Contacts of the helix formed by residues 369 - 396 (chain F) in PDB entry 6V3O
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 GLU 369 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E ARG* 3.2 13.4 + - - -
229E GLU* 4.2 13.5 - - - +
330F LEU 5.5 1.3 - - - +
331F SER 4.8 7.6 - - - +
332F MET 4.2 3.6 - - - +
365F ILE* 4.1 1.7 - - + +
366F PRO* 3.0 44.9 + - - +
367F PRO 3.0 2.6 - - - -
368F ASN* 1.3 84.8 - - - +
370F PRO* 1.3 68.3 - - - +
371F TYR 3.4 2.2 - - - -
372F ARG* 2.6 55.7 + - + -
373F VAL* 3.1 24.7 + - - +
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Residues in contact with PRO 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332F MET 3.2 20.0 - - - +
333F TRP* 3.6 18.8 - - - +
335F CYS* 3.6 27.1 - - + -
339F LEU* 4.2 11.2 - - + -
343F ALA* 4.2 24.0 - - + +
367F PRO 4.0 6.7 - - - +
368F ASN* 3.4 7.9 - - - +
369F GLU* 1.3 87.5 - - - +
371F TYR* 1.3 64.8 + - + +
373F VAL* 3.0 16.1 + - + +
374F ILE* 3.3 13.3 + - - +
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Residues in contact with TYR 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F LEU* 3.9 31.2 - - + +
332F MET* 3.7 35.7 - - + -
334F ARG 2.9 28.2 + - - -
335F CYS* 3.8 6.5 - - + -
339F LEU* 3.4 20.4 - - + -
369F GLU 3.4 0.2 - - - -
370F PRO* 1.3 76.2 - - + +
372F ARG* 1.3 58.9 + - - +
374F ILE* 3.5 7.4 - - - +
375F LEU* 3.1 37.5 + - + +
419F CYS* 3.8 24.5 - - + -
422F SER* 3.0 20.5 + - - -
423F LEU* 3.5 39.0 + - + +
426F CYS* 4.7 0.7 - - - +
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Residues in contact with ARG 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E ARG* 3.2 3.6 - - - +
185E SER* 3.5 7.9 - - - -
1002E SO4 2.9 38.9 + - - -
327F MET* 2.8 40.2 + - + +
328F PHE* 3.0 31.3 + - - +
330F LEU 3.5 14.7 + - - +
331F SER* 3.8 7.8 + - - -
365F ILE* 3.8 30.3 - - + +
369F GLU* 2.6 50.3 + - + +
371F TYR* 1.3 77.9 - - - +
373F VAL* 1.3 58.4 + - - +
375F LEU* 4.3 0.2 - - - +
376F GLY* 3.0 24.1 + - - -
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Residues in contact with VAL 373 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F ALA* 3.9 27.6 - - + +
346F LEU* 4.1 16.8 - - + +
347F HIS* 4.7 10.3 - - + +
365F ILE* 4.2 16.4 - - + +
366F PRO 3.6 18.2 - - - +
367F PRO* 4.5 7.6 - - + +
369F GLU 3.1 17.9 - - - +
370F PRO* 3.0 9.9 + - + +
372F ARG* 1.3 78.9 - - - +
374F ILE* 1.3 60.9 + - - +
376F GLY* 3.5 1.6 + - - -
377F HIS* 3.2 19.2 + - - +
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Residues in contact with ILE 374 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339F LEU* 4.1 11.7 - - + -
342F ARG* 4.1 14.1 - - + +
343F ALA* 5.6 3.8 - - - -
346F LEU* 3.9 21.8 - - + -
370F PRO 3.3 8.6 + - - +
371F TYR 3.5 11.0 - - - +
373F VAL* 1.3 76.0 - - - +
375F LEU* 1.3 65.5 + - + +
377F HIS* 3.0 5.9 + - + +
378F VAL* 2.9 31.2 + - + +
415F PRO* 3.7 34.1 - - + +
418F LEU* 3.9 27.4 - - + -
419F CYS* 3.7 21.1 - - - -
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Residues in contact with LEU 375 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F ILE* 3.5 18.6 - - + +
326F LEU* 3.9 33.2 - - + +
327F MET* 3.5 35.4 - - + +
330F LEU* 4.1 15.3 - - + -
371F TYR* 3.1 23.1 + - + +
374F ILE* 1.3 81.7 - - + +
376F GLY* 1.3 56.1 + - - +
378F VAL* 3.1 6.5 + - + +
379F ARG 3.0 24.1 + - - -
416F LEU* 3.4 33.0 - - + -
419F CYS* 4.8 10.1 - - + -
436F LEU* 6.0 0.7 - - + -
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Residues in contact with GLY 376 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F MET* 3.8 6.1 - - - +
365F ILE* 5.4 2.2 - - - -
372F ARG 3.0 18.3 + - - -
373F VAL* 3.9 1.8 - - - -
374F ILE 3.2 0.2 - - - -
375F LEU* 1.3 76.7 - - - +
377F HIS* 1.3 61.6 + - - +
379F ARG* 3.1 27.6 + - - +
380F ASP* 3.1 30.0 + - - +
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Residues in contact with HIS 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F ARG* 4.4 17.0 + - - -
346F LEU* 3.9 28.9 - - + +
373F VAL 3.2 12.4 + - - +
374F ILE* 3.0 12.8 + - - +
376F GLY* 1.3 74.2 - - - +
378F VAL* 1.3 67.7 + - - +
380F ASP* 3.3 13.3 + - + +
381F LYS* 3.1 52.7 + - + +
415F PRO* 6.1 2.2 - - - +
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Residues in contact with VAL 378 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F ILE* 4.0 17.5 - - + -
374F ILE* 2.9 21.7 + - + +
375F LEU* 3.1 11.2 + - - +
377F HIS* 1.3 79.9 - - + +
379F ARG* 1.3 57.9 + - - +
381F LYS 3.4 0.7 + - - -
382F LEU* 2.9 29.1 + - + +
406F PHE* 3.5 15.3 - - + -
412F PHE* 3.6 31.4 - - + -
415F PRO* 3.6 34.8 - - + -
416F LEU* 4.4 8.5 - - + -
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Residues in contact with ARG 379 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F ILE* 5.0 8.7 - - + +
323F ILE* 4.2 9.4 - - + -
324F GLU* 4.0 23.8 + - - -
327F MET* 3.3 29.8 - - + +
365F ILE* 5.3 6.5 - - - +
375F LEU 3.0 9.7 + - - +
376F GLY* 3.1 32.9 + - - +
378F VAL* 1.3 73.8 - - - +
380F ASP* 1.3 74.4 + - - +
382F LEU* 3.5 12.8 - - + +
383F TYR* 2.9 47.0 + - + -
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Residues in contact with ASP 380 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376F GLY 3.1 17.5 + - - +
377F HIS* 3.3 19.7 + - + +
379F ARG* 1.3 96.1 + - - +
381F LYS* 1.3 62.8 + - + +
383F TYR* 3.1 11.0 + - - +
384F ASN* 3.1 27.9 + - - +
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Residues in contact with LYS 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F HIS* 3.1 41.4 + - + +
378F VAL 3.8 1.3 - - - +
380F ASP* 1.3 76.4 - - + +
382F LEU* 1.3 57.0 + - - +
384F ASN* 3.2 5.0 + - - +
385F THR* 2.8 33.7 + - - +
403F GLU 4.2 11.3 + - - -
404F SER* 3.7 16.1 - - - +
405F SER 3.2 20.4 + - - -
406F PHE* 3.5 37.3 - - + -
411F GLU* 3.0 25.5 + - - +
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Residues in contact with LEU 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F ALA* 4.0 12.2 - - + +
319F TYR* 3.8 34.3 - - + -
320F ILE* 3.7 19.3 - - + +
323F ILE* 4.1 12.3 - - + -
378F VAL* 2.9 33.8 + - + +
379F ARG* 3.5 14.8 - - - +
380F ASP 3.1 0.2 - - - -
381F LYS* 1.3 76.8 - - - +
383F TYR* 1.3 57.0 + - - +
385F THR* 2.3 30.7 + - + +
386F ARG* 2.9 15.1 + - - +
406F PHE* 4.0 17.9 - - + -
412F PHE* 4.2 10.5 - - + -
448F LEU* 5.3 6.1 - - + -
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Residues in contact with TYR 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E TYR 4.9 11.1 + - - -
359E ILE* 4.3 16.1 - - + +
320F ILE* 3.8 40.1 - - + +
324F GLU* 4.1 11.1 + - - -
379F ARG* 2.9 37.9 + - - -
380F ASP* 3.1 11.6 + - - +
382F LEU* 1.3 75.7 - - - +
384F ASN* 1.3 60.5 + - - +
386F ARG* 3.4 21.5 + - - +
387F GLU* 3.0 39.2 + - + +
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Residues in contact with ASN 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380F ASP* 3.1 16.3 + - - +
381F LYS* 3.2 6.2 + - - +
383F TYR* 1.3 76.9 - - - +
385F THR* 1.3 60.0 + - - +
387F GLU* 3.3 3.1 + - - -
388F ARG* 2.8 32.7 + - - +
400F ILE* 3.9 14.4 - - + +
404F SER* 3.0 48.7 + - - +
405F SER* 4.8 1.1 - - - -
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Residues in contact with THR 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312F ARG 5.9 0.6 - - - -
316F ALA* 3.8 11.0 - - - +
381F LYS 2.8 20.5 + - - +
382F LEU* 2.3 35.3 + - + +
384F ASN* 1.3 74.3 - - - +
386F ARG* 1.3 61.7 + - - -
388F ARG* 3.4 4.8 + - - +
389F ALA* 3.1 22.5 + - - +
405F SER* 3.7 9.8 - - - -
406F PHE* 3.0 50.5 - - + +
448F LEU* 6.4 0.7 - - + -
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Residues in contact with ARG 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E LYS* 4.0 9.5 + - - +
357E TYR 4.7 2.8 + - - -
358E TYR 2.4 32.8 + - - +
359E ILE* 4.1 4.6 + - - +
362E TRP* 3.6 27.1 - - - +
312F ARG 5.3 0.4 - - - -
313F MET* 4.0 29.1 - - + +
316F ALA* 3.8 13.7 - - + -
317F ASN* 3.1 37.7 + - - +
320F ILE* 4.8 7.6 - - + -
382F LEU 2.9 11.3 + - - +
383F TYR* 3.7 18.1 - - - +
385F THR* 1.3 81.7 + - - +
387F GLU* 1.3 85.6 + - - +
389F ALA* 3.2 8.1 + - - +
390F ARG* 2.9 28.0 + - - +
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Residues in contact with GLU 387 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E LYS* 3.9 12.1 - - - +
383F TYR* 3.0 25.8 + - + +
384F ASN* 4.0 1.8 - - - +
386F ARG* 1.3 106.6 + - - +
388F ARG* 1.3 67.2 + - - +
390F ARG* 3.0 34.8 + - - +
391F HIS* 2.9 30.0 + - + +
400F ILE* 3.7 21.1 - - + -
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Residues in contact with ARG 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384F ASN 2.8 18.3 + - - +
385F THR* 3.5 6.3 - - - +
387F GLU* 1.3 75.4 - - - +
389F ALA* 1.3 63.4 + - - +
391F HIS* 2.9 13.7 + - - +
392F LEU* 3.0 39.9 + - + +
398F SER* 3.6 27.4 + - - +
400F ILE* 2.8 43.1 + - + +
401F SER* 4.6 1.0 - - - +
402F ALA* 4.3 21.2 - - - +
405F SER* 4.5 19.5 + - - -
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Residues in contact with ALA 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F LEU* 3.9 24.8 - - + +
312F ARG* 4.5 11.0 - - + -
313F MET* 3.7 23.1 - - + +
385F THR 3.1 10.3 + - - +
386F ARG* 3.5 8.1 - - - +
388F ARG* 1.3 79.2 - - - +
390F ARG* 1.3 63.6 + - - +
392F LEU* 3.5 7.8 + - - +
393F LEU* 3.0 25.3 + - - +
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Residues in contact with ARG 390 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356E LYS* 3.2 47.1 - - - +
362E TRP* 5.1 10.5 - - + -
313F MET* 4.0 26.6 - - + -
386F ARG* 2.9 17.5 + - - +
387F GLU* 3.0 31.8 + - - +
389F ALA* 1.3 76.8 - - - +
391F HIS* 1.3 101.0 + - - +
393F LEU* 3.4 4.5 + - - +
394F ALA* 3.0 40.2 + - - +
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Residues in contact with HIS 391 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F GLU* 2.9 21.2 + - - +
388F ARG 2.9 3.1 + - - +
390F ARG* 1.3 116.0 + - - +
392F LEU* 1.3 66.4 + - - +
393F LEU 3.1 1.3 - - - -
394F ALA* 3.0 5.9 + - - +
395F SER* 2.9 23.0 + - - -
396F GLY 3.5 0.3 + - - -
397F VAL 3.5 14.0 + - - +
398F SER* 3.1 24.9 - - - +
400F ILE* 4.9 9.7 - - + +
399G GLU* 3.9 27.7 + - - -
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Residues in contact with LEU 392 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F GLU* 5.7 0.5 - - - +
305F ARG* 3.4 33.7 + - - +
309F LEU* 3.8 17.4 - - + +
388F ARG* 3.0 59.4 + - + +
389F ALA* 3.9 3.4 - - - +
391F HIS* 1.3 75.7 - - - +
393F LEU* 1.3 58.4 + - - +
396F GLY* 3.0 49.0 + - - +
397F VAL* 3.8 9.2 - - - +
398F SER* 3.5 17.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 393 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E TRP* 4.5 10.5 - - + -
302F GLU* 5.4 3.1 - - - +
306F ASP* 3.3 53.2 - - + +
309F LEU* 3.7 12.5 - - + +
310F LEU* 3.7 31.2 - - + +
313F MET* 4.5 12.3 - - - -
389F ALA 3.0 18.5 + - - +
390F ARG* 3.6 4.9 - - - +
392F LEU* 1.3 78.0 - - - +
394F ALA* 1.3 63.0 + - - +
396F GLY 4.8 0.3 + - - -
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Residues in contact with ALA 394 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F ARG* 3.0 32.6 + - - +
391F HIS* 3.0 9.0 + - - +
393F LEU* 1.3 80.0 - - - +
395F SER* 1.3 63.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 395 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F HIS 2.9 8.6 + - - -
394F ALA* 1.3 78.3 - - - +
396F GLY* 1.3 58.0 + - - +
397F VAL* 2.8 27.7 + - - +
401G SER* 6.2 0.3 - - - -
----------------------------------------------------------
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Residues in contact with GLY 396 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F ARG* 4.2 11.7 + - - -
391F HIS 3.5 0.2 + - - -
392F LEU* 3.0 36.5 + - - +
393F LEU 4.6 0.2 - - - -
394F ALA 3.9 0.2 - - - -
395F SER* 1.3 73.7 - - - +
397F VAL* 1.3 57.1 + - - +
----------------------------------------------------------
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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