Contacts of the helix formed by residues 405 - 438 (chain A) in PDB entry 3QMK
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 GLN 405 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ALA 4.6 3.8 + - - -
401A ALA* 5.1 3.2 - - + +
403A PRO 3.0 7.3 + - - +
404A PRO* 1.3 71.7 - - - +
406A ALA* 1.3 65.8 + - - +
407A GLU* 4.9 1.6 - - + +
408A ARG* 4.0 23.4 - - + +
409A VAL* 3.1 26.3 + - - +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A PRO 3.8 3.0 + - - -
405A GLN* 1.3 71.1 - - - +
407A GLU* 1.3 59.1 + - - +
409A VAL* 3.1 6.2 + - - +
410A LEU* 2.9 33.0 + - + +
476A GLU* 6.0 3.6 - - + -
477A LEU* 3.8 28.3 - - + +
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Residues in contact with GLU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLN* 3.6 1.7 - - + +
406A ALA* 1.3 77.7 - - - +
408A ARG* 1.3 57.1 + - - +
410A LEU* 3.7 8.3 - - - +
411A LEU* 3.0 38.7 + - + +
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Residues in contact with ARG 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLY 5.2 1.2 + - - -
397A ALA* 4.1 14.5 + - - +
398A ALA* 3.8 32.6 - - + +
401A ALA* 3.7 24.0 - - - +
405A GLN* 3.6 23.0 + - + +
406A ALA 3.2 1.0 - - - -
407A GLU* 1.3 75.0 - - - +
409A VAL* 1.3 59.9 + - - +
410A LEU 3.1 1.3 - - - -
411A LEU* 3.2 9.4 + - - +
412A ALA* 2.9 31.7 + - + +
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Residues in contact with VAL 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE* 4.0 9.0 - - + -
398A ALA* 3.2 41.7 - - + +
399A LEU* 3.3 30.3 - - + +
404A PRO* 4.9 5.2 - - + -
405A GLN 3.1 21.1 + - - +
406A ALA 3.7 3.6 - - - +
408A ARG* 1.3 76.8 - - - +
410A LEU* 1.3 57.8 + - + +
412A ALA* 3.4 1.4 + - - +
413A LEU* 2.9 29.6 + - + +
467A LEU* 4.8 3.1 - - + -
477A LEU* 4.1 21.1 - - + -
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ALA 2.9 15.8 + - - +
407A GLU* 3.7 9.2 - - - +
409A VAL* 1.3 76.5 - - + +
411A LEU* 1.3 60.5 + - - +
413A LEU* 3.4 9.1 + - + +
414A ARG* 2.9 29.5 + - - +
477A LEU* 4.5 15.5 - - + -
480A GLN* 3.4 44.2 - - + +
481A ILE* 4.5 4.9 - - + +
484A LEU* 3.9 24.2 - - + +
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A GLU* 3.0 27.9 + - + +
408A ARG* 3.2 7.4 + - - +
410A LEU* 1.3 76.0 - - + +
412A ALA* 1.3 57.3 + - - +
414A ARG* 3.4 8.7 - - + +
415A ARG* 3.0 27.9 + - - +
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ALA 4.7 2.4 - - - +
394A GLY* 4.0 7.6 - - - +
395A PHE* 3.6 30.3 - - - +
398A ALA* 4.1 6.7 - - + -
408A ARG* 2.9 18.9 + - + +
409A VAL 3.6 5.8 - - - +
410A LEU 3.2 0.2 - - - -
411A LEU* 1.3 74.2 - - - +
413A LEU* 1.3 60.2 + - - +
414A ARG 3.1 1.3 - - - -
415A ARG* 3.1 8.5 + - - +
416A TYR* 2.9 27.2 + - - +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A PHE* 3.5 39.6 - - + -
409A VAL* 2.9 19.9 + - + +
410A LEU* 3.9 8.3 - - + +
412A ALA* 1.3 75.5 - - - +
414A ARG* 1.3 58.4 + - - +
416A TYR* 3.3 11.1 + - + +
417A LEU* 2.9 44.2 + - + +
464A LEU* 3.9 27.1 - - + +
467A LEU* 4.6 9.4 - - + -
481A ILE* 4.4 18.4 - - + -
484A LEU* 4.0 18.8 - - + -
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU 2.9 18.2 + - - +
411A LEU* 3.4 13.2 - - + +
413A LEU* 1.3 78.2 - - - +
415A ARG* 1.3 56.4 + - - +
417A LEU* 3.3 7.2 + - - +
418A ARG* 3.0 37.3 + - + +
484A LEU* 4.6 21.3 - - + +
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Residues in contact with ARG 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ALA* 4.0 10.6 - - + +
411A LEU 3.0 14.7 + - - +
412A ALA* 3.1 10.5 + - - +
414A ARG* 1.3 72.8 - - - +
416A TYR* 1.3 65.9 + - - +
418A ARG* 3.3 10.8 + - - +
419A ALA* 2.9 22.9 + - - +
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Residues in contact with TYR 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 4.3 11.4 - - + -
391A ALA* 3.6 18.1 - - + +
392A LEU* 3.9 33.7 - - + -
395A PHE* 4.4 9.0 - + + -
412A ALA 2.9 13.7 + - - +
413A LEU* 3.5 21.3 - - + +
415A ARG* 1.3 76.8 - - - +
417A LEU* 1.3 81.1 + - + +
419A ALA* 3.0 13.7 + - - +
420A GLU* 2.7 52.9 + - + +
459A ARG* 3.6 10.5 + - - +
460A VAL* 3.8 6.7 - - - -
463A SER* 2.7 39.1 + - - -
464A LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 2.9 43.4 + - + +
414A ARG* 3.6 4.7 - - - +
416A TYR* 1.3 86.3 - - + +
418A ARG* 1.3 58.8 + - + +
420A GLU* 3.3 4.9 + - - +
421A GLN* 2.9 28.2 + - - +
460A VAL* 3.8 32.1 - - + -
464A LEU* 4.9 7.4 - - + -
484A LEU* 4.3 30.1 - - + +
485A LEU* 5.3 3.6 - - - +
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Residues in contact with ARG 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ARG* 3.0 24.6 + - + +
415A ARG* 3.6 8.3 - - - +
416A TYR 3.2 0.4 - - - -
417A LEU* 1.3 74.1 - - + +
419A ALA* 1.3 59.7 + - - +
421A GLN* 3.5 24.2 + - - +
422A LYS* 2.9 28.4 + - - +
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Residues in contact with ALA 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ILE* 4.7 5.2 - - - +
387A GLN* 4.1 7.9 - - + +
388A ARG* 3.7 33.6 - - + +
391A ALA* 4.0 10.3 - - + -
415A ARG 2.9 13.6 + - - +
416A TYR 3.0 9.1 + - - +
418A ARG* 1.3 78.4 - - - +
420A GLU* 1.3 61.8 + - - +
422A LYS* 3.2 17.9 + - - +
423A GLU* 3.3 11.1 + - - +
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Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG* 3.3 15.0 - - + -
416A TYR* 2.7 50.0 + - + +
417A LEU* 3.7 8.1 - - + +
419A ALA* 1.3 77.7 - - - +
421A GLN* 1.3 61.2 + - - +
423A GLU* 3.0 8.1 + - - +
424A GLN* 3.0 21.5 + - - +
456A ILE* 3.4 13.6 - - + +
459A ARG* 2.6 48.3 + - - +
460A VAL* 3.8 25.8 - - + -
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Residues in contact with GLN 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A LEU 2.9 18.1 + - - +
418A ARG* 3.5 28.0 + - - +
419A ALA 3.3 0.2 - - - -
420A GLU* 1.3 75.8 - - - +
422A LYS* 1.3 57.6 + - - +
424A GLN* 3.2 16.8 + - - +
425A ARG* 2.8 56.8 + - + +
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Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 6.2 0.2 - - - -
384A ILE* 4.5 22.9 - - + -
387A GLN* 3.8 24.2 - - + +
418A ARG 2.9 13.2 + - - +
419A ALA* 3.4 13.5 - - - +
420A GLU 3.1 0.2 - - - -
421A GLN* 1.3 78.0 - - - +
423A GLU* 1.3 56.4 + - - +
425A ARG* 3.5 9.6 + - - +
426A HIS* 3.0 29.3 + - - +
429A ARG* 5.5 0.5 + - - -
1C SGN 3.1 35.7 + - - -
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Residues in contact with GLU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ILE* 3.6 26.6 - - + +
385A ASN* 4.3 4.9 - - - +
388A ARG* 2.7 33.7 + - - -
419A ALA 3.3 5.1 + - - +
420A GLU* 3.0 10.1 + - - +
422A LYS* 1.3 75.6 - - - +
424A GLN* 1.3 61.0 + - - +
426A HIS* 3.6 7.5 - - + +
427A THR* 2.8 31.8 + - - -
452A HIS* 2.5 37.8 + - + +
456A ILE* 3.9 4.5 - - + -
459A ARG* 2.8 21.2 + - - -
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Residues in contact with GLN 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A GLU 3.0 11.5 + - - +
421A GLN* 3.5 23.0 + - - +
423A GLU* 1.3 75.3 - - - +
425A ARG* 1.3 67.2 + - - +
427A THR* 3.2 4.0 + - - -
428A LEU* 3.0 32.5 + - + +
453A LEU* 3.8 19.5 + - + +
456A ILE* 3.6 22.6 - - + +
326B ASN* 3.3 29.9 + - - +
330B ARG* 5.9 2.8 - - - +
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Residues in contact with ARG 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLN* 2.8 46.5 + - + +
422A LYS* 3.8 7.6 - - - +
424A GLN* 1.3 74.9 - - + +
426A HIS* 1.3 59.3 + - - +
428A LEU* 3.3 3.9 + - + -
429A ARG* 2.8 63.0 + - - +
319B GLU* 3.0 39.2 + - - -
322B MET* 3.7 20.5 - - + +
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Residues in contact with HIS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA* 5.7 2.2 - - + -
380A VAL* 3.7 23.5 - - + +
381A ILE* 4.4 19.2 - - + +
384A ILE* 3.8 17.6 - - + +
422A LYS* 3.0 19.0 + - + +
423A GLU* 3.6 7.9 - - + +
425A ARG* 1.3 78.2 - - - +
427A THR* 1.3 66.8 + - - +
429A ARG* 4.0 11.8 - - - +
430A HIS* 3.0 31.4 + + + +
452A HIS* 6.3 1.1 - + - -
2C IDS 3.0 29.7 + - - -
3C SGN 3.6 13.2 + - - -
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Residues in contact with THR 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLU 2.8 20.0 + - - -
424A GLN 3.2 6.9 + - - -
426A HIS* 1.3 83.9 - - - +
428A LEU* 1.3 62.6 + - - +
430A HIS* 4.0 3.4 - - - +
431A TYR* 3.3 22.0 + - - +
445A MET* 5.5 0.3 - - - +
449A VAL* 4.1 30.1 - - + +
452A HIS* 3.5 36.5 + - + +
453A LEU* 4.1 15.7 - - + -
456A ILE* 4.1 2.8 - - - +
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Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLN* 3.0 29.8 + - + +
425A ARG* 3.7 7.6 - - + +
427A THR* 1.3 77.1 - - - +
429A ARG* 1.3 53.1 + - - +
431A TYR* 3.2 9.3 + - - +
432A GLN* 2.8 35.2 + - - +
449A VAL* 5.0 2.2 - - + -
453A LEU* 3.7 30.7 - - + -
322B MET* 3.9 29.6 - - + +
325B ILE* 3.8 25.9 - - + +
326B ASN* 3.8 35.2 - - + +
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Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LYS 5.5 0.2 + - - -
425A ARG* 2.8 72.5 + - - +
426A HIS* 4.0 13.6 - - - +
428A LEU* 1.3 73.7 - - - +
430A HIS* 1.3 52.7 + - - +
432A GLN* 2.9 13.8 + - - +
433A HIS* 2.7 34.0 + - + +
318B GLU* 3.2 37.5 + - - +
319B GLU* 4.6 0.6 + - - -
322B MET* 3.8 13.0 - - - +
2C IDS 3.3 38.5 + - - -
3C SGN 2.9 24.9 - - - +
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Residues in contact with HIS 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A HIS* 3.0 27.9 + + + +
427A THR* 4.0 4.3 - - - +
429A ARG* 1.3 76.9 - - - +
431A TYR* 1.3 57.8 + - - +
433A HIS* 3.5 3.3 + - - +
434A VAL* 2.9 56.1 + - + +
445A MET* 3.5 27.1 - - + +
3C SGN 3.2 30.6 + - - +
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Residues in contact with TYR 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A THR 3.3 12.1 + - - +
428A LEU* 3.2 7.5 + - - +
430A HIS* 1.3 76.1 - - - +
432A GLN* 1.3 64.9 + - - +
434A VAL* 3.2 1.9 + - - +
435A ALA* 3.0 23.0 + - + +
442A ALA* 3.6 26.5 - - + -
445A MET* 3.7 22.9 - - + +
446A ARG* 3.6 15.5 - - + +
449A VAL* 3.8 29.2 - - + -
325B ILE* 3.6 50.3 - - + -
329B MET* 3.9 12.6 - - + -
358B LEU* 3.7 15.2 + - + +
361B LEU* 6.1 0.2 - - - +
362B GLU* 2.8 29.7 + - + +
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Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU 2.8 20.2 + - - +
429A ARG* 2.9 22.7 + - - +
431A TYR* 1.3 73.7 - - - +
433A HIS* 1.3 67.7 + - - +
435A ALA* 3.5 3.9 + - - -
436A ALA* 3.1 25.3 + - - +
318B GLU* 3.9 42.7 + - - +
321B ARG* 4.1 24.8 - - + +
322B MET* 4.5 3.8 - - + -
325B ILE* 4.0 18.6 - - + -
365B VAL* 3.6 12.6 - - + +
369B ARG* 4.0 19.3 + - - +
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Residues in contact with HIS 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG 2.7 21.0 + - - +
430A HIS* 3.5 7.5 + - - +
431A TYR 3.1 0.2 - - - -
432A GLN* 1.3 81.9 - - - +
434A VAL* 1.3 69.9 + - - +
435A ALA 3.1 0.4 - - - -
436A ALA* 3.1 13.7 + - - +
437A VAL* 3.2 30.3 + - + +
318B GLU* 6.0 1.6 - - - +
369B ARG* 5.1 5.2 - - - -
3C SGN 3.2 68.7 + - - +
4C IDS 2.8 37.4 + - - -
----------------------------------------------------------
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Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A HIS* 2.9 45.6 + - + +
431A TYR 3.7 1.3 - - - +
433A HIS* 1.3 80.2 - - - +
435A ALA* 1.3 55.5 + - - +
437A VAL* 4.5 4.9 - - - -
438A ASP* 2.7 46.5 + - + +
441A LYS* 3.7 11.7 - - + -
442A ALA* 3.6 18.2 - - - +
445A MET* 3.6 31.2 - - - -
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Residues in contact with ALA 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A TYR* 3.0 18.9 + - + +
432A GLN* 3.6 8.5 - - - +
434A VAL* 1.3 79.8 - - - +
436A ALA* 1.3 60.1 + - - +
437A VAL 3.3 0.9 + - - -
438A ASP 4.0 4.3 + - - -
439A PRO* 4.2 5.9 - - - +
442A ALA* 3.7 21.0 - - + +
362B GLU* 4.2 20.2 - - + +
365B VAL* 4.1 16.6 - - + -
366B SER* 3.5 20.8 + - - -
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Residues in contact with ALA 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLN* 3.1 18.7 + - - +
433A HIS* 3.1 9.1 + - - +
435A ALA* 1.3 78.2 - - - +
437A VAL* 1.3 63.4 + - + +
365B VAL* 3.7 16.4 - - + -
366B SER* 4.2 12.1 + - - +
369B ARG* 3.6 49.6 - - + +
----------------------------------------------------------
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Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A HIS* 3.2 33.8 + - + +
434A VAL* 4.4 3.4 - - - +
436A ALA* 1.3 89.8 - - + +
438A ASP* 1.3 68.7 + - + +
439A PRO* 4.1 3.1 - - - -
366B SER* 5.7 0.4 - - - -
369B ARG* 4.3 17.0 - - + +
3C SGN 4.5 7.4 - - - +
4C IDS 5.2 1.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL* 2.7 25.2 + - + +
437A VAL* 1.3 83.6 - - + +
439A PRO* 1.3 67.9 - - - +
440A GLU* 3.4 3.9 - - - +
441A LYS* 2.9 45.9 + - + +
442A ALA 3.2 6.2 + - - -
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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