - - -
267A MET* 3.1 7.1 + - - +
269A LYS* 1.3 89.7 - - - +
271A GLU* 1.3 64.7 + - - +
273A ALA* 3.4 4.4 + - - +
274A ARG* 3.2 26.7 + - - +
411A THR* 3.6 19.3 - - + -
415A SER* 4.2 2.0 - - - -
221B ASN 3.8 19.3 - - - -
222B TYR 3.3 17.0 - - - -
223B ILE 3.2 15.9 - - - -
224B ASP* 3.2 43.1 - - + +
225B PRO* 3.6 21.5 - - + -
226B ARG* 3.9 5.8 - - - +
251B PHE* 4.9 5.8 - + - -
253B TRP* 4.0 7.2 - + - -
262B PHE* 3.9 2.5 - + - -
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET* 2.8 32.5 + - + +
268A VAL* 3.2 9.8 + - + +
270A PHE* 1.3 76.1 - - - +
272A LYS* 1.3 56.9 + - - +
274A ARG* 3.1 26.5 + - - +
275A LYS* 3.1 24.6 + - - +
226B ARG* 2.6 37.9 + - - +
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 3.0 31.8 + - + +
269A LYS* 3.8 14.6 - - - +
270A PHE 3.3 0.4 - - - -
271A GLU* 1.3 75.6 - - - +
273A ALA* 1.3 57.5 + - - +
275A LYS* 3.2 1.9 + - + -
276A LEU* 2.9 26.3 + - - +
401A MET* 3.3 25.7 - - + +
402A ASP 4.9 2.0 - - - +
403A GLY* 3.1 39.4 + - - +
405A SER* 5.7 0.4 + - - -
408A VAL* 4.0 21.4 - - + +
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Residues in contact with ALA 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LYS 3.3 6.7 + - - +
270A PHE 3.4 6.2 + - - +
272A LYS* 1.3 74.4 - - - +
274A ARG* 1.3 56.2 + - - +
276A LEU* 3.4 5.5 + - - +
277A LYS* 3.1 21.3 + - - +
408A VAL* 3.9 13.3 - - + +
411A THR* 3.7 29.6 - - + -
412A TYR* 3.6 23.2 - - - +
262B PHE* 3.6 20.8 - - + -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE 3.2 10.5 + - - +
271A GLU* 3.1 42.7 + - - +
273A ALA* 1.3 71.3 - - - +
275A LYS* 1.3 64.7 + - - +
277A LYS* 3.3 20.1 - - - +
278A ASP* 3.6 12.1 - - - +
224B ASP* 4.0 0.2 - - - -
226B ARG* 3.9 12.4 - - - +
260B PHE* 3.4 27.8 - - - -
261B ASP 2.6 24.5 + - - +
262B PHE* 3.1 47.3 + - + +
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A GLU 3.1 17.4 + - - +
272A LYS* 3.2 6.2 + - - +
274A ARG* 1.3 73.0 - - - +
276A LEU* 1.3 65.0 + - - +
278A ASP* 3.4 10.8 + - - +
279A LYS* 3.4 18.9 + - - +
401A MET* 3.9 19.6 - - + +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A LYS 2.9 13.5 + - - +
273A ALA 3.4 8.3 - - - +
275A LYS* 1.3 72.7 - - - +
277A LYS* 1.3 56.4 + - - +
278A ASP 3.1 2.5 - - - -
279A LYS* 2.8 3.9 + - + +
280A VAL* 2.8 47.2 + - + +
283A ILE* 3.6 29.6 - - + -
401A MET* 3.8 5.6 - - - -
404A LEU* 3.7 20.4 - - + -
408A VAL* 3.9 8.7 - - + +
409A PHE* 3.8 42.4 - - + +
412A TYR* 3.7 26.2 - - + -
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ALA 3.1 10.6 + - - +
274A ARG* 3.3 14.1 - - - +
276A LEU* 1.3 75.4 - - - +
278A ASP* 1.3 73.7 + - - +
280A VAL* 3.8 11.8 - - - +
281A ASP* 5.1 1.9 + - - +
412A TYR* 3.5 29.7 + - + +
416A ILE* 4.3 16.6 - - + -
419A ASP* 5.7 0.2 - - - -
261B ASP* 5.9 2.6 - - - +
262B PHE* 3.2 38.3 + - + +
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Residues in contact with ASP 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ARG 3.6 12.9 + - - +
275A LYS* 3.4 10.2 + - - +
276A LEU 3.1 0.8 - - - -
277A LYS* 1.3 93.0 + - - +
279A LYS* 1.3 59.4 + - - +
280A VAL 3.4 0.4 - - - -
281A ASP* 5.1 1.6 + - - +
282A ASP* 3.6 10.2 - - - +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS 3.4 11.6 + - - +
276A LEU* 2.8 9.6 + - - +
278A ASP* 1.3 77.0 - - - +
280A VAL* 1.3 64.9 + - - +
281A ASP 3.5 1.8 - - - -
282A ASP* 3.2 21.4 + - + +
283A ILE* 3.2 27.3 + - + +
400A PHE* 4.8 14.1 - - + +
401A MET* 4.9 9.6 - - + -
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 2.8 38.8 + - + +
277A LYS 3.8 9.6 - - - +
278A ASP 3.4 1.6 - - - -
279A LYS* 1.3 76.4 - - - +
281A ASP* 1.3 71.5 + - - +
283A ILE* 3.0 17.7 + - - +
284A ARG* 3.1 56.0 + - - +
409A PHE* 4.4 11.0 - - + -
412A TYR* 3.8 29.2 - - + +
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Residues in contact with ASP 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LYS 5.1 2.0 + - - +
278A ASP 5.1 1.5 + - - +
279A LYS 3.5 0.8 - - - -
280A VAL* 1.3 90.3 - - - +
282A ASP* 1.3 64.1 + - - +
284A ARG* 3.5 15.0 + - - +
285A ALA* 3.2 28.1 + - - +
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Residues in contact with ASP 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASP 3.6 15.2 - - - +
279A LYS* 3.2 15.2 + - + +
281A ASP* 1.3 80.0 - - - +
283A ILE* 1.3 63.9 + - + +
285A ALA* 4.0 6.3 - - - +
286A SER* 3.3 20.6 + - - -
400A PHE* 4.1 8.8 - - + -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 3.6 30.7 - - + -
279A LYS* 3.2 20.4 + - + +
280A VAL* 3.0 8.0 + - - +
282A ASP* 1.3 76.7 - - - +
284A ARG* 1.3 61.6 + - + +
286A SER* 3.3 3.6 + - - -
287A TYR* 2.9 37.1 + - + +
305A MET* 3.8 22.6 - - + +
397A LEU* 5.0 0.7 - - + -
400A PHE* 3.6 34.3 - - + -
404A LEU* 3.8 18.4 - - + -
409A PHE* 4.2 18.4 - - + -
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 3.2 41.3 - - - +
281A ASP* 3.8 14.9 + - - +
282A ASP 3.4 0.2 - - - -
283A ILE* 1.3 76.0 - - + +
285A ALA* 1.3 58.5 + - - +
286A SER 3.2 0.2 - - - -
287A TYR* 3.6 16.0 - - + +
288A MET* 3.1 53.4 + - + +
309A ASP* 2.7 41.7 + - - +
310A ARG* 3.4 36.1 - - - +
412A TYR* 4.1 14.6 + - - -
413A ASN* 5.6 0.6 + - - -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASP 3.2 15.3 + - - +
282A ASP* 4.2 6.5 - - - +
284A ARG* 1.3 77.9 - - - +
286A SER* 1.3 62.0 + - - +
288A MET* 3.7 6.9 + - - +
289A GLU* 3.3 22.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A ASP 3.3 14.3 + - - -
283A ILE 3.3 10.5 + - - -
284A ARG 3.2 0.2 - - - -
285A ALA* 1.3 80.3 - - - +
287A TYR* 1.3 60.9 + - - +
289A GLU* 3.4 7.7 + - - +
290A ASP* 3.3 29.5 + - - +
305A MET* 5.7 0.2 - - - +
396A HIS* 4.6 4.2 + - - -
400A PHE* 3.3 27.2 - - - -
----------------------------------------------------------
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Residues in contact with TYR 287 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 2.9 31.2 + - + +
284A ARG* 3.6 28.5 - - + +
286A SER* 1.3 74.4 - - - +
288A MET* 1.3 70.1 + - + +
290A ASP* 3.1 11.2 + - - +
291A PHE* 3.0 43.0 + + - -
302A ALA* 3.5 17.0 - - - +
305A MET* 3.8 50.6 - - + +
306A TYR* 3.8 29.0 - + + -
309A ASP* 2.8 29.9 + - + +
310A ARG* 3.7 13.2 + - - -
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ARG* 3.1 48.1 + - + +
285A ALA* 4.0 7.0 - - - +
286A SER 3.3 0.2 - - - -
287A TYR* 1.3 85.9 - - + +
289A GLU* 1.3 60.6 + - - +
291A PHE* 3.6 42.2 - - + +
292A LYS* 4.4 3.3 + - - +
306A TYR* 6.1 0.4 - - + -
310A ARG* 5.5 4.5 - - - +
364A LEU* 4.5 16.4 - - + -
----------------------------------------------------------
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Residues in contact with GLU 289 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ALA 3.3 13.5 + - - +
286A SER* 3.6 9.6 - - - +
287A TYR 3.3 0.2 - - - -
288A MET* 1.3 76.3 - - - +
290A ASP* 1.3 64.0 + - - +
291A PHE 3.3 0.2 - - - -
292A LYS* 3.3 19.4 + - - +
293A SER* 4.0 2.8 + - - -
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A SER* 3.3 18.5 + - - +
287A TYR* 3.1 16.9 + - - +
289A GLU* 1.3 76.5 - - - +
291A PHE* 1.3 64.9 + - - +
292A LYS 3.0 2.0 - - - -
293A SER* 3.0 22.7 + - - -
298A VAL* 3.6 27.4 - - + +
299A ALA* 3.6 10.9 - - - -
301A ARG* 4.2 12.5 + - - -
302A ALA* 3.6 15.5 - - + +
305A MET* 5.4 1.2 - - - +
396A HIS* 4.3 10.0 + - - -
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Residues in contact with PHE 291 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 3.0 30.5 + + - -
288A MET* 3.6 41.1 - - + +
289A GLU 3.3 0.2 - - - -
290A ASP* 1.3 76.8 - - - +
292A LYS* 1.3 58.3 + - + +
293A SER 3.3 3.7 + - - +
299A ALA* 4.6 0.5 - - - +
302A ALA* 3.5 34.1 - - + -
303A VAL* 3.8 3.8 - - + -
306A TYR* 3.9 5.8 - + + -
364A LEU* 4.0 11.7 - - + -
366A GLU* 4.5 20.9 - - + -
367A VAL* 3.3 32.5 - - + -
370A LEU* 3.7 42.2 - - + +
373A ARG* 5.4 0.5 + - - -
----------------------------------------------------------
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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