Contacts of the helix formed by residues 378 - 403 (chain C) in PDB entry 3OMA
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 LYS 378 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PHE* 3.6 22.7 - - + -
376C GLU* 3.2 41.1 + - + +
377C LEU* 1.3 78.8 - - - +
379C THR* 1.3 66.7 + - - +
380C PRO* 3.3 7.2 - - + -
381C MET* 2.9 14.1 + - - +
382C LEU* 3.1 10.6 + - - +
450C GLU* 3.7 34.2 + - + +
454C LYS* 4.6 2.9 - - - +
531C TRP* 4.4 13.2 - - + -
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Residues in contact with THR 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C LYS* 1.3 69.3 - - - +
380C PRO* 1.4 65.6 - - - +
382C LEU* 3.1 20.6 + - - +
383C TRP* 3.1 35.2 + - + +
437C TYR* 3.4 24.5 - - + -
448C TYR* 3.4 14.7 - - - -
450C GLU* 2.9 21.8 + - - -
453C GLY* 3.1 40.0 - - - +
454C LYS* 3.2 3.0 + - - +
457C PHE* 5.3 0.4 - - + -
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Residues in contact with PRO 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C VAL* 3.4 15.1 - - + +
305C PHE* 3.9 23.1 - - + -
378C LYS* 3.4 12.8 - - + -
379C THR* 1.4 88.7 - - - +
381C MET* 1.3 59.4 + - - +
383C TRP* 3.4 12.4 + - + +
384C ALA 3.2 16.8 + - - -
434C ALA* 3.9 20.5 - - - +
437C TYR* 3.7 10.3 - - + +
438C PHE* 3.7 25.1 - - + +
448C TYR* 3.4 14.4 - - - +
531C TRP* 4.1 2.7 - - + -
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Residues in contact with MET 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C VAL* 3.9 6.2 - - - +
302C ILE* 4.2 26.2 - - - +
305C PHE* 3.8 34.9 - - + -
306C ALA 4.1 3.8 - - - +
370C MET* 4.4 12.8 - - + -
375C ILE* 4.1 24.7 - - + -
376C GLU 3.5 22.9 - - - +
377C LEU* 4.4 5.6 - - + -
378C LYS 2.9 10.4 + - - +
380C PRO* 1.3 77.1 - - - +
382C LEU* 1.3 65.5 + - - +
384C ALA* 3.2 1.8 + - - -
385C LEU* 3.0 56.3 + - + +
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Residues in contact with LEU 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C LEU* 4.1 32.8 - - + +
378C LYS 3.1 12.6 + - - +
379C THR* 3.1 11.1 + - - +
381C MET* 1.3 75.9 - - - +
383C TRP* 1.3 56.8 + - - +
385C LEU* 3.3 8.3 + - + +
386C GLY 2.9 25.5 + - - -
454C LYS* 3.9 29.4 - - + -
457C PHE* 3.1 48.9 - - + -
458C TRP* 4.1 19.5 - - + +
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Residues in contact with TRP 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C THR* 3.1 46.3 + - + +
380C PRO* 3.6 7.2 - - + +
382C LEU* 1.3 76.8 - - - +
384C ALA* 1.3 52.0 + - - +
386C GLY* 3.4 1.7 + - - -
387C PHE* 2.8 32.9 + - - +
430C PHE* 3.4 67.5 - + - +
433C PHE* 3.5 37.2 - + + -
434C ALA* 3.7 9.2 - - + -
437C TYR* 3.4 16.2 - + - -
456C HIS* 3.3 28.9 - + - -
457C PHE* 3.6 29.9 - + - +
460C MET* 3.7 23.1 - - + -
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C VAL* 4.4 14.6 - - + +
301C VAL* 3.9 16.4 - - + -
302C ILE* 3.9 25.4 - - + -
380C PRO 3.2 13.9 + - - +
381C MET 3.2 7.3 + - - +
383C TRP* 1.3 76.2 - - - +
385C LEU* 1.3 57.5 + - - +
387C PHE* 3.2 10.8 - - - +
388C LEU* 3.1 29.6 + - - +
434C ALA* 4.5 3.8 - - + +
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Residues in contact with LEU 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ILE* 4.9 2.7 - - + -
370C MET* 3.3 33.4 - - - -
377C LEU* 3.9 20.2 - - + -
381C MET* 3.0 37.8 + - + +
382C LEU* 3.8 8.1 - - + +
384C ALA* 1.3 73.4 - - - +
386C GLY* 1.3 66.2 + - - +
388C LEU* 3.1 22.5 + - + +
389C PHE* 3.2 14.4 + - - +
76D ILE* 4.2 18.4 - - + +
80D VAL* 3.7 23.8 - - + -
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Residues in contact with GLY 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C LEU 2.9 14.7 + - - -
383C TRP 3.6 3.4 - - - -
385C LEU* 1.3 75.4 - - - +
387C PHE* 1.3 61.5 + - - +
389C PHE* 3.3 3.6 + - - -
390C LEU* 2.9 38.1 + - - +
430C PHE* 4.0 13.9 - - - -
457C PHE* 4.4 8.4 - - - -
461C PHE* 4.5 7.6 - - - -
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Residues in contact with PHE 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL* 4.5 2.5 - - + -
294C ALA* 4.2 14.6 - - + -
295C PHE* 3.7 35.7 - + - -
298C VAL* 3.8 28.7 - - + -
363C ILE* 5.3 0.2 - - + -
366C TRP* 4.2 15.0 - + - -
383C TRP 2.8 15.3 + - - +
384C ALA* 3.2 13.7 - - - +
386C GLY* 1.3 76.1 - - - +
388C LEU* 1.3 63.9 + - + +
391C PHE* 2.9 56.7 + + + +
426C LEU 4.4 3.6 - - - -
427C GLY* 3.0 42.0 - - - -
428C ALA* 4.1 1.6 - - - -
430C PHE* 4.0 9.1 - - + -
431C GLY 4.1 5.4 - - - +
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C VAL* 4.6 0.4 - - + -
302C ILE* 3.8 20.6 - - + -
363C ILE* 4.3 17.5 - - + +
366C TRP* 3.4 47.8 - - + -
367C ILE* 4.6 4.0 - - + -
370C MET* 4.2 19.3 - - + -
384C ALA 3.1 16.9 + - - +
385C LEU* 3.1 15.9 + - + +
387C PHE* 1.3 83.5 - - + +
389C PHE* 1.3 58.3 + - - +
392C THR* 2.8 30.0 + - - -
72D VAL* 4.6 2.1 - - - +
76D ILE* 3.7 24.5 - - + -
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Residues in contact with PHE 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C LEU 3.2 8.9 + - - +
386C GLY* 3.9 5.4 - - - +
388C LEU* 1.3 79.6 - - - +
390C LEU* 1.3 90.5 + - + +
392C THR* 3.3 7.9 + - - -
393C VAL* 3.1 46.6 + - + +
422C TYR* 5.8 0.2 - + - -
461C PHE* 4.1 20.4 - + + -
465C ASN* 4.7 5.6 - - - -
69D THR* 4.3 7.6 - - + -
72D VAL* 5.3 1.8 - - + -
73D THR* 3.0 44.0 - - + -
76D ILE* 4.3 10.3 - - + +
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Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLY 2.9 16.9 + - - +
389C PHE* 1.3 96.7 - - + +
391C PHE* 1.3 59.6 + - - +
393C VAL* 3.3 4.0 + - - +
394C GLY* 3.0 25.1 + - - -
422C TYR* 3.7 17.0 - - + +
426C LEU* 3.1 39.9 - - + +
430C PHE* 3.4 39.7 - - + -
461C PHE* 3.9 9.2 - - + -
465C ASN* 3.5 31.9 - - - +
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Residues in contact with PHE 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.8 43.7 - - + -
288C TYR* 6.4 0.2 - + - -
291C VAL* 3.9 12.1 - - + -
295C PHE* 3.6 20.9 - + - -
359C THR* 3.5 29.8 - - + -
363C ILE* 4.0 19.1 - - + -
366C TRP* 5.8 0.2 - + - -
387C PHE* 2.9 48.9 + + + +
388C LEU* 4.6 1.1 - - - +
390C LEU* 1.3 73.3 - - - +
392C THR* 1.3 53.3 + - - +
394C GLY 3.6 0.7 - - - +
395C GLY* 2.7 30.0 + - - -
422C TYR 4.5 6.5 - - - -
423C VAL* 3.9 24.5 - - + -
426C LEU 4.2 1.4 + - - -
427C GLY* 4.7 1.8 - - - -
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Residues in contact with THR 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 4.2 25.7 - - + +
363C ILE* 3.8 18.7 - - - +
388C LEU 2.8 22.4 + - - -
389C PHE* 3.3 7.1 + - + +
390C LEU 3.2 0.4 - - - -
391C PHE* 1.3 76.7 - - - +
393C VAL* 1.3 66.2 + - - +
395C GLY* 3.2 0.3 + - - -
396C VAL* 3.0 31.0 + - + +
68D ILE* 5.0 0.7 - - + -
69D THR* 4.0 21.8 - - + +
72D VAL* 4.0 23.9 - - + +
----------------------------------------------------------
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Residues in contact with VAL 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C PHE* 3.1 37.3 + - + +
390C LEU* 3.3 6.9 + - - +
392C THR* 1.3 75.6 - - - +
394C GLY* 1.3 61.8 + - - +
396C VAL* 3.4 10.0 - - - +
397C THR* 3.3 21.1 + - - +
422C TYR* 3.9 28.9 - - + -
469C PHE* 4.8 9.9 - - + -
472C HIS* 4.8 4.9 - - + +
3D TRD 4.0 20.2 - - + -
69D THR* 4.0 23.3 - - + -
----------------------------------------------------------
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Residues in contact with GLY 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU 3.0 11.5 + - - -
391C PHE 3.8 0.4 - - - -
393C VAL* 1.3 76.5 - - - +
395C GLY* 1.3 60.2 + - - +
397C THR* 3.0 11.8 + - - -
398C GLY 3.2 0.3 + - - -
419C HIS* 2.7 28.2 + - - -
422C TYR* 3.5 23.3 - - - +
423C VAL* 3.5 16.8 - - - -
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Residues in contact with GLY 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.5 47.1 - - - +
391C PHE 2.7 21.5 + - - -
392C THR 3.2 0.4 + - - -
394C GLY* 1.3 73.4 - - - +
396C VAL* 1.3 57.0 + - - +
398C GLY* 3.1 16.1 + - - -
399C ILE 3.2 8.7 + - - -
419C HIS* 5.0 0.4 - - - -
423C VAL* 3.6 4.9 - - - +
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Residues in contact with VAL 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 4.3 21.5 - - + -
392C THR* 3.0 20.3 + - + +
393C VAL* 3.4 16.8 - - - +
395C GLY* 1.3 73.4 - - - +
397C THR* 1.3 59.7 + - - +
399C ILE* 3.2 10.6 + - - +
400C VAL* 3.1 27.4 + - - +
3D TRD 4.2 5.8 - - + -
65D ILE* 3.7 37.8 - - + +
68D ILE* 4.4 18.6 - - + -
69D THR* 3.8 20.9 - - - +
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Residues in contact with THR 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C VAL 3.3 14.5 + - - +
394C GLY* 3.0 16.3 + - - -
396C VAL* 1.3 74.4 - - + +
398C GLY* 1.3 58.6 + - - +
400C VAL* 3.3 8.4 + - - +
401C LEU* 3.0 32.8 + - - +
415C TYR* 3.5 26.2 - - - +
419C HIS* 3.2 23.8 - - - +
472C HIS* 3.8 23.1 + - + +
3D TRD 3.9 20.0 - - + -
65D ILE* 4.7 1.3 - - + -
----------------------------------------------------------
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Residues in contact with GLY 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.3 29.4 - - - +
394C GLY 3.2 6.7 + - - -
395C GLY 3.1 9.5 + - - -
397C THR* 1.3 78.5 - - - +
399C ILE* 1.3 55.6 + - - +
401C LEU* 3.2 2.6 + - - +
402C SER 3.0 22.7 + - - -
419C HIS* 3.4 24.8 + - - -
----------------------------------------------------------
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Residues in contact with ILE 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.7 54.7 - - + -
352C THR 4.5 1.8 - - - +
353C MET* 4.2 20.0 - - + +
356C ALA* 3.7 23.3 - - + +
395C GLY 3.2 3.8 + - - +
396C VAL* 3.2 10.3 + - + +
398C GLY* 1.3 73.9 - - - +
400C VAL* 1.3 63.9 - - - +
402C SER* 2.6 25.3 + - - +
403C GLN* 3.5 12.8 - - + +
61D ILE* 5.4 3.1 - - + -
65D ILE* 5.3 5.2 - - + -
112D LEU* 4.2 17.7 - - + -
115D ILE* 5.0 12.1 - - + -
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Residues in contact with VAL 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C VAL 3.1 15.0 + - - +
397C THR* 3.5 8.1 - - - +
398C GLY 3.3 0.2 - - - -
399C ILE* 1.3 75.7 - - - +
401C LEU* 1.3 62.4 + - - +
403C GLN* 3.2 27.4 + - - +
406C VAL* 4.0 11.1 - - + +
410C TYR* 3.7 31.2 - - + -
415C TYR* 3.7 14.1 - - + +
58D ASP* 3.9 10.5 - - - +
61D ILE* 3.8 23.6 - - + -
62D LEU* 5.7 0.7 - - - +
65D ILE* 3.6 22.9 - - + -
----------------------------------------------------------
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Residues in contact with LEU 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.4 29.7 - - + +
336C TYR* 3.6 6.6 - - - -
397C THR 3.0 19.1 + - - +
398C GLY* 3.2 7.6 + - - +
400C VAL* 1.3 76.6 - - - +
402C SER* 1.3 60.7 + - - +
407C ASP* 3.3 41.2 - - - +
410C TYR* 3.6 27.4 - - + -
415C TYR* 3.7 13.5 - - + -
416C VAL* 3.7 19.3 - - + -
419C HIS* 3.7 38.6 - - + -
----------------------------------------------------------
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Residues in contact with SER 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C HEA 3.1 10.1 + - - -
336C TYR* 2.7 24.3 + - - -
349C MET* 3.2 12.4 - - - +
352C THR* 3.5 34.1 - - - -
353C MET* 3.8 8.0 - - - +
398C GLY 3.0 10.4 + - - -
399C ILE* 2.6 26.9 + - - +
401C LEU* 1.3 75.8 - - - +
403C GLN* 1.3 69.1 + - - +
404C ALA 3.1 5.2 + - - -
----------------------------------------------------------
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Residues in contact with GLN 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C MET* 3.8 11.0 - - - +
353C MET* 3.1 30.9 - - - +
399C ILE* 3.5 14.7 + - + +
400C VAL 3.3 9.8 - - - +
401C LEU 3.2 1.5 - - - -
402C SER* 1.3 92.1 + - - +
404C ALA* 1.3 65.1 + - - +
405C SER* 3.2 2.2 - - - -
406C VAL* 2.9 15.8 + - + +
407C ASP* 2.9 20.8 + - - +
61D ILE* 3.8 19.7 - - + -
115D ILE* 3.5 15.4 - - + +
119D SER* 2.6 38.7 + - - +
----------------------------------------------------------
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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