Contacts of the helix formed by residues 390 - 413 (chain F) in PDB entry 3IFS
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 ASN 390 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F HIS* 5.6 1.8 + - - -
95F MSE 5.5 0.2 - - - +
96F LEU* 3.7 11.2 - - - +
388F GLU* 3.5 30.1 + - + +
389F LEU* 1.3 76.3 - - - +
391F GLU* 1.3 72.7 + - - +
392F TYR* 3.5 10.7 + - - +
393F THR* 2.7 43.5 + - - -
394F PHE* 3.0 22.3 + - - +
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Residues in contact with GLU 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F LEU* 4.0 15.9 - - + +
224F GLY 4.7 1.2 - - - +
225F LEU* 3.5 29.7 - - + +
226F ASN* 2.7 56.6 + - - +
229F GLU* 4.3 5.3 - - + +
230F MSE 3.3 24.1 - - + +
390F ASN* 1.3 80.8 - - - +
392F TYR* 1.3 64.8 + - - +
394F PHE* 3.3 2.4 + - - +
395F GLY 3.1 18.9 + - - -
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Residues in contact with TYR 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F HIS* 3.9 39.5 - + + +
229F GLU* 3.5 35.8 + - + +
232F LYS* 3.7 12.1 - - + -
233F GLY* 3.3 42.0 - - - -
236F ALA* 3.2 20.5 - - + +
390F ASN* 3.3 11.3 + - - +
391F GLU* 1.3 78.4 - - - +
393F THR* 1.3 64.3 + - - +
396F TYR* 3.2 21.7 + + - +
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Residues in contact with THR 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F HIS* 2.9 29.9 + - + +
5F VAL* 4.0 16.6 - - + -
386F ILE* 3.5 22.4 - - + -
387F PRO* 4.2 2.7 - - + -
388F GLU* 3.3 26.6 + - - +
389F LEU* 5.1 0.4 - - - -
390F ASN* 2.7 32.8 + - - -
392F TYR* 1.3 70.2 - - - +
394F PHE* 1.3 60.4 + - - +
396F TYR* 3.3 1.5 + - - +
397F LEU* 2.8 30.4 + - + +
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Residues in contact with PHE 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F GLY* 4.1 10.3 - - - -
91F ALA* 4.4 2.9 - - + -
92F ALA* 3.5 37.2 - - + -
95F MSE 3.8 28.2 - - + -
96F LEU* 4.1 11.4 - - + -
211F VAL* 4.3 13.7 - - + -
212F LEU* 4.8 2.9 - - + -
230F MSE 3.6 33.2 - - + -
281F PHE* 4.1 18.4 - + - -
284F TRP* 6.2 1.8 - + - -
390F ASN 3.0 13.3 + - - +
391F GLU 3.3 7.2 + - - +
393F THR* 1.3 76.5 - - - +
395F GLY* 1.3 58.6 + - - +
397F LEU* 3.8 4.7 - - - +
398F VAL* 2.8 59.5 + - + +
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Residues in contact with GLY 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F LEU* 4.6 3.5 - - - +
230F MSE 3.6 28.3 - - - -
234F ALA* 3.5 21.9 - - - +
391F GLU 3.1 11.9 + - - -
392F TYR 3.4 0.4 + - - -
393F THR 3.4 0.2 - - - -
394F PHE* 1.3 79.8 - - - +
396F TYR* 1.3 61.9 + - - +
398F VAL* 3.7 5.2 - - - +
399F TYR* 3.1 18.2 + - - +
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Residues in contact with TYR 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F THR* 3.1 20.6 - - - -
4F HIS* 3.4 22.8 + - + -
5F VAL* 3.4 35.2 - - + -
233F GLY* 3.4 16.4 - - - +
234F ALA* 4.3 0.9 - - - +
236F ALA* 3.7 11.0 - - + -
237F GLY* 3.3 27.5 - - - -
240F ASP* 2.6 34.4 + - - +
241F PHE* 3.4 26.1 - + - -
392F TYR* 3.2 18.4 + + + +
393F THR* 3.6 8.3 - - - +
395F GLY* 1.3 75.7 - - - +
397F LEU* 1.3 57.1 + - - +
399F TYR* 3.4 3.3 + - - +
400F PHE* 3.0 23.6 + - + +
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Residues in contact with LEU 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 4.1 17.9 - - + -
95F MSE 4.9 12.1 - - + -
278F LEU* 5.7 0.2 - - + -
281F PHE* 3.6 33.7 - - + -
330F LEU* 4.8 0.4 - - + -
384F VAL* 3.9 21.8 - - + -
386F ILE* 3.7 31.2 - - + -
393F THR* 2.8 18.6 + - + +
394F PHE* 3.8 4.3 - - - +
396F TYR* 1.3 75.5 - - - +
398F VAL* 1.3 65.0 + - - +
400F PHE* 3.3 7.2 + - + +
401F PHE* 3.1 47.6 + - + -
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Residues in contact with VAL 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211F VAL* 3.7 19.7 - - + -
212F LEU* 4.2 11.0 - - + -
281F PHE* 4.3 9.4 - - + -
284F TRP* 3.8 19.1 - - + -
394F PHE* 2.8 55.7 + - + +
395F GLY* 3.7 5.6 - - - +
397F LEU* 1.3 77.5 - - - +
399F TYR* 1.3 58.2 + - - +
401F PHE 3.4 0.3 + - - -
402F GLU* 3.0 52.3 + - - +
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Residues in contact with TYR 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F HIS* 5.4 0.5 - - - -
48F TRP* 3.7 18.2 - + - -
49F VAL* 2.7 47.7 + - - +
52F PRO* 3.9 22.0 - - + -
212F LEU* 5.3 2.5 - - + -
234F ALA* 4.0 11.0 - - + +
237F GLY 3.6 19.7 - - - -
238F ARG* 3.4 28.3 + - + +
241F PHE* 4.2 5.2 - + + -
395F GLY 3.1 17.2 + - - +
396F TYR 3.8 3.8 - - - +
397F LEU 3.3 0.2 - - - -
398F VAL* 1.3 73.5 - - - +
400F PHE* 1.3 67.8 + - - +
402F GLU* 4.1 14.6 - - - -
403F LYS* 3.0 49.4 + - + +
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Residues in contact with PHE 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F VAL* 4.7 10.3 - - + -
6F THR 5.7 0.2 - - - -
7F PHE* 4.2 15.9 - + + -
241F PHE* 3.5 36.9 - + + -
250F PRO* 3.7 11.9 - - + -
251F ALA* 3.5 29.2 - - - +
254F TYR* 4.1 26.0 - + + -
384F VAL* 4.2 14.6 - - + -
396F TYR 3.0 15.2 + - - +
397F LEU* 3.4 16.6 - - + +
398F VAL 3.3 0.2 - - - -
399F TYR* 1.3 75.1 - - - +
401F PHE* 1.3 95.9 + + - +
404F ALA* 3.0 28.4 + - - +
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Residues in contact with PHE 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F TYR* 3.7 33.7 - + - -
271F LEU* 4.4 5.4 - - + -
281F PHE* 3.7 27.8 - + - -
284F TRP* 4.0 5.4 - + + -
285F TRP* 3.6 26.2 - + - -
288F LEU* 3.7 16.7 - - + +
289F PHE* 3.8 3.6 - + + -
330F LEU* 3.9 19.5 - - + -
384F VAL* 4.3 7.4 - - + -
397F LEU* 3.1 44.8 + - + +
398F VAL 4.0 2.5 - - - +
400F PHE* 1.3 91.4 - + - +
402F GLU* 1.3 61.0 + - - +
404F ALA* 3.7 2.7 - - - +
405F CYS* 2.8 31.5 + - - +
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Residues in contact with GLU 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F TRP* 3.6 35.4 - - + +
209F PHE* 3.6 48.5 - - + +
211F VAL* 4.3 4.0 - - - +
212F LEU* 4.9 6.3 - - - +
284F TRP* 4.1 14.3 - - + -
288F LEU* 4.1 8.7 - - + -
398F VAL* 3.0 41.7 + - + +
399F TYR* 3.8 15.6 - - - +
401F PHE* 1.3 74.5 - - - +
403F LYS* 1.3 63.9 + - - +
405F CYS* 3.3 4.5 + - - +
406F ALA 3.1 17.5 + - - -
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Residues in contact with LYS 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ILE* 4.1 19.9 - - + +
36F HIS* 2.8 38.7 + - - -
48F TRP* 3.9 15.0 - - + -
49F VAL* 4.6 1.8 - - + -
241F PHE* 2.8 38.5 + - + +
242F GLY* 3.8 4.0 - - - -
251F ALA* 4.3 7.2 - - + -
252F TYR* 3.1 24.9 + - + -
399F TYR* 3.0 41.8 + - + +
400F PHE 4.0 2.2 - - - +
402F GLU* 1.3 73.2 - - - +
404F ALA* 1.3 65.4 + - - +
406F ALA* 3.3 3.8 + - - +
407F MSE 3.1 22.9 + - - +
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Residues in contact with ALA 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F ALA* 3.5 29.5 - - + +
254F TYR* 3.7 27.1 - - + -
255F ALA* 3.5 5.2 - - - +
289F PHE* 4.4 1.3 - - + -
400F PHE* 3.0 19.3 + - + +
401F PHE* 3.7 6.7 - - - +
403F LYS* 1.3 75.7 - - - +
405F CYS* 1.3 57.7 + - - +
407F MSE 3.3 2.6 + - - -
408F SER* 2.8 31.3 + - - -
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Residues in contact with CYS 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F PHE* 4.5 4.5 - - + -
288F LEU* 3.5 27.4 - - + -
289F PHE* 3.6 28.2 - - + -
292F SER* 3.2 38.1 - - - -
293F GLU* 4.4 1.9 - - - +
401F PHE 2.8 18.3 + - - +
402F GLU 3.5 5.4 - - - +
403F LYS 3.2 0.2 - - - -
404F ALA* 1.3 76.2 - - - +
406F ALA* 1.3 62.1 + - - +
408F SER* 3.7 1.3 - - - -
409F GLY* 3.0 22.3 + - - -
416F PRO* 4.7 2.1 - - - +
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Residues in contact with ALA 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ILE* 3.8 20.2 - - + -
48F TRP* 3.8 20.9 - - + -
209F PHE* 5.2 0.6 - - - -
402F GLU 3.1 6.3 + - - -
403F LYS* 3.3 8.5 + - - +
405F CYS* 1.3 75.7 - - - +
407F MSE 1.3 64.0 + - - +
409F GLY 3.6 0.2 + - - -
410F TYR* 3.1 28.9 + - - -
416F PRO* 4.1 4.9 - - - +
417F PHE* 3.8 28.9 - - + -
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Residues in contact with MSE 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 3.7 31.6 - - + +
31F THR* 3.5 31.2 - - + -
32F HIS* 3.9 5.4 - - - +
35F ILE* 4.1 5.9 - - + +
252F TYR* 3.5 48.7 - - + +
255F ALA* 3.4 18.6 - - + -
403F LYS 3.1 10.4 + - - +
404F ALA 3.6 7.0 - - - +
406F ALA* 1.3 80.8 - - - +
408F SER* 1.3 57.0 + - - +
410F TYR* 3.9 0.7 - - - -
411F LEU* 3.0 51.8 + - + +
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Residues in contact with SER 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F ALA* 3.5 13.0 - - - +
258F ARG* 2.8 21.9 + - - -
259F ASN* 3.0 27.0 + - - +
289F PHE* 4.4 1.6 - - - -
293F GLU* 2.5 23.8 + - - +
404F ALA 2.8 21.9 + - - -
405F CYS* 3.7 6.1 - - - -
407F MSE 1.3 72.2 - - - +
409F GLY* 1.3 58.7 + - - +
411F LEU* 3.3 1.4 + - - -
412F LEU* 2.9 26.7 + - - +
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Residues in contact with GLY 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F GLU* 3.1 14.8 + - - -
405F CYS 3.0 15.2 + - - -
406F ALA 4.1 0.7 - - - -
408F SER* 1.3 74.4 - - - +
410F TYR* 1.3 62.2 + - - +
412F LEU* 3.2 2.1 + - - +
413F GLY 3.0 17.2 + - - -
414F VAL* 3.2 30.1 + - - +
416F PRO* 4.1 11.0 - - - -
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Residues in contact with TYR 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F THR* 3.3 34.6 + - + +
34F ALA* 4.9 7.5 + - + -
35F ILE* 3.6 27.8 - - + -
40F GLY* 3.7 15.9 + - - -
41F ALA* 2.7 42.5 + - + -
43F ASN 4.6 2.4 + - - -
46F LEU* 4.7 6.8 - - - +
406F ALA 3.1 22.5 + - - +
409F GLY* 1.3 77.1 - - - +
411F LEU* 1.3 63.0 + - - +
413F GLY* 3.1 13.5 + - - -
414F VAL 4.0 8.1 - - - -
416F PRO* 3.7 15.0 - - + +
417F PHE* 3.5 23.2 - + - -
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Residues in contact with LEU 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F LEU* 4.7 11.4 - - + -
27F ALA* 4.3 24.0 - - + +
28F VAL* 4.7 2.9 - - + +
31F THR* 4.1 11.7 - - - +
255F ALA* 4.2 8.1 - - + +
256F VAL* 3.8 37.7 - - + -
259F ASN* 4.0 12.7 - - + +
407F MSE 3.0 46.0 + - + +
408F SER 3.3 4.2 + - - +
410F TYR* 1.3 76.4 - - - +
412F LEU* 1.3 61.7 + - - +
413F GLY* 3.4 1.0 + - - -
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Residues in contact with LEU 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ASN* 3.6 14.1 + - - +
262F TYR* 3.8 31.9 - - + -
293F GLU* 3.8 43.3 - - + +
298F LYS* 4.4 21.0 + - + +
299F GLY* 4.1 12.1 - - - +
300F ILE 5.4 0.7 - - - +
408F SER 2.9 13.3 + - - +
409F GLY 3.4 8.1 - - - +
410F TYR 3.2 0.2 - - - -
411F LEU* 1.3 76.9 - - - +
413F GLY* 1.3 59.9 + - - +
414F VAL* 4.0 17.3 - - + -
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Residues in contact with GLY 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F ASP* 4.8 2.3 - - - +
298F LYS* 4.2 12.0 + - - -
409F GLY 3.0 3.4 + - - -
410F TYR 3.1 12.2 + - - -
411F LEU 4.3 0.7 - - - -
412F LEU* 1.3 79.5 - - - +
414F VAL* 1.3 64.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il