Contacts of the helix formed by residues 392 - 417 (chain C) in PDB entry 5UQ9
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 ASP 392 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ALA* 3.5 39.2 - - - +
382C ARG* 5.1 6.2 + - - +
386C LEU* 4.1 16.2 - - + +
388C ASN 4.1 0.8 + - - -
389C LEU 3.2 5.3 + - - +
391C LEU* 1.3 80.2 - - - +
393C ASP* 1.3 78.3 + - - +
394C PHE* 3.3 22.1 + - - +
395C PHE* 3.6 23.0 - - + -
396C LYS* 3.0 26.8 + - - +
303D LYS* 5.0 0.7 - - - -
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Residues in contact with ASP 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C ARG* 2.8 39.1 + - - +
391C LEU 4.1 1.0 + - - -
392C ASP* 1.3 87.1 - - - +
394C PHE* 1.3 69.9 + - - +
396C LYS* 4.0 4.6 - - - +
397C SER* 3.0 30.5 + - - -
303D LYS* 5.3 3.8 - - - +
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Residues in contact with PHE 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C GLU* 5.1 8.1 - - + -
328C TYR* 3.2 27.8 - + - -
372C PHE* 5.2 1.3 - + - -
375C LYS* 3.5 42.2 - - + -
378C ASP* 6.1 0.7 - - - +
392C ASP* 3.3 11.7 + - - +
393C ASP* 1.3 87.6 - - - +
395C PHE* 1.3 75.3 + + - +
397C SER* 3.3 5.7 + - - -
398C ALA* 2.8 32.6 + - + +
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Residues in contact with PHE 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C ILE* 3.8 30.5 - - + -
372C PHE* 3.4 34.3 - + - -
375C LYS 3.5 17.5 - - - -
376C ILE* 3.4 21.1 - - + -
379C ALA* 3.6 26.0 - - + -
389C LEU* 3.3 33.0 - - + +
390C LEU* 4.7 3.1 - - - +
392C ASP* 3.5 21.0 + - + -
394C PHE* 1.3 87.6 - + - +
396C LYS* 1.3 63.5 + - - +
398C ALA* 4.1 4.3 - - + -
399C VAL* 3.0 29.8 + - - +
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Residues in contact with LYS 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU* 4.0 12.8 + - - +
392C ASP 3.0 19.5 + - - +
393C ASP* 4.0 3.8 - - - +
395C PHE* 1.3 79.1 - - - +
397C SER* 1.3 69.4 + - - +
399C VAL* 4.0 2.5 - - + +
400C GLU* 3.0 40.9 + - - +
430C TYR* 5.2 1.8 - - - +
303D LYS* 3.1 47.8 - - - +
304D LEU* 3.8 24.0 - - + +
305D LYS* 3.5 26.6 - - - +
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Residues in contact with SER 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ASP 3.0 18.3 + - - -
394C PHE* 3.8 5.6 - - - -
396C LYS* 1.3 86.4 + - - +
398C ALA* 1.3 57.1 + - - +
400C GLU* 3.8 2.8 - - - +
401C ASN* 2.9 30.5 + - - +
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Residues in contact with ALA 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C TYR* 3.7 31.0 - - + +
332C ILE* 3.8 12.8 - - + -
394C PHE* 2.8 27.1 + - + +
395C PHE* 3.8 2.7 - - - +
396C LYS 3.2 0.2 - - - -
397C SER* 1.3 76.8 - - - +
399C VAL* 1.3 62.2 + - - +
401C ASN* 3.2 6.6 + - - +
402C CYS* 3.1 30.6 + - - -
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Residues in contact with VAL 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ALA* 4.9 9.6 - - + +
332C ILE* 4.1 22.7 - - + -
333C ILE* 5.2 2.5 - - + -
390C LEU* 4.0 18.6 - - + -
395C PHE 3.0 19.1 + - - +
396C LYS* 4.1 3.1 - - - +
398C ALA* 1.3 74.9 - - - +
400C GLU* 1.3 57.8 + - - +
402C CYS* 3.1 5.8 + - - +
403C GLN* 2.9 29.5 + - + +
406C TRP* 4.3 15.9 - - + -
430C TYR* 3.5 42.4 - - + +
304D LEU* 5.9 0.2 - - + -
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Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LYS* 3.0 35.6 + - - +
397C SER* 3.8 4.9 - - - +
399C VAL* 1.3 77.8 - - - +
401C ASN* 1.3 61.3 + - - +
402C CYS 3.4 0.5 + - - -
403C GLN* 3.7 23.3 + - - +
404C ASP 4.9 1.4 + - - -
430C TYR* 4.8 2.2 + - - +
305D LYS* 3.4 45.0 + - - +
308D GLN* 3.2 24.5 + - - -
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Residues in contact with ASN 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C LYS* 3.4 30.7 + - - +
397C SER 2.9 18.7 + - - +
398C ALA* 3.6 8.3 - - - +
399C VAL 3.2 0.4 - - - -
400C GLU* 1.3 76.7 - - - +
402C CYS* 1.3 60.7 + - - +
403C GLN 3.6 0.2 - - - -
404C ASP* 5.3 1.2 + - - +
405C SER* 5.5 1.0 + - - -
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Residues in contact with CYS 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ARG* 6.0 1.1 - - - -
325C LYS* 3.5 45.8 - - + +
328C TYR* 3.8 24.5 - - - -
329C ALA* 3.9 12.3 - - + -
398C ALA* 3.1 23.3 + - - +
399C VAL 3.1 5.3 + - - +
401C ASN* 1.3 85.1 - - - +
403C GLN* 1.3 51.5 + - - +
404C ASP 3.4 2.5 - - - -
405C SER* 3.4 3.9 + - - -
406C TRP* 2.7 34.9 + - - +
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Residues in contact with GLN 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399C VAL* 2.9 15.0 + - + +
400C GLU* 3.7 20.5 + - - +
401C ASN 3.6 2.2 - - - -
402C CYS* 1.3 77.5 - - - +
404C ASP* 1.3 63.8 + - - +
406C TRP* 3.1 14.8 + - + +
407C ARG* 2.7 71.7 + - + +
430C TYR* 4.4 11.3 + - + -
305D LYS 3.3 16.5 + - - -
306D GLY* 3.0 34.5 + - - -
307D PRO* 3.1 3.0 - - - +
308D GLN* 5.0 0.4 - - - +
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Residues in contact with ASP 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400C GLU 4.9 1.6 + - - -
401C ASN 5.3 0.8 + - - +
402C CYS 3.4 0.6 - - - -
403C GLN* 1.3 78.0 - - - +
405C SER* 1.3 63.5 + - - +
407C ARG* 3.6 6.9 + - - +
408C ARG* 3.1 45.3 + - - +
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Residues in contact with SER 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C ASP* 2.8 49.0 + - - +
325C LYS* 3.7 29.7 + - - +
401C ASN 5.6 0.6 + - - -
402C CYS 3.4 2.9 + - - -
403C GLN 3.3 0.2 - - - -
404C ASP* 1.3 76.4 - - - +
406C TRP* 1.3 65.1 + - - +
408C ARG* 3.3 14.9 + - - +
409C ALA 3.1 18.2 + - - -
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Residues in contact with TRP 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C LYS* 4.7 0.4 - - - +
326C ALA* 3.5 30.8 + - + +
329C ALA* 3.6 23.1 - - + -
330C SER* 3.3 27.5 + - - -
333C ILE* 3.7 16.2 - - + -
399C VAL* 4.3 11.7 - - + -
402C CYS 2.7 22.9 + - - +
403C GLN* 3.1 17.4 + - + +
405C SER* 1.3 75.5 - - - +
407C ARG* 1.3 63.2 + - + +
409C ALA* 3.3 2.3 + - - +
410C VAL* 3.1 28.4 + - + +
423C PHE* 3.8 11.9 + - - +
426C ALA* 3.4 21.8 - - + -
427C LEU* 3.3 43.3 - - + -
430C TYR* 4.2 16.4 - + + -
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Residues in contact with ARG 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C GLN* 2.7 49.2 + - - +
404C ASP* 4.2 6.5 - - - +
406C TRP* 1.3 75.6 - - - +
408C ARG* 1.3 57.2 + - - +
411C SER* 2.8 35.8 + - - -
427C LEU* 3.7 25.4 - - + +
430C TYR* 4.4 1.6 - - - -
431C ASP* 2.4 44.0 + - - -
434C ARG* 4.0 1.4 - - - +
307D PRO* 3.7 20.6 - - - +
414D VAL* 2.5 51.0 + - + +
415D GLN* 4.3 13.0 - - + +
417D GLY* 3.4 9.5 - - - -
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Residues in contact with ARG 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PHE* 3.9 6.2 - - + -
322C ASP* 2.5 48.3 + - - +
404C ASP* 3.1 46.1 + - - +
405C SER* 3.3 19.7 + - - +
406C TRP 3.3 0.2 - - - -
407C ARG* 1.3 76.7 - - - +
409C ALA* 1.3 60.0 + - - +
411C SER* 4.1 4.4 - - - -
412C THR* 2.8 36.4 + - - +
415D GLN* 5.9 4.7 - - - +
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.4 9.3 - - + +
319C PHE* 3.9 14.9 - - + -
322C ASP* 3.8 22.8 - - + +
323C ILE* 4.3 9.6 - - + +
326C ALA* 4.2 10.5 - - + -
405C SER 3.1 17.7 + - - +
406C TRP 3.7 3.8 - - - +
408C ARG* 1.3 75.1 - - - +
410C VAL* 1.3 64.0 + - + +
412C THR* 4.0 1.2 - - - -
413C GLY* 3.1 19.1 + - - -
420C MET* 3.8 8.9 - - + +
423C PHE* 6.0 0.2 - - + -
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Residues in contact with VAL 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ALA* 5.6 0.2 - - + -
406C TRP* 3.1 35.9 + - + +
407C ARG 3.4 3.6 + - - +
409C ALA* 1.3 74.6 - - + +
411C SER* 1.3 65.9 + - - +
413C GLY* 3.4 1.6 + - - -
414C VAL* 3.0 32.3 + - + +
420C MET* 3.6 18.4 - - + +
423C PHE* 4.4 10.5 - - + +
424C THR* 4.0 24.0 - - + -
427C LEU* 4.0 11.4 - - + -
414D VAL* 3.7 30.7 - - + -
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Residues in contact with SER 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C ARG 2.8 24.1 + - - -
408C ARG* 4.1 5.6 - - - -
410C VAL* 1.3 76.1 - - - +
412C THR* 1.3 62.2 + - - +
414C VAL* 3.4 4.7 + - - +
415C GLN* 3.2 27.5 + - - +
411D SER* 3.2 28.9 + - - +
414D VAL* 3.5 14.4 - - - +
415D GLN* 3.5 20.2 - - - +
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Residues in contact with THR 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C VAL* 4.1 11.4 - - + -
310C PHE* 3.9 21.3 - - + -
312C PHE* 4.5 11.1 - - + -
319C PHE* 3.4 32.1 - - + -
408C ARG* 2.8 28.1 + - - +
409C ALA 4.0 0.2 - - - -
411C SER* 1.3 77.2 - - - +
413C GLY* 1.3 57.1 + - - +
415C GLN* 3.3 7.2 + - - +
416C ALA* 2.9 26.9 + - - +
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Residues in contact with GLY 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 4.1 16.8 - - - +
208C VAL* 4.9 0.2 - - - -
319C PHE* 5.1 0.2 - - - -
409C ALA 3.1 12.2 + - - -
412C THR* 1.3 77.3 - - - +
414C VAL* 1.3 60.5 + - - +
416C ALA* 3.4 4.8 + - - -
417C GLY 3.1 3.3 + - - -
418C ILE 3.0 29.2 + - - +
420C MET* 3.6 26.0 - - - -
431D ASP* 5.0 0.2 - - - +
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Residues in contact with VAL 414 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C VAL* 3.0 31.6 + - + +
411C SER* 3.7 8.3 - - - +
412C THR 3.2 0.2 - - - -
413C GLY* 1.3 77.5 - - - +
415C GLN* 1.3 60.6 + - + +
417C GLY 3.3 1.2 + - - -
418C ILE 5.3 1.3 - - - +
420C MET* 5.5 1.8 - - - -
424C THR* 5.0 8.5 - - + -
407D ARG* 2.9 57.7 + - + +
410D VAL* 3.8 23.1 - - + -
411D SER* 4.5 4.5 - - - +
414D VAL* 5.5 0.2 - - + -
427D LEU* 3.6 26.5 - - + -
431D ASP* 5.4 1.1 - - - -
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Residues in contact with GLN 415 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C PRO* 3.4 21.5 - - - +
309C LYS 5.8 0.2 - - - +
310C PHE* 3.6 32.5 - - + +
411C SER 3.2 16.7 + - - +
412C THR* 3.8 1.3 - - - +
414C VAL* 1.3 77.0 - - + +
416C ALA* 1.3 59.7 + - - +
404D ASP* 5.0 3.3 + - - +
407D ARG* 3.8 37.5 + - - +
408D ARG* 4.0 11.1 - - - +
411D SER* 4.4 10.8 - - - +
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Residues in contact with ALA 416 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ASP 5.6 1.1 - - - +
208C VAL* 3.7 25.4 - - + -
307C PRO* 3.4 11.3 - - - +
310C PHE* 3.5 30.3 - - + +
412C THR 2.9 16.9 + - - +
413C GLY 3.9 1.1 - - - +
414C VAL 3.2 0.4 - - - -
415C GLN* 1.3 76.7 - - - +
417C GLY* 1.3 62.9 + - - +
418C ILE* 3.8 13.1 - - + +
434D ARG* 4.7 0.7 + - - -
----------------------------------------------------------
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Residues in contact with GLY 417 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C PRO* 3.8 4.3 - - - -
413C GLY 3.1 4.2 + - - -
414C VAL 3.3 1.6 + - - -
415C GLN 3.3 3.8 + - - -
416C ALA* 1.3 79.6 - - - +
418C ILE* 1.3 61.7 + - - +
407D ARG* 3.5 11.2 - - - -
431D ASP* 3.4 21.9 - - - +
434D ARG* 2.9 28.3 + - - -
435D HIS* 3.2 12.3 + - - -
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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