Contacts of the helix formed by residues 361 - 386 (chain C) in PDB entry 5NC5
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 361 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C TYR* 4.0 10.3 - - - -
359C LEU 3.1 22.0 + - - -
360C GLN* 1.3 80.1 - - - +
362C PHE* 1.3 64.7 + - - +
363C ARG* 3.4 23.7 + - - +
364C ALA* 3.3 24.9 + - - +
365C THR* 3.0 22.0 + - - -
417C GLU* 4.7 6.7 + - - -
497C LEU* 5.3 1.7 - - - +
498C LYS* 5.0 12.3 + - - +
509C LYS* 5.5 2.9 - - - +
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Residues in contact with PHE 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C PHE* 4.8 13.5 - + - -
356C TYR* 3.3 37.9 - + - -
361C ASN* 1.3 73.7 + - - +
363C ARG* 1.3 66.1 + - + +
365C THR* 3.2 4.2 + - - -
366C LEU* 2.9 31.0 + - + +
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Residues in contact with ARG 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ASN* 3.3 12.2 + - - +
362C PHE* 1.3 81.2 - - + +
364C ALA* 1.3 63.6 + - - +
366C LEU* 3.2 14.3 + - - +
367C ILE* 3.3 18.3 + - - +
495C THR 5.3 1.0 + - - -
496C MET* 3.4 53.8 + - + +
497C LEU* 5.3 2.9 - - + -
498C LYS* 3.9 33.6 - - - +
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Residues in contact with ALA 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C LEU* 3.1 25.6 - - + +
361C ASN* 3.3 25.5 + - - +
362C PHE 3.4 0.2 - - - -
363C ARG* 1.3 77.0 - - - +
365C THR* 1.3 65.3 + - - +
367C ILE* 3.4 7.4 + - - +
368C PRO* 3.0 21.3 - - - +
413C VAL* 4.4 2.9 - - + +
417C GLU* 4.5 5.6 - - - +
497C LEU* 3.6 27.7 - - + +
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Residues in contact with THR 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C PHE* 3.5 30.1 - - + +
355C MET* 3.6 11.7 - - + -
356C TYR* 3.4 47.6 - - + +
359C LEU* 3.8 13.7 - - - +
361C ASN 3.0 19.8 + - - -
362C PHE 3.9 2.9 - - - -
364C ALA* 1.3 76.3 - - - +
366C LEU* 1.3 61.7 + - - +
367C ILE 3.3 0.5 + - - -
368C PRO* 3.5 5.0 - - - +
369C THR* 2.8 25.7 + - - +
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Residues in contact with LEU 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C PHE* 4.7 11.4 - - + -
362C PHE* 2.9 21.3 + - + +
363C ARG* 3.6 8.3 - - - +
364C ALA 3.1 0.6 - - - -
365C THR* 1.3 78.9 - - - +
367C ILE* 1.3 61.9 + - - +
369C THR* 3.4 19.8 - - + -
370C ILE* 3.0 41.3 + - + +
496C MET* 4.2 11.2 - - + -
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Residues in contact with ILE 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ARG 3.3 16.8 - - - +
364C ALA* 3.7 5.2 - - - +
366C LEU* 1.3 78.4 - - - +
368C PRO* 1.3 68.8 - - + +
370C ILE* 3.4 20.4 + - - +
371C ALA 3.9 2.3 + - - -
413C VAL* 3.5 23.6 - - + -
489C THR* 3.9 23.1 + - + +
492C LEU* 4.0 24.8 - - + +
493C CYS* 3.9 26.2 - - - +
496C MET* 3.5 18.2 - - + -
497C LEU* 4.0 19.3 - - + +
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Residues in contact with PRO 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C MET* 3.3 34.5 - - + -
359C LEU* 4.3 7.9 - - + -
364C ALA 3.0 26.5 - - - +
365C THR 3.5 4.5 - - - +
367C ILE* 1.3 87.3 - - + +
369C THR* 1.3 60.1 + - - +
370C ILE 3.1 0.2 - - - -
371C ALA* 3.1 19.4 + - - +
372C VAL 3.9 0.2 + - - -
406C VAL* 3.7 12.2 - - + +
409C ALA* 3.7 28.3 - - + +
410C ILE* 4.2 11.9 - - + +
413C VAL* 4.0 9.0 - - + -
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Residues in contact with THR 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ILE* 6.0 6.1 - - + -
352C PHE* 3.5 24.9 - - + +
355C MET* 3.3 16.9 - - - +
365C THR 2.8 22.6 + - - -
366C LEU* 3.2 23.5 + - + -
367C ILE 3.2 1.0 - - - -
368C PRO* 1.3 74.5 - - - +
370C ILE* 1.3 64.5 + - + +
372C VAL* 3.2 12.9 + - + +
373C PRO* 3.1 17.4 - - + +
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Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TRP* 4.0 28.0 - - + -
20C MET* 6.2 1.3 - - + -
366C LEU* 3.0 26.4 + - + +
367C ILE 3.5 8.5 - - - +
369C THR* 1.3 76.6 - - + +
371C ALA* 1.3 65.1 + - - +
373C PRO* 3.1 17.6 - - + +
374C VAL* 3.5 15.6 - - + +
488C LEU* 3.7 28.9 - - + -
492C LEU* 4.0 14.8 - - + -
496C MET* 4.1 16.8 - - + -
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Residues in contact with ALA 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ILE 3.9 2.1 + - - +
368C PRO* 3.1 17.2 + - + +
370C ILE* 1.3 80.2 - - - +
372C VAL* 1.3 56.7 + - - +
374C VAL* 3.4 2.9 + - - -
375C VAL* 2.8 35.0 + - + +
405C LEU* 3.7 18.2 - - + +
406C VAL* 5.0 0.7 - - + -
409C ALA* 4.4 13.7 - - + -
484C VAL* 3.8 29.6 - - + -
489C THR* 5.2 0.4 - - - +
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Residues in contact with VAL 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ILE* 4.0 26.7 - - + -
351C VAL* 5.9 1.3 - - + -
369C THR* 3.2 11.3 + - + +
370C ILE 3.0 1.4 - - - -
371C ALA* 1.3 76.5 - - - +
373C PRO* 1.3 75.7 - - + +
376C LEU* 2.9 48.2 + - + +
402C ILE* 4.2 12.3 - - + +
405C LEU* 3.6 17.9 - - + -
406C VAL* 3.7 27.6 - - + -
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Residues in contact with PRO 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MET* 3.6 21.3 - - - -
369C THR* 3.1 14.8 - - + +
370C ILE* 3.1 17.9 - - + +
372C VAL* 1.3 92.0 - - + +
374C VAL* 1.3 56.6 + - - +
376C LEU* 4.7 2.5 - - + -
377C LEU* 2.9 43.0 + - + +
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Residues in contact with VAL 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TRP* 6.1 0.2 - - + -
16C ALA* 3.6 37.9 - - + -
19C ILE* 3.2 24.0 - - + +
20C MET* 3.5 22.4 - - + -
370C ILE* 3.5 23.8 - - + +
371C ALA* 3.4 6.3 + - - +
372C VAL 3.3 0.4 - - - -
373C PRO* 1.3 75.7 - - - +
375C VAL* 1.3 59.0 + - - +
378C GLY* 3.1 19.8 + - - -
480C LEU* 4.5 1.7 - - + +
484C VAL* 3.6 25.6 - - + -
488C LEU* 4.6 3.6 - - + -
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Residues in contact with VAL 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C ALA* 2.8 25.4 + - + +
374C VAL* 1.3 70.8 - - - +
376C LEU* 1.3 63.2 + - + +
378C GLY 3.4 0.5 + - - -
379C THR* 2.9 31.8 + - - +
405C LEU* 3.9 26.7 - - + -
477C ALA* 3.4 39.5 - - + +
480C LEU* 3.6 10.3 - - + +
481C SER* 3.8 20.6 - - - +
484C VAL* 3.7 24.2 - - + -
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Residues in contact with LEU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 5.7 4.9 - - + -
348C ILE* 4.7 7.4 - - + -
372C VAL* 2.9 39.8 + - + +
373C PRO* 4.2 2.0 - - + +
375C VAL* 1.3 76.6 - - + +
377C LEU* 1.3 68.1 + - + +
379C THR* 2.8 16.5 + - - +
380C PHE* 2.9 22.2 + - + -
398C MET* 3.7 44.3 - - + +
401C ALA* 5.3 3.6 - - + -
402C ILE* 3.8 15.0 - - + -
405C LEU* 4.1 17.5 - - + -
477C ALA* 5.6 1.8 - - + -
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Residues in contact with LEU 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C MET* 3.4 51.6 - - + +
23C GLY* 3.1 10.9 - - - -
24C GLY* 3.9 15.9 - - - +
27C ILE* 3.7 28.9 - - + -
373C PRO* 2.9 26.0 + - + +
376C LEU* 1.3 76.3 - - + +
378C GLY* 1.3 65.4 + - - +
380C PHE* 2.9 15.2 + - + +
381C ALA 3.0 9.4 + - - -
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Residues in contact with GLY 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ILE* 3.4 26.7 - - - +
374C VAL 3.1 12.0 + - - -
375C VAL 3.8 1.1 - - - -
377C LEU* 1.3 78.1 - - - +
379C THR* 1.3 61.4 + - - +
381C ALA* 3.1 12.2 + - - +
382C VAL* 3.0 24.3 + - - +
480C LEU* 3.7 12.1 - - - -
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Residues in contact with THR 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C VAL* 2.9 15.9 + - - +
376C LEU* 2.8 13.1 + - - -
378C GLY* 1.3 73.3 - - - +
380C PHE* 1.3 61.0 + - - +
382C VAL* 3.3 5.2 + - - +
383C LEU* 2.9 30.6 + - + +
398C MET* 4.1 10.8 - - + -
473C THR* 3.9 36.6 - - + +
476C SER* 3.9 12.8 - - - +
477C ALA* 3.5 27.4 + - + +
480C LEU* 4.0 2.6 - - - +
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Residues in contact with PHE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLY 4.0 4.3 - - - +
26C ALA* 3.8 3.9 - - - +
27C ILE* 3.5 34.3 - - + -
30C LEU* 3.7 22.3 - - + +
344C LEU* 5.9 1.3 - - + -
376C LEU* 2.9 28.7 + - + -
377C LEU* 2.9 8.9 + - + +
379C THR* 1.3 76.2 - - - +
381C ALA* 1.3 56.7 + - - +
383C LEU* 3.3 10.6 + - + +
384C ALA* 2.9 29.6 + - - +
390C ILE* 3.7 25.8 - - + -
395C MET* 3.7 16.8 - - + -
398C MET* 3.4 32.3 - - + -
1102C D10 4.1 20.0 - - + -
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Residues in contact with ALA 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ALA* 4.1 13.0 - - + +
23C GLY* 3.9 17.8 - - - +
26C ALA* 4.0 10.8 - - - -
377C LEU 3.0 10.3 + - - +
378C GLY* 3.1 14.6 - - - +
380C PHE* 1.3 76.0 - - - +
382C VAL* 1.3 57.8 + - + +
384C ALA* 3.1 5.5 + - - +
385C ALA* 3.0 27.6 + - - +
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Residues in contact with VAL 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C GLY 3.0 16.5 + - - +
379C THR 3.6 7.6 - - - +
381C ALA* 1.3 70.5 - - + +
383C LEU* 1.3 70.5 + - + +
385C ALA* 2.8 18.6 + - - +
386C PHE* 3.1 40.5 + - + -
472C ILE* 4.4 8.3 - - + -
476C SER* 3.8 31.6 - - - +
480C LEU* 5.3 3.4 - - + -
1105C HEX 4.6 19.7 - - + -
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Residues in contact with LEU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 4.8 7.6 - - + -
379C THR* 2.9 21.4 + - + +
380C PHE* 3.5 16.2 - - + +
382C VAL* 1.3 78.7 - - + +
384C ALA* 1.3 64.1 + - - +
386C PHE 3.4 0.9 + - - -
387C GLY 3.1 3.6 + - - -
388C PHE* 2.9 45.6 + - + +
389C SER 4.6 5.2 - - - +
390C ILE* 5.8 0.9 - - - -
394C THR* 3.9 24.0 - - + +
395C MET* 5.8 0.4 - - + -
398C MET* 4.0 26.0 - - + -
472C ILE* 3.7 36.3 - - + -
473C THR* 4.3 8.1 - - - +
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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
----------------------------------------------------------
26C ALA* 3.7 21.1 - - + -
29C LYS* 5.9 4.5 - - + -
30C LEU* 3.8 19.9 - - + +
380C PHE 2.9 14.0 + - - +
381C ALA 3.5 7.9 - - - +
382C VAL 3.1 0.2 - - - -
383C LEU* 1.3 78.2 - - - +
385C ALA* 1.3 62.9 + - - +
387C GLY* 3.2 14.4 + - - +
388C PHE 4.7 0.9 - - - -
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Residues in contact with ALA 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C ALA 3.0 11.8 + - - +
382C VAL* 2.8 13.5 + - - +
384C ALA* 1.3 78.9 - - - +
386C PHE* 1.3 74.0 + - + +
387C GLY 3.8 0.3 + - - -
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Residues in contact with PHE 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C VAL* 3.1 43.7 + - + -
385C ALA* 1.3 89.5 - - + +
387C GLY* 1.3 63.8 + - - +
388C PHE* 3.2 23.7 + + + -
472C ILE* 3.7 17.0 - - + -
1105C HEX 4.0 25.1 - - + -
1108C D12 4.1 28.3 - - + +
1109C DD9 4.8 24.2 - - + -
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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