Contacts of the helix formed by residues 402 - 437 (chain A) in PDB entry 3PIK
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 TYR 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A SER* 3.8 23.7 - - - -
182A PHE* 6.2 0.4 - + - -
183A VAL* 3.8 20.5 - - + +
196A ALA* 3.5 43.3 - - + -
199A GLN* 3.7 17.7 - - + +
200A ALA* 4.0 18.9 - - + +
392A ARG* 4.8 2.4 + - - -
395A TYR* 3.4 40.6 - + + -
401A SER* 1.3 72.6 - - - +
403A LEU* 1.3 59.6 + - - +
405A VAL* 2.8 46.8 + - + +
406A LEU* 3.0 19.8 + - + +
409A GLU* 4.3 5.4 + - - -
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Residues in contact with LEU 403 (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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199A GLN* 4.2 23.6 + - - +
401A SER* 3.0 15.2 + - - +
402A TYR* 1.3 78.4 - - - +
404A GLU* 1.3 57.0 + - - +
406A LEU* 3.9 19.1 - - + -
407A ASP* 2.9 48.7 + - - +
410A ARG* 4.4 5.2 - - - +
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Residues in contact with GLU 404 (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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387A THR* 6.2 0.2 - - - +
391A ALA* 3.8 15.8 - - + +
400A VAL* 3.7 34.8 - - + +
401A SER* 3.2 17.9 + - - +
402A TYR 3.0 0.6 - - - -
403A LEU* 1.3 79.1 - - - +
405A VAL* 1.3 61.7 + - + +
407A ASP* 4.0 4.5 - - - +
408A ALA* 3.2 24.3 + - - +
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Residues in contact with VAL 405 (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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388A LEU* 4.2 6.3 - - + -
391A ALA* 3.9 31.0 - - + +
392A ARG* 3.7 31.2 - - + +
395A TYR* 3.9 18.8 - - + -
402A TYR* 2.8 40.5 + - + +
404A GLU* 1.3 75.4 - - + +
406A LEU* 1.3 66.2 + - - +
408A ALA* 3.2 3.9 + - - +
409A GLU* 2.9 32.7 + - - +
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Residues in contact with LEU 406 (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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199A GLN* 3.9 39.5 - - + +
203A VAL* 3.4 38.1 - - + -
402A TYR* 3.0 23.1 + - + +
403A LEU* 3.8 16.2 - - + +
405A VAL* 1.3 77.0 - - - +
407A ASP* 1.3 57.4 + - - +
409A GLU* 3.2 11.0 + - - +
410A ARG* 2.9 64.6 + - - +
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Residues in contact with ASP 407 (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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403A LEU* 2.9 33.6 + - - +
404A GLU* 4.0 5.8 - - - +
406A LEU* 1.3 76.4 - - - +
408A ALA* 1.3 62.6 + - - +
410A ARG* 3.5 25.0 + - - +
411A SER* 3.2 33.3 + - - -
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Residues in contact with ALA 408 (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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384A LEU* 4.9 7.3 - - - +
387A THR* 4.0 22.2 - - + +
388A LEU* 3.8 32.1 - - + +
391A ALA* 4.7 0.9 - - + -
404A GLU 3.2 16.9 + - - +
405A VAL* 3.7 3.6 - - - +
407A ASP* 1.3 80.8 - - - +
409A GLU* 1.3 61.5 + - - +
411A SER* 4.0 3.9 - - - -
412A LEU* 3.0 25.9 + - - +
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Residues in contact with GLU 409 (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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175A ASN* 6.0 0.3 - - - +
176A TYR* 3.4 44.6 + - + +
179A SER* 3.0 26.9 + - - -
203A VAL* 4.7 2.8 - - - +
388A LEU* 3.8 22.4 - - + +
392A ARG* 3.4 10.7 + - - +
402A TYR* 4.3 6.2 + - - -
405A VAL* 2.9 29.8 + - - +
406A LEU* 3.5 19.5 - - + +
408A ALA* 1.3 76.4 - - - +
410A ARG* 1.3 63.6 + - + +
412A LEU* 3.3 6.8 + - - +
413A PHE* 2.9 20.1 + - - +
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Residues in contact with ARG 410 (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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176A TYR* 4.1 6.3 - - - +
203A VAL* 4.5 16.3 - - + +
403A LEU* 4.4 9.3 - - - +
406A LEU* 2.9 58.3 + - + +
407A ASP* 3.5 28.0 + - - +
409A GLU* 1.3 75.5 - - - +
411A SER* 1.3 59.2 + - - +
413A PHE* 3.3 5.1 + - - +
414A ALA* 2.9 30.0 + - - +
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Residues in contact with SER 411 (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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380A TYR* 4.4 8.6 + - - -
384A LEU* 3.9 25.6 - - - -
407A ASP* 3.2 21.4 + - - -
408A ALA* 4.0 1.3 - - - -
410A ARG* 1.3 75.0 - - - +
412A LEU* 1.3 60.2 - - - +
414A ALA* 3.4 6.1 + - - +
415A THR* 2.9 34.7 + - - -
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Residues in contact with LEU 412 (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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381A LEU* 3.0 34.1 - - + -
384A LEU* 4.1 16.5 - - + +
385A GLN* 4.0 31.4 - - + +
388A LEU* 3.5 34.1 - - + -
408A ALA 3.0 16.7 + - - +
409A GLU* 3.5 5.8 - - - +
411A SER* 1.3 77.6 - - - +
413A PHE* 1.3 62.6 + - - +
415A THR* 3.3 2.4 + - - -
416A ARG* 3.0 38.0 + - + +
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Residues in contact with PHE 413 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ILE* 4.0 16.6 - - + -
169A ALA* 3.9 13.5 - - + -
172A THR* 3.2 36.8 - - + -
176A TYR* 4.1 11.4 - + - +
207A THR* 4.3 19.7 - - + -
210A ASP* 3.4 31.0 - - + -
409A GLU 2.9 17.2 + - - +
410A ARG* 3.7 4.5 - - - +
412A LEU* 1.3 77.4 - - - +
414A ALA* 1.3 62.0 + - - +
416A ARG* 3.3 9.7 + - + +
417A GLN* 3.1 47.2 + - + -
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Residues in contact with ALA 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A ARG 2.9 18.0 + - - +
411A SER* 3.9 7.0 - - - +
413A PHE* 1.3 76.5 - - - +
415A THR* 1.3 58.8 + - - +
417A GLN* 3.4 14.5 + - - +
418A THR* 2.9 33.4 + - - +
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Residues in contact with THR 415 (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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377A GLN* 3.6 29.3 + - + +
380A TYR* 3.5 14.2 - - + -
381A LEU* 3.9 33.0 - - + +
384A LEU* 3.3 14.7 - - - +
411A SER 2.9 20.7 + - - -
412A LEU* 3.7 4.5 - - - -
414A ALA* 1.3 75.7 - - - +
416A ARG* 1.3 59.3 + - - +
418A THR* 3.2 6.8 + - - +
419A LEU* 2.8 29.8 + - + +
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Residues in contact with ARG 416 (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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168A ILE* 3.5 33.2 - - + +
171A GLU* 3.1 33.5 + - - +
172A THR* 4.1 16.3 + - - +
381A LEU* 3.8 21.6 - - + +
385A GLN* 6.1 2.2 - - - +
412A LEU* 3.0 33.7 + - - +
413A PHE* 3.6 12.3 - - - +
415A THR* 1.3 75.6 - - - +
417A GLN* 1.3 62.0 + - - +
419A LEU* 3.4 8.8 + - - +
420A LEU* 3.1 27.0 + - - +
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Residues in contact with GLN 417 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLN* 2.9 41.8 + - - +
168A ILE* 3.8 10.3 - - + -
210A ASP* 3.4 15.6 - - - +
213A LYS* 5.1 0.7 + - - -
214A ARG* 2.9 24.6 + - - +
413A PHE* 3.1 53.1 + - + +
414A ALA* 3.7 12.6 - - - +
415A THR 3.3 0.2 - - - -
416A ARG* 1.3 76.1 - - - +
418A THR* 1.3 63.0 + - - +
420A LEU 3.4 0.3 + - - -
421A ASP* 3.1 16.0 + - - +
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Residues in contact with THR 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A GLN* 4.1 24.2 - - - +
414A ALA* 2.9 19.6 + - - +
415A THR* 3.2 8.2 + - - -
417A GLN* 1.3 76.2 - - - +
419A LEU* 1.3 59.0 + - - +
421A ASP* 3.2 10.9 + - + +
422A LEU* 2.9 39.2 + - + +
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Residues in contact with LEU 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A ILE* 4.0 23.8 - - + +
377A GLN* 3.5 39.3 - - + +
378A GLN* 4.2 17.3 - - + +
381A LEU* 3.7 32.1 - - + -
415A THR 2.8 16.5 + - - +
416A ARG* 3.6 6.7 - - - +
418A THR* 1.3 74.9 - - - +
420A LEU* 1.3 65.0 + - + +
422A LEU* 3.3 5.6 + - + +
423A ASN* 3.0 35.2 + - - +
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Residues in contact with LEU 420 (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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161A LEU* 3.6 15.3 - - + +
164A ALA* 3.6 37.7 - - + +
165A GLN* 3.4 37.7 - - + +
168A ILE* 3.6 24.0 - - + -
416A ARG 3.1 14.8 + - - +
417A GLN 3.6 0.4 - - - +
419A LEU* 1.3 78.4 - - + +
421A ASP* 1.3 61.6 + - - +
423A ASN* 3.4 7.7 + - + +
424A TYR* 3.1 18.2 + - - +
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Residues in contact with ASP 421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 3.6 20.5 - - - +
165A GLN* 3.1 17.1 + - - +
214A ARG* 5.0 8.1 + - - -
417A GLN* 3.1 21.0 + - - +
418A THR* 3.2 11.3 + - - +
420A LEU* 1.3 75.4 - - - +
422A LEU* 1.3 59.7 + - + +
424A TYR* 3.4 7.6 + - + +
425A ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 422 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU* 4.0 19.8 - - + +
373A GLN* 3.6 54.1 - - + +
374A ILE* 3.6 18.2 - - + +
377A GLN* 4.2 14.4 - - + +
418A THR* 2.9 35.8 + - + +
419A LEU* 3.7 5.6 - - - +
420A LEU 3.2 0.2 - - - -
421A ASP* 1.3 75.4 - - + +
423A ASN* 1.3 60.0 + - - +
425A ALA* 3.2 6.6 + - + +
426A ARG* 2.9 28.8 + - - +
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Residues in contact with ASN 423 (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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242A ASN* 6.0 2.2 - - - +
243A SER* 5.4 4.9 - - - +
374A ILE* 4.3 17.3 - - - +
378A GLN* 5.4 2.7 + - - +
419A LEU* 3.0 31.5 + - - +
420A LEU* 3.8 7.8 - - + +
422A LEU* 1.3 73.9 - - - +
424A TYR* 1.3 62.5 + - - +
426A ARG* 2.7 40.3 + - - +
427A GLN* 3.0 32.2 + - - +
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Residues in contact with TYR 424 (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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154A GLN* 3.9 10.1 + - - +
157A PHE* 3.6 24.2 - - + -
158A ASN* 3.3 48.4 + - - +
161A LEU* 3.8 25.8 - - + -
420A LEU 3.1 13.1 + - - +
421A ASP* 3.5 9.6 - - - +
423A ASN* 1.3 77.7 - - - +
425A ALA* 1.3 66.7 + - + +
427A GLN* 3.1 14.9 - - - +
428A VAL* 2.9 49.9 + - + +
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Residues in contact with ALA 425 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU* 3.7 21.3 - - + +
421A ASP 2.9 14.2 + - - +
422A LEU* 3.5 12.6 - - + +
424A TYR* 1.3 81.4 - - + +
426A ARG* 1.3 58.5 + - - +
428A VAL* 3.4 6.8 + - - +
429A ASN* 2.9 30.7 + - - +
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Residues in contact with ARG 426 (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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243A SER* 4.2 25.3 + - - +
367A ARG* 6.1 2.2 - - - +
370A LEU* 3.8 15.0 - - + +
371A ASN* 2.8 45.1 + - - +
374A ILE* 3.6 33.2 - - + +
378A GLN* 5.6 1.6 - - - +
422A LEU 2.9 17.1 + - - +
423A ASN* 2.7 35.1 + - - +
424A TYR 3.2 0.2 - - - -
425A ALA* 1.3 76.9 - - - +
427A GLN* 1.3 58.2 + - - +
429A ASN* 3.1 3.1 + - - +
430A GLU* 2.9 43.5 + - + +
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Residues in contact with GLN 427 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A PHE* 3.3 45.9 + - + +
160A GLN* 5.7 0.4 - - - +
161A LEU* 6.0 0.6 - - - +
241A VAL* 3.8 23.2 - - - +
242A ASN 4.2 14.2 - - - +
243A SER* 5.4 1.0 - - - -
245A SER* 4.9 0.5 - - - -
246A LEU* 3.6 22.5 - - + +
423A ASN* 3.0 20.5 + - - +
424A TYR* 3.1 24.7 - - - +
426A ARG* 1.3 76.0 - - - +
428A VAL* 1.3 61.0 + - - +
430A GLU* 3.3 1.6 + - - -
431A ILE* 3.0 35.8 + - + +
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Residues in contact with VAL 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLN* 3.4 34.3 - - + +
157A PHE* 5.6 0.9 - - + -
424A TYR* 2.9 59.9 + - + +
425A ALA* 3.7 6.3 - - - +
427A GLN* 1.3 76.3 - - + +
429A ASN* 1.3 59.2 + - - +
431A ILE* 3.2 9.1 + - + +
432A SER* 2.8 39.3 + - - +
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Residues in contact with ASN 429 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A ALA* 2.8 47.1 - - - +
366A LEU* 3.5 25.4 - - + +
367A ARG* 3.3 17.3 + - - +
370A LEU* 4.1 9.6 - - + -
425A ALA 2.9 19.0 + - - +
426A ARG 3.6 3.6 - - - +
428A VAL* 1.3 77.5 - - + +
430A GLU* 1.3 62.4 + - - +
432A SER* 3.2 7.9 + - - -
433A LEU* 2.8 29.8 + - - +
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Residues in contact with GLU 430 (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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40A PHE* 3.7 7.5 - - + -
246A LEU* 3.9 16.2 - - + -
248A SER* 3.1 24.1 - - - -
249A VAL* 4.0 5.0 + - - +
367A ARG* 2.6 59.2 + - - +
371A ASN* 5.5 0.2 - - - +
426A ARG* 2.9 34.6 + - + +
427A GLN* 3.7 5.6 - - - +
429A ASN* 1.3 77.2 - - - +
431A ILE* 1.3 58.3 + - - +
433A LEU* 3.3 6.0 + - - +
434A TYR* 3.0 29.5 + - - +
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Residues in contact with ILE 431 (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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40A PHE* 4.2 7.9 - - + -
41A PHE* 3.9 20.6 - - + -
150A SER* 3.5 37.5 - - - +
153A ALA* 4.1 8.5 - - + -
154A GLN* 4.2 11.9 - - + -
157A PHE* 3.8 34.1 - - + -
246A LEU* 3.8 12.8 - - + -
427A GLN 3.0 25.8 + - - +
428A VAL* 3.5 9.2 - - + +
430A GLU* 1.3 77.2 - - - +
432A SER* 1.3 57.4 + - - +
434A TYR* 3.4 3.8 + - + +
435A THR* 2.8 34.4 + - - +
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Residues in contact with SER 432 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER* 4.8 2.7 - - - -
154A GLN* 4.2 8.9 + - - +
363A ALA* 4.8 4.0 - - - -
428A VAL* 2.8 37.4 + - - +
429A ASN* 3.2 13.6 + - - -
431A ILE* 1.3 73.5 - - - +
433A LEU* 1.3 57.4 + - - +
435A THR* 3.7 6.0 - - - -
436A ALA* 2.8 31.9 + - - +
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Residues in contact with LEU 433 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A VAL* 3.5 28.5 - - + -
251A LEU* 4.4 1.8 - - + -
360A VAL* 4.3 15.5 - - + +
363A ALA* 3.9 26.4 - - + +
364A LEU* 4.0 27.1 - - + -
367A ARG* 3.8 24.9 - - + +
429A ASN* 2.8 17.2 + - - +
430A GLU* 3.5 8.5 - - - +
431A ILE 3.2 0.2 - - - -
432A SER* 1.3 73.2 - - - +
434A TYR* 1.3 66.3 + - - +
436A ALA* 3.1 2.9 + - - -
437A LEU* 3.0 44.5 + - + +
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Residues in contact with TYR 434 (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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34A ASN* 3.1 37.3 - - + +
35A ALA* 2.7 32.6 + - + -
36A GLY 3.2 0.2 - - - -
37A TRP* 2.9 30.0 + - + -
40A PHE* 3.5 52.7 - + + -
41A PHE* 4.9 4.9 - + - -
149A VAL* 5.5 4.3 - - + -
249A VAL* 4.1 12.0 - - + +
430A GLU 3.0 16.6 + - - +
431A ILE* 3.5 4.9 - - + +
433A LEU* 1.3 78.3 - - - +
435A THR* 1.3 67.9 + - - +
437A LEU* 3.3 3.2 + - - -
439A GLY* 2.9 22.2 + - - -
440A GLY 3.1 23.3 + - - -
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Residues in contact with THR 435 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 3.9 26.7 + - + +
147A LEU* 4.3 14.4 - - + -
149A VAL* 6.1 0.3 - - - +
150A SER* 3.4 33.6 + - - +
431A ILE* 2.8 19.9 + - - +
432A SER* 3.8 5.4 - - - -
434A TYR* 1.3 82.5 - - - +
436A ALA* 1.3 57.8 + - - +
438A GLY* 2.8 21.8 + - - -
439A GLY* 3.5 8.7 + - - +
453A SO4 3.8 9.7 + - - +
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Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU* 4.2 2.6 - - - +
263A ARG* 2.9 46.9 + - - +
359A GLU* 4.0 18.2 - - + +
360A VAL* 3.8 26.3 - - + +
432A SER 2.8 22.4 + - - +
433A LEU* 3.1 6.7 + - - +
435A THR* 1.3 72.8 - - - +
437A LEU* 1.3 58.4 + - - +
438A GLY 3.1 0.7 - - - -
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 4.4 3.8 - - + -
34A ASN* 3.5 29.5 - - - +
249A VAL* 4.5 4.0 - - + -
251A LEU* 3.7 29.8 - - + -
255A LEU* 4.3 11.2 - - + -
259A ILE* 4.0 47.2 - - + +
260A LEU* 5.7 0.9 - - - -
262A GLN* 5.7 2.1 - - - +
263A ARG* 4.8 3.1 + - - -
360A VAL* 4.0 27.6 - - + -
433A LEU* 3.0 38.0 + - + +
435A THR 3.1 0.2 - - - -
436A ALA* 1.3 75.6 - - - +
438A GLY* 1.3 57.9 + - - +
439A GLY 3.5 1.3 - - - -
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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