Contacts of the helix formed by residues 252 - 285 (chain A) in PDB entry 4KJW
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 LEU 252 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA* 4.9 5.6 - - + +
248A PRO 3.9 10.5 - - - +
249A LEU* 3.3 32.5 + - + +
251A THR* 1.3 79.8 - - - +
253A TRP* 1.3 57.8 + - - +
254A LEU 3.0 0.2 - - - -
255A TYR* 2.9 28.3 + - + +
256A LEU* 3.4 9.0 + - - +
423A LEU* 3.8 27.1 - - + -
424A PRO* 4.2 28.7 - - + -
427A ILE* 4.2 26.6 - - + +
227B ILE* 4.3 15.5 - - + -
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Residues in contact with TRP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU 4.9 0.2 + - - -
250A ASN* 3.2 21.9 + - - -
251A THR 4.1 1.3 - - - -
252A LEU* 1.3 77.3 - - - +
254A LEU* 1.3 84.2 + - + +
255A TYR 3.2 0.2 - - - -
256A LEU* 3.6 12.0 + - + +
257A ILE* 3.3 60.6 + - + +
379A PHE* 4.0 20.6 - + - -
382A TYR* 3.1 36.2 + + - -
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR* 3.1 16.0 + - - +
252A LEU 3.0 0.6 + - - -
253A TRP* 1.3 114.7 - - + +
255A TYR* 1.3 59.7 + - - +
257A ILE* 3.7 5.1 + - + +
258A LEU* 3.2 12.3 + - - +
371A PHE* 3.2 34.8 - - + -
375A ALA* 4.3 4.0 - - + -
379A PHE* 3.8 16.8 - - + -
382A TYR* 3.9 18.8 - - + -
384A LEU* 3.8 29.2 - - + -
389A PHE* 3.7 20.2 - - + -
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Residues in contact with TYR 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA* 4.2 8.9 - - + +
251A THR* 3.6 33.5 - - + +
252A LEU* 2.9 14.2 + - - +
254A LEU* 1.3 77.2 - - - +
256A LEU* 1.3 59.8 + - - +
257A ILE 3.2 0.2 - - - -
258A LEU* 3.2 5.6 + - + +
259A GLY 2.8 24.8 + - - -
384A LEU* 5.3 0.9 - - - +
388A THR* 3.2 43.3 + - - -
389A PHE* 3.4 33.6 - + - -
392A ALA* 3.7 5.8 - - + -
424A PRO* 3.5 45.1 - - + +
427A ILE* 4.2 6.5 - - + -
428A THR* 3.3 27.6 + - - +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A LEU 3.4 5.3 + - - +
253A TRP* 3.9 13.2 - - - +
254A LEU 3.5 0.2 - - - -
255A TYR* 1.3 77.6 - - - +
257A ILE* 1.3 63.3 + - + +
259A GLY* 3.4 1.1 + - - +
260A ILE* 3.1 42.3 + - + +
427A ILE* 3.7 24.3 - - + +
431A GLY* 4.4 19.5 - - - +
434A LEU* 6.4 2.0 - - + -
435A LEU* 6.5 0.2 - - + -
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TRP* 3.3 44.3 + - + +
254A LEU* 3.7 13.0 - - + +
255A TYR 3.2 0.2 - - - -
256A LEU* 1.3 79.3 - - + +
258A LEU* 1.3 62.3 + - - +
260A ILE* 3.1 14.6 + - + +
261A ILE* 3.0 29.8 + - + +
371A PHE* 4.0 19.5 - - + -
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU 3.2 11.3 + - - +
255A TYR* 3.2 9.3 + - + +
257A ILE* 1.3 78.8 - - - +
259A GLY* 1.3 62.0 + - - +
261A ILE* 3.3 13.8 + - + +
262A PHE* 3.1 39.7 + - + -
367A LEU* 4.5 4.9 - - + +
368A GLY* 4.3 7.6 - - - -
371A PHE* 3.6 40.4 - - + -
389A PHE* 3.5 33.4 - - + +
392A ALA* 4.6 2.5 - - + -
393A GLY* 4.5 5.6 - - - +
428A THR* 3.8 17.7 - - + +
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Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A TYR 2.8 12.9 + - - -
256A LEU 3.8 2.5 - - - -
257A ILE 3.2 0.4 - - - -
258A LEU* 1.3 73.6 - - - +
260A ILE* 1.3 54.0 + - - +
262A PHE* 3.2 4.0 + - - +
263A GLY 2.7 29.1 + - - -
428A THR* 3.2 32.2 - - - +
431A GLY* 3.6 8.5 - - - -
432A ALA* 3.2 13.1 - - - -
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Residues in contact with ILE 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 3.1 35.2 + - + +
257A ILE* 3.1 14.8 + - + +
259A GLY* 1.3 77.6 - - - +
261A ILE* 1.3 59.6 + - + +
263A GLY* 2.8 15.4 + - - -
264A ILE* 3.1 20.2 + - + +
431A GLY 4.0 6.7 - - - +
435A LEU* 3.7 35.6 - - + +
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 3.0 20.1 + - + +
258A LEU* 3.5 12.3 - - + +
259A GLY 3.3 0.2 - - - -
260A ILE* 1.3 78.4 - - + +
262A PHE* 1.3 61.8 + - - +
264A ILE* 3.7 12.7 + - + +
265A PHE* 3.5 20.9 + - + +
367A LEU* 5.0 17.5 - - + -
371A PHE* 3.7 35.7 - - + -
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Residues in contact with PHE 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 3.1 43.9 + - + +
259A GLY 3.4 8.3 - - - +
261A ILE* 1.3 76.6 - - + +
263A GLY* 1.3 57.5 + - - +
265A PHE* 4.5 4.5 - + - -
266A GLY 2.9 27.7 + - - -
337A PHE* 6.0 0.2 - + - -
363A LEU 5.1 0.2 - - - -
364A GLY* 3.5 23.3 - - - -
367A LEU* 3.5 30.7 - - + -
368A GLY 4.6 0.4 - - - -
393A GLY* 3.4 24.0 - - - -
396A ALA* 3.5 22.7 - - + +
397A LEU* 3.6 36.8 - - + -
400A ALA* 3.3 9.1 - - - +
428A THR* 4.9 0.7 - - + -
432A ALA* 4.1 13.2 - - + -
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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
----------------------------------------------------------
259A GLY 2.7 12.9 + - - -
260A ILE 2.8 8.8 + - - -
262A PHE* 1.3 79.0 - - - +
264A ILE* 1.3 54.3 + - - -
267A PRO* 3.3 8.5 - - - +
400A ALA* 4.5 0.4 - - - -
432A ALA 3.3 22.4 - - - -
435A LEU* 3.2 29.8 - - - +
436A ALA* 3.2 11.1 + - - -
439A THR* 3.5 0.3 + - - -
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Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ILE* 3.1 19.6 + - + +
261A ILE* 3.8 15.0 - - + +
263A GLY* 1.3 77.7 - - - +
265A PHE* 1.3 67.6 + - + +
267A PRO* 4.1 3.8 - - - +
268A ILE* 3.2 31.2 + - + +
435A LEU* 4.3 17.3 - - + -
439A THR* 4.3 18.6 + - + -
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Residues in contact with PHE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ILE* 3.5 15.5 + - + +
262A PHE* 3.2 5.7 + + - +
264A ILE* 1.3 84.7 - - + +
266A GLY* 1.3 57.1 + - - +
268A ILE* 3.1 14.5 + - + +
269A PHE* 2.8 63.7 + + + -
272A TRP* 4.7 17.7 - + - -
337A PHE* 3.8 35.0 - + - -
341A VAL* 4.5 8.1 - - + -
363A LEU* 5.9 0.7 - - + -
367A LEU* 4.7 12.3 - - + -
397A LEU* 4.1 26.2 - - + -
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Residues in contact with GLY 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE 2.9 16.1 + - - -
265A PHE* 1.3 78.4 - - - +
267A PRO* 1.3 56.5 - - - +
269A PHE* 3.1 1.0 + - - +
270A ASN* 2.7 31.9 + - - +
397A LEU* 4.2 5.4 - - - -
400A ALA* 3.8 15.3 - - - -
401A SER* 3.2 22.4 + - - -
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Residues in contact with PRO 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY 3.3 14.6 - - - +
264A ILE 4.1 3.8 - - - +
265A PHE 3.8 1.8 - - - -
266A GLY* 1.3 89.3 - - - +
268A ILE* 1.3 57.3 + - + +
270A ASN* 3.1 12.5 + - + +
271A LYS* 2.9 41.0 + - - +
400A ALA 4.0 7.8 - - - +
436A ALA* 3.6 20.6 - - + +
439A THR* 3.5 27.6 - - - +
440A GLY 4.9 0.2 - - - -
441A GLY* 3.6 21.8 - - - +
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 3.2 26.5 - - + +
265A PHE* 3.1 18.9 + - + +
267A PRO* 1.3 72.9 - - + +
269A PHE* 1.3 67.5 + - - +
271A LYS* 3.2 24.0 + - + +
272A TRP* 3.2 49.8 + - + +
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Residues in contact with PHE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A PHE* 2.8 43.5 + + + +
266A GLY 3.5 6.1 - - - +
268A ILE* 1.3 74.5 - - - +
270A ASN* 1.3 64.2 + - - +
272A TRP* 3.1 13.1 + + - +
273A VAL* 3.1 27.3 + - + +
341A VAL* 4.4 18.4 - - + -
344A THR* 4.2 11.2 - - + -
345A LEU* 3.8 25.8 - - + -
356A ILE* 3.9 24.7 - - + -
360A MET* 3.9 21.3 - - + -
363A LEU* 4.2 19.7 - - + -
397A LEU* 4.4 4.7 - - + -
401A SER* 3.7 18.6 - - - +
444A LEU* 5.5 1.1 - - + -
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Residues in contact with ASN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY 2.7 12.8 + - - +
267A PRO* 3.2 14.6 - - + +
269A PHE* 1.3 78.7 - - - +
271A LYS* 1.3 60.5 + - + +
273A VAL* 3.1 17.7 - - - +
274A LEU* 3.4 20.2 - - + +
400A ALA 4.6 2.2 + - - -
401A SER* 3.0 38.2 + - - +
441A GLY* 6.0 0.2 - - - -
442A LYS 2.5 35.1 + - - +
444A LEU* 3.2 25.6 - - + +
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Residues in contact with LYS 271 (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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267A PRO* 2.9 25.5 + - - +
268A ILE* 3.2 16.5 + - + +
270A ASN* 1.3 75.0 - - - +
272A TRP* 1.3 60.2 + - + +
274A LEU* 3.2 8.7 + - - +
275A GLY* 2.6 36.2 + - - -
439A THR 5.8 4.0 + - - -
440A GLY 5.9 3.4 - - - -
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Residues in contact with TRP 272 (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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265A PHE* 4.7 14.8 - + - -
268A ILE* 3.2 34.0 + - + +
269A PHE* 3.1 17.6 + + - +
271A LYS* 1.3 84.0 - - + +
273A VAL* 1.3 52.6 + - - +
275A GLY* 4.9 1.1 - - - -
276A MET* 2.7 42.9 + - + +
341A VAL* 3.9 30.3 - - + -
345A LEU* 3.7 21.1 - - + -
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PHE* 3.1 20.5 + - + +
270A ASN* 3.1 26.2 - - - +
272A TRP* 1.3 72.9 - - - +
274A LEU* 1.3 61.3 + - - +
277A GLN* 3.2 19.8 + - - +
345A LEU* 3.6 13.6 - - + +
348A PHE* 3.7 30.7 - - + -
349A SER* 2.8 31.5 + - - +
356A ILE* 4.4 4.9 - - + -
444A LEU* 3.9 27.1 - - + -
448A ILE* 5.1 0.7 - - + -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 3.4 17.9 + - + +
271A LYS* 3.2 9.5 + - - +
273A VAL* 1.3 78.5 - - + +
275A GLY* 1.3 61.6 + - - +
277A GLN* 3.2 30.6 - - - +
278A ASP* 3.4 3.1 + - - -
444A LEU* 4.3 8.7 - - + -
447A ALA* 4.4 20.9 - - + +
448A ILE* 3.9 24.7 - - + -
451A ARG* 2.8 44.7 + - + +
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Residues in contact with GLY 275 (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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271A LYS 2.6 21.0 + - - -
272A TRP* 3.8 1.6 - - - -
274A LEU* 1.3 74.4 - - - +
276A MET* 1.3 59.1 + - - +
278A ASP* 3.3 13.0 + - - +
279A LEU* 3.1 26.2 + - - +
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Residues in contact with MET 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TRP* 2.7 27.6 + - + +
274A LEU 3.3 0.2 - - - -
275A GLY* 1.3 71.8 - - - +
277A GLN* 1.3 64.4 + - - +
278A ASP 3.2 0.2 - - - -
279A LEU* 3.9 29.8 - - + +
280A LEU* 3.2 40.2 + - + +
345A LEU* 4.3 31.2 - - + +
346A LEU* 4.8 10.8 - - + -
349A SER* 3.6 19.3 - - - +
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Residues in contact with GLN 277 (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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273A VAL* 3.2 18.9 + - - +
274A LEU* 3.2 17.9 + - - +
275A GLY 3.2 0.2 - - - -
276A MET* 1.3 79.8 - - - +
278A ASP* 1.3 63.6 + - - +
280A LEU* 4.1 1.4 - - - +
281A HIS* 3.2 22.3 + - - +
348A PHE* 4.4 13.7 + - - -
349A SER* 3.5 26.1 - - - +
448A ILE* 4.0 28.0 - - - +
451A ARG* 3.1 26.2 + - - +
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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 LEU 3.7 7.9 - - - +
275A GLY* 3.3 12.8 + - - +
276A MET 3.2 0.2 - - - -
277A GLN* 1.3 76.0 - - - +
279A LEU* 1.3 66.2 + - - +
281A HIS* 2.9 21.8 + - - +
282A ARG* 3.3 19.4 + - - +
451A ARG* 3.3 28.8 + - - -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLY 3.1 13.1 + - - +
276A MET* 4.3 26.7 - - + +
278A ASP* 1.3 78.9 - - - +
280A LEU* 1.3 71.8 + - + +
282A ARG* 3.5 35.3 + - - +
283A VAL* 3.7 11.2 - - + +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A MET* 3.2 37.5 + - + +
277A GLN 4.3 2.0 - - - +
279A LEU* 1.3 86.4 - - + +
281A HIS* 1.3 62.0 + - - +
282A ARG 3.2 1.1 - - - -
283A VAL* 3.3 20.7 + - + +
284A HIS* 3.0 24.6 - - - +
294A MET* 3.8 21.9 - - + +
298A ILE* 4.5 7.2 - - + -
345A LEU 4.7 1.8 - - - +
346A LEU* 4.1 18.8 - - + +
349A SER 4.1 5.4 - - - +
350A SER* 3.7 35.2 - - - +
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Residues in contact with HIS 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLN 3.2 15.0 + - - +
278A ASP* 2.9 15.3 + - - +
280A LEU* 1.3 76.3 - - - +
282A ARG* 1.3 54.9 + - + +
284A HIS* 3.2 20.1 + + - -
285A GLY* 2.6 49.2 + - - -
286A GLY* 3.9 24.7 - - - -
291A TRP* 4.6 9.9 - + - -
455A LYS* 5.2 12.7 + - - -
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Residues in contact with ARG 282 (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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278A ASP* 3.7 18.7 + - - +
279A LEU* 3.6 25.9 - - - +
280A LEU 3.2 0.4 - - - -
281A HIS* 1.3 78.0 - - + +
283A VAL* 1.3 64.3 + - + +
284A HIS 3.2 0.7 + - - -
285A GLY* 3.6 8.1 + - - +
290A LYS* 5.8 1.0 + - - -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.7 19.7 - - + +
280A LEU* 3.5 20.9 - - + +
281A HIS 3.2 0.6 - - - -
282A ARG* 1.3 77.7 - - + +
284A HIS* 1.3 57.1 + - - +
290A LYS* 3.8 19.2 + - - +
294A MET* 3.7 29.2 - - + -
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 3.0 25.4 + - - +
281A HIS* 3.2 34.1 - - + -
282A ARG 4.3 0.4 - - - -
283A VAL* 1.3 79.6 - - - +
285A GLY* 1.3 56.0 + - - +
286A GLY 2.8 28.2 + - - -
287A ASN* 2.8 24.7 + - - +
290A LYS* 3.5 17.3 + - + +
291A TRP* 3.3 72.1 + + + +
294A MET* 3.5 22.8 - - + +
350A SER 4.8 1.2 + - - -
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A HIS* 2.6 37.3 + - - -
282A ARG* 3.6 8.6 + - - -
284A HIS* 1.3 71.0 - - - +
286A GLY* 1.3 55.0 + - - -
287A ASN 3.5 0.9 - - - -
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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