Contacts of the helix formed by residues 405 - 438 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ALA 4.9 1.6 + - - -
401B ALA* 5.2 1.9 - - + +
403B PRO* 3.5 17.6 - - + +
404B PRO* 1.3 68.9 - - - +
406B ALA* 1.3 66.7 + - - +
407B GLU* 2.9 7.8 + - + +
408B ARG* 2.9 35.8 + - + +
409B VAL* 3.0 14.2 + - - +
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Residues in contact with ALA 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B PRO 3.4 6.3 + - - -
405B GLN* 1.3 69.9 - - - +
407B GLU* 1.3 56.4 + - - +
409B VAL* 3.9 2.9 - - - -
410B LEU* 3.0 30.7 + - - +
473B LEU* 3.4 28.9 - - + -
476B GLU* 3.4 24.5 - - - +
477B LEU* 3.4 18.2 - - + +
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 2.9 6.6 + - + +
406B ALA* 1.3 80.1 - - - +
408B ARG* 1.3 58.3 + - - +
410B LEU* 3.5 4.2 + - - +
411B LEU* 3.1 39.8 + - + +
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Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ALA* 3.9 11.9 - - + +
405B GLN* 2.9 30.4 + - + +
407B GLU* 1.3 76.8 - - - +
409B VAL* 1.3 60.8 + - + +
411B LEU* 3.4 7.7 + - - +
412B ALA* 3.0 29.6 + - - +
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Residues in contact with VAL 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 4.2 8.6 - - + -
398B ALA* 3.5 36.8 - - + +
399B LEU* 3.6 27.4 - - + -
404B PRO* 4.8 0.4 - - + -
405B GLN 3.0 20.1 + - - +
406B ALA* 3.9 5.2 - - - +
408B ARG* 1.3 75.8 - - + +
410B LEU* 1.3 65.5 + - - +
412B ALA* 3.2 2.6 + - - +
413B LEU* 2.9 24.0 + - + +
467B LEU* 4.0 10.1 - - + -
473B LEU* 4.0 14.1 - - + -
477B LEU* 3.7 18.6 - - + -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B ALA 3.0 20.2 + - - +
407B GLU* 3.6 6.5 - - - +
409B VAL* 1.3 78.2 - - - +
411B LEU* 1.3 66.1 - - + +
413B LEU* 3.7 4.1 - - + +
414B ARG* 2.9 28.6 + - + +
477B LEU* 3.8 15.0 - - + +
480B GLN* 3.6 50.5 - - + +
481B ILE* 4.3 13.7 - - + -
484B LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B GLU* 3.1 23.1 + - + +
408B ARG* 3.9 7.6 - - - +
410B LEU* 1.3 88.3 - - + +
412B ALA* 1.3 63.8 + - - +
414B ARG* 3.4 15.7 + - - +
415B ARG* 3.2 22.3 + - - +
418B ARG* 5.7 0.5 + - - -
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Residues in contact with ALA 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ALA 4.5 3.3 - - - +
394B GLY 3.8 10.8 - - - +
395B PHE* 3.5 30.5 - - + +
398B ALA* 4.2 5.8 - - + -
408B ARG 3.0 18.1 + - - +
409B VAL 3.7 3.6 - - - +
411B LEU* 1.3 74.5 - - - +
413B LEU* 1.3 65.1 + - - +
415B ARG* 3.4 9.9 + - - +
416B TYR* 3.1 21.7 + - - +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.5 31.5 - - + -
409B VAL* 2.9 18.4 + - + +
410B LEU* 3.7 7.4 - - + +
412B ALA* 1.3 74.6 - - - +
414B ARG* 1.3 66.3 + - - +
416B TYR* 3.2 13.0 + - + +
417B LEU* 2.9 46.5 + - + +
464B LEU* 3.7 28.9 - - + +
467B LEU* 4.2 9.2 - - + -
477B LEU* 5.8 0.2 - - + -
481B ILE* 3.6 39.0 - - + -
484B LEU* 4.8 3.4 - - + -
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Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU* 2.9 19.5 + - + +
411B LEU* 3.5 17.0 - - - +
413B LEU* 1.3 76.9 - - - +
415B ARG* 1.3 57.2 + - - +
417B LEU* 3.2 5.5 + - - +
418B ARG* 2.9 80.4 + - - +
484B LEU* 3.6 39.2 - - + +
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B GLN* 4.9 2.0 + - - +
390B ALA* 3.5 35.6 + - - +
391B ALA* 3.8 21.0 - - + +
394B GLY* 5.1 8.7 - - - -
411B LEU 3.2 10.2 + - - +
412B ALA* 3.7 10.5 - - - +
413B LEU 3.3 0.2 - - - -
414B ARG* 1.3 78.4 - - - +
416B TYR* 1.3 62.4 + - - +
418B ARG* 3.4 24.0 + - - +
419B ALA* 3.1 21.1 + - - +
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Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ARG* 4.0 17.9 - - + -
391B ALA* 3.6 16.6 - - + +
392B LEU* 4.0 33.9 - - + -
395B PHE* 4.7 7.0 - + + -
412B ALA 3.1 14.1 + - - +
413B LEU* 3.5 15.3 - - + +
415B ARG* 1.3 75.0 - - - +
417B LEU* 1.3 84.6 + - + +
419B ALA* 3.1 12.6 + - - +
420B GLU* 2.8 48.2 + - + +
459B ARG* 3.5 13.3 + - - +
460B VAL* 4.4 4.3 - - - -
463B SER* 2.6 39.9 + - - -
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B LEU* 2.9 41.9 + - + +
414B ARG* 3.2 4.0 + - - +
416B TYR* 1.3 92.6 - - + +
418B ARG* 1.3 58.1 + - + +
420B GLU* 3.3 4.7 + - - +
421B GLN* 2.9 28.6 + - - +
460B VAL* 3.7 33.2 - - + -
464B LEU* 4.5 4.3 - - + -
481B ILE* 5.0 0.7 - - + -
484B LEU* 4.0 28.7 - - + +
485B LEU* 3.8 24.2 - - + +
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Residues in contact with ARG 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU 5.7 0.4 + - - -
414B ARG* 2.9 85.8 + - + +
415B ARG* 3.6 23.2 - - - +
416B TYR 3.2 0.2 - - - -
417B LEU* 1.3 77.4 - - + +
419B ALA* 1.3 57.7 + - - +
421B GLN* 3.4 8.3 + - - +
422B LYS* 3.0 27.4 + - - +
425B ARG* 5.0 2.9 + - - -
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ILE* 4.6 6.0 - - - +
387B GLN* 4.2 12.1 - - + +
388B ARG* 3.8 34.8 - - + +
391B ALA* 4.5 0.7 - - + -
415B ARG* 3.1 13.2 + - + +
416B TYR* 3.1 12.5 + - - +
418B ARG* 1.3 74.3 - - - +
420B GLU* 1.3 64.4 + - - +
422B LYS* 3.3 10.2 + - - +
423B GLU* 3.2 19.8 + - - +
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Residues in contact with GLU 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ARG* 3.1 15.8 - - + -
416B TYR* 2.8 42.8 + - + +
417B LEU 3.7 7.4 - - - +
418B ARG 3.3 0.2 - - - -
419B ALA* 1.3 76.3 - - - +
421B GLN* 1.3 57.1 + - - +
423B GLU* 3.3 6.9 + - - +
424B GLN* 2.9 27.5 + - - +
456B ILE* 3.8 15.0 - - + +
459B ARG* 2.7 48.0 + - - +
460B VAL* 3.6 33.0 - - + -
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Residues in contact with GLN 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B LEU 2.9 18.2 + - - +
418B ARG* 3.5 9.0 - - - +
419B ALA 3.2 0.2 - - - -
420B GLU* 1.3 75.1 - - - +
422B LYS* 1.3 60.0 + - - +
424B GLN* 3.1 15.4 + - - +
425B ARG* 2.8 49.1 + - - +
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Residues in contact with LYS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SO4 3.1 32.8 + - - +
384B ILE* 4.5 20.2 - - + -
387B GLN* 3.8 24.2 - - - +
418B ARG 3.0 13.7 + - - +
419B ALA* 3.4 13.0 - - - +
420B GLU 3.2 0.2 - - - -
421B GLN* 1.3 75.9 - - - +
423B GLU* 1.3 59.0 + - - +
425B ARG* 3.2 17.7 + - - +
426B HIS* 2.8 31.0 + - + +
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ILE* 6.2 0.4 - - - +
384B ILE* 3.7 24.5 - - + +
385B ASN* 4.3 5.7 - - - +
388B ARG* 3.2 17.6 + - - +
419B ALA 3.2 7.0 + - - +
420B GLU* 3.3 9.9 + - - +
422B LYS* 1.3 77.7 - - - +
424B GLN* 1.3 62.1 + - - +
426B HIS* 3.7 7.4 - - + +
427B THR* 2.9 31.1 + - - +
452B HIS* 2.7 31.3 + - + +
456B ILE* 3.7 8.7 - - + -
459B ARG* 2.7 33.2 + - - -
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASN* 2.8 35.4 + - - +
420B GLU 2.9 15.7 + - - +
421B GLN* 3.1 16.6 + - - +
423B GLU* 1.3 76.8 - - - +
425B ARG* 1.3 66.2 + - - +
427B THR* 3.1 5.3 + - - -
428B LEU* 2.9 30.0 + - + +
453B LEU* 3.9 17.7 - - + +
456B ILE* 4.0 17.7 - - + +
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Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A MET* 3.7 17.7 - - + +
1B SO4 2.8 52.5 + - - +
418B ARG 5.0 2.2 + - - -
421B GLN* 2.8 40.1 + - - +
422B LYS* 3.7 18.3 - - - +
424B GLN* 1.3 76.7 - - + +
426B HIS* 1.3 58.4 + - - +
428B LEU* 3.3 6.0 + - + +
429B ARG* 2.8 39.4 + - - +
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Residues in contact with HIS 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SO4 4.6 1.3 + - - +
3B SO4 4.2 12.4 + - - -
377B ALA* 5.5 1.2 + - - -
380B VAL* 3.6 31.7 - - + +
381B ILE* 4.1 25.9 - - + +
384B ILE* 3.9 17.5 - - + +
422B LYS* 2.8 17.0 + - + +
423B GLU* 3.7 6.5 + - - +
425B ARG* 1.3 76.2 - - - +
427B THR* 1.3 67.0 + - - +
429B ARG* 3.6 19.9 - - - +
430B HIS* 3.1 33.5 + + + +
452B HIS* 6.1 1.2 - - - -
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Residues in contact with THR 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLU* 2.9 19.4 + - - +
424B GLN 3.1 8.0 + - - -
426B HIS* 1.3 82.7 + - - +
428B LEU* 1.3 63.1 + - - +
430B HIS* 3.5 4.3 + - - +
431B TYR* 3.2 21.1 + - - +
448B GLN* 6.1 0.2 - - - +
449B VAL* 4.0 26.5 - - + +
452B HIS* 3.2 45.0 + - + +
453B LEU* 4.0 16.4 - - + -
456B ILE* 4.0 1.9 - - - +
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A MET* 4.3 23.9 - - + +
325A ILE* 3.8 29.2 - - + +
326A ASN* 3.5 37.5 - - + +
329A MET* 4.8 0.2 - - + -
424B GLN* 2.9 30.9 + - + +
425B ARG* 3.7 8.1 - - + +
427B THR* 1.3 77.8 - - - +
429B ARG* 1.3 57.1 + - - +
431B TYR* 3.3 8.5 + - - +
432B GLN* 2.9 28.2 + - - +
449B VAL* 5.3 2.7 - - + -
453B LEU* 3.9 26.9 - - + -
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Residues in contact with ARG 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 3.6 29.3 + - - +
322A MET* 3.8 18.9 - - - +
1B SO4 2.9 46.3 + - - -
3B SO4 3.4 25.2 + - - +
425B ARG* 2.8 30.0 + - - +
426B HIS* 3.6 26.6 - - - +
428B LEU* 1.3 71.5 - - - +
430B HIS* 1.3 60.1 + - - +
432B GLN* 3.0 16.9 + - - +
433B HIS* 2.8 27.4 + - - +
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Residues in contact with HIS 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SO4 3.1 31.6 + - - +
426B HIS* 3.1 29.0 + + + +
427B THR* 3.9 4.7 - - - +
429B ARG* 1.3 76.7 - - - +
431B TYR* 1.3 61.8 + - - +
433B HIS* 3.4 4.2 + - - +
434B VAL* 3.1 41.8 + - + +
445B MET* 3.4 31.8 - - + +
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Residues in contact with TYR 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 3.8 44.9 - - + -
329A MET* 3.9 18.4 - - + -
358A LEU* 3.9 11.4 - - + +
362A GLU* 2.5 33.6 + - + +
427B THR 3.2 12.5 + - - +
428B LEU* 3.5 8.1 - - - +
429B ARG 3.2 0.2 - - - -
430B HIS* 1.3 80.2 - - - +
432B GLN* 1.3 61.9 + - - +
434B VAL* 3.2 3.3 + - - +
435B ALA* 3.1 21.0 + - + +
442B ALA* 3.6 27.1 - - + -
445B MET* 3.8 27.6 - - + -
446B ARG* 3.7 15.6 - - + +
449B VAL* 3.9 20.4 - - + -
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Residues in contact with GLN 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 3.6 48.4 + - - +
321A ARG* 4.4 15.5 - - + -
322A MET* 4.3 7.6 - - + -
325A ILE* 4.2 18.6 - - + -
365A VAL* 3.8 9.8 - - + +
369A ARG* 3.9 19.9 + - - -
428B LEU 2.9 16.1 + - - +
429B ARG* 3.0 24.2 + - - +
431B TYR* 1.3 75.8 - - - +
433B HIS* 1.3 65.9 + - - +
435B ALA* 3.4 6.0 + - - +
436B ALA* 3.1 27.4 + - - +
----------------------------------------------------------
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Residues in contact with HIS 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ARG* 4.9 5.4 - - - -
3B SO4 4.0 23.5 + - - +
429B ARG 2.8 17.2 + - - +
430B HIS* 3.7 5.4 + - - +
431B TYR 3.2 0.2 - - - -
432B GLN* 1.3 85.5 - - - +
434B VAL* 1.3 71.5 + - - +
436B ALA* 3.2 5.6 + - - +
437B VAL* 3.2 42.4 + - + +
4C IDS 2.7 34.4 + - - -
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B HIS* 3.1 44.1 + - + +
431B TYR 3.7 4.7 - - - +
433B HIS* 1.3 82.3 - - - +
435B ALA* 1.3 54.3 + - - +
437B VAL* 4.4 4.3 - - - -
438B ASP* 2.7 46.3 + - + +
441B LYS* 3.8 11.7 - - + -
442B ALA* 3.6 24.9 - - - +
445B MET* 3.7 16.6 - - - -
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Residues in contact with ALA 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLU* 3.9 24.8 - - + +
365A VAL* 4.0 12.3 - - + -
366A SER* 3.3 22.5 - - - -
431B TYR* 3.1 13.4 + - + +
432B GLN* 3.7 9.6 - - - +
434B VAL* 1.3 76.6 - - - +
436B ALA* 1.3 64.8 + - - +
437B VAL 3.4 0.2 + - - -
439B PRO* 3.5 10.3 - - - +
442B ALA* 3.6 21.7 - - + +
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Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A VAL* 3.6 20.6 - - + +
366A SER* 4.0 9.8 + - - +
369A ARG* 3.4 55.2 - - + +
370A GLN* 5.4 1.9 - - - +
432B GLN* 3.1 18.7 + - - +
433B HIS* 3.2 8.9 + - - +
435B ALA* 1.3 79.2 - - - +
437B VAL* 1.3 59.2 + - - +
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Residues in contact with VAL 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ARG* 3.9 22.2 - - + +
433B HIS* 3.2 40.1 + - + +
434B VAL* 4.1 3.8 - - - +
436B ALA* 1.3 84.8 - - - +
438B ASP* 1.3 66.0 + - + +
439B PRO* 3.7 6.8 - - - +
4C IDS 4.5 10.3 - - - +
----------------------------------------------------------
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Residues in contact with ASP 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 2.7 25.3 + - + +
437B VAL* 1.3 82.7 - - + +
439B PRO* 1.3 64.0 - - - +
440B GLU* 3.8 7.4 + - - +
441B LYS* 3.1 35.7 + - + +
442B ALA 3.1 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