Contacts of the helix formed by residues 403 - 429 (chain B) in PDB entry 5FN3
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 ASP 403 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 5.2 9.0 + - - +
101B LYS* 3.1 26.7 + - - +
396B ALA 4.1 4.9 - - - +
397B SER* 3.0 26.8 - - - +
398B ALA 4.6 3.1 - - - +
400B ALA* 3.6 29.0 - - - +
401B SER 3.1 6.2 - - - +
402B GLY* 1.3 74.7 - - - +
404B TRP* 1.3 75.7 + - + +
406B THR* 3.2 7.7 + - - -
407B THR* 3.2 25.9 + - - +
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Residues in contact with TRP 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 5.4 2.2 - - - -
97B VAL* 4.3 15.3 - - + -
98B ALA* 6.0 2.0 - - - -
101B LYS* 4.6 33.3 - - + +
402B GLY 2.6 5.9 + - - -
403B ASP* 1.3 84.6 + - - +
405B ASN* 1.3 66.2 + - - +
407B THR* 3.0 24.8 - - + +
408B ILE* 2.9 32.5 + - + +
135C ILE* 3.6 45.8 + - + +
136C ASN* 3.6 8.1 - - - +
139C ALA* 3.5 32.0 - - + +
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Residues in contact with ASN 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B GLY* 3.0 12.8 + - - +
404B TRP* 1.3 79.8 - - - +
406B THR* 1.3 59.6 + - - +
408B ILE* 3.1 12.5 - - - +
409B ALA 2.9 24.9 + - - -
449B THR* 5.2 2.5 - - + -
453B VAL* 6.1 0.4 - - + +
454B GLN* 5.3 3.7 + - + +
457B MET* 3.7 28.7 - - - +
458B ASP* 4.3 7.3 + - - -
132C PHE* 3.3 38.6 + - + +
135C ILE* 3.5 12.7 - - - +
136C ASN* 2.8 34.4 + - - +
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Residues in contact with THR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ALA* 5.1 0.7 - - - -
400B ALA* 4.3 4.9 - - - -
402B GLY* 3.2 26.2 + - - -
403B ASP 3.2 7.7 + - - -
404B TRP 3.2 0.4 - - - -
405B ASN* 1.3 76.4 - - - +
407B THR* 1.4 58.4 + - - +
409B ALA* 3.2 3.5 + - - +
410B CYS* 2.8 34.8 + - - -
446B TYR* 3.4 48.2 - - + +
449B THR* 3.7 24.1 - - + +
450B ASP* 3.7 12.1 + - - +
454B GLN* 4.8 0.3 - - - +
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Residues in contact with THR 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 4.5 11.3 - - + +
393B VAL* 2.8 39.3 + - + +
396B ALA* 3.9 8.7 - - - +
397B SER* 3.4 16.5 + - - -
403B ASP 3.2 16.2 + - - +
404B TRP* 3.0 40.4 + - + +
406B THR* 1.4 79.0 - - - +
408B ILE* 1.3 59.0 + - + +
410B CYS* 3.2 4.7 + - - +
411B PHE* 2.9 28.2 + - - +
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B TRP* 2.9 20.3 + - + +
405B ASN* 3.1 18.2 - - - +
407B THR* 1.3 80.3 - - + +
409B ALA* 1.3 57.6 + - - +
411B PHE* 3.2 20.4 + - + +
412B VAL* 2.9 37.7 + - + +
128C ILE* 4.4 6.1 - - + -
131C VAL* 3.8 33.0 - - + -
132C PHE* 3.6 21.5 - - + -
135C ILE* 5.7 8.1 - - + -
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ASN 2.9 12.9 + - - +
406B THR 3.2 9.4 + - - +
408B ILE* 1.3 78.6 - - - +
410B CYS* 1.3 56.3 - - - +
412B VAL* 3.2 3.8 + - - +
413B ALA* 2.9 28.6 + - - +
445B PHE* 4.1 8.3 - - + +
449B THR* 3.9 22.0 - - + +
43C LEU* 3.7 35.6 - - + +
132C PHE* 3.9 4.3 - - + -
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Residues in contact with CYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B LEU* 3.6 21.5 - - + -
393B VAL* 4.8 1.6 - - + -
396B ALA* 4.2 5.6 - - + -
406B THR 2.8 29.2 + - - -
407B THR* 3.2 8.9 + - - +
409B ALA* 1.3 75.7 - - - +
411B PHE* 1.3 56.3 + - - +
413B ALA* 3.2 6.4 + - - +
414B ILE* 2.9 34.6 + - - +
442B GLY* 3.9 8.3 - - - +
445B PHE* 4.3 0.9 - - - -
446B TYR* 3.3 50.7 - - - -
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 3.7 33.4 - - + -
93B MET* 3.6 45.1 - - + -
94B VAL* 4.7 10.1 - - + -
97B VAL* 5.8 2.2 - - + -
393B VAL* 4.1 9.3 - - + +
407B THR 2.9 12.5 + - - +
408B ILE* 3.2 22.7 - - + +
410B CYS* 1.3 77.4 - - - +
412B VAL* 1.3 67.3 - - + +
414B ILE* 3.2 3.7 + - - +
415B LEU* 2.9 56.3 + - + +
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Residues in contact with VAL 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ILE* 2.9 22.5 + - + +
409B ALA 3.5 2.2 - - - +
411B PHE* 1.3 87.0 - - + +
413B ALA* 1.3 58.4 + - - +
415B LEU* 3.2 8.8 + - + +
416B ILE* 2.9 28.0 + - + +
36C VAL* 4.5 6.7 - - + +
39C ALA* 4.4 9.6 - - + -
40C PHE* 4.0 24.5 - - + +
43C LEU* 3.2 33.2 - - + -
128C ILE* 4.5 15.7 - - + -
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Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ALA 2.9 10.5 + - - +
410B CYS 3.3 10.1 - - - +
412B VAL* 1.3 77.0 - - - +
414B ILE* 1.3 57.4 + - - +
416B ILE* 3.2 12.3 + - - +
417B GLY* 2.8 26.3 + - - -
441B PHE* 3.8 6.2 - - + +
442B GLY* 3.6 19.3 - - - +
445B PHE* 3.2 38.8 - - + -
40C PHE* 4.9 1.1 - - - -
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 5.0 3.8 - - + -
93B MET* 3.6 22.7 - - + -
389B TYR* 3.1 66.0 - - + +
392B LEU* 3.3 36.8 - - + -
393B VAL* 4.5 0.4 - - + -
410B CYS 2.9 13.2 + - - +
411B PHE* 3.2 7.4 + - - +
413B ALA* 1.3 77.3 - - - +
415B LEU* 1.3 59.5 - - + +
417B GLY* 3.2 2.1 + - - -
418B LEU* 2.9 29.9 + - + +
438B SER* 3.9 16.2 - - - +
442B GLY* 4.4 2.0 - - - -
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Residues in contact with LEU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 3.5 31.7 - - + +
89B VAL* 5.3 5.6 - - + -
90B THR* 4.5 19.5 - - + +
93B MET* 4.3 13.5 - - + -
411B PHE* 2.9 51.5 + - + +
412B VAL* 3.2 10.7 + - - +
414B ILE* 1.3 79.6 - - + +
416B ILE* 1.3 57.9 + - - +
418B LEU* 3.2 8.0 + - + +
419B CYS* 2.9 25.7 + - - +
36C VAL* 4.1 31.4 - - + -
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Residues in contact with ILE 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B VAL 2.9 11.2 + - - +
413B ALA 3.2 10.1 + - - +
415B LEU* 1.3 75.5 - - - +
417B GLY* 1.3 63.0 + - - +
419B CYS* 3.2 17.8 + - + +
420B LEU* 2.9 35.2 + - + +
441B PHE* 4.4 11.4 - - + -
36C VAL* 3.3 36.3 - - + +
37C ALA* 3.8 8.5 - - + -
40C PHE* 3.4 63.5 - - + -
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Residues in contact with GLY 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ALA 2.8 13.4 + - - -
414B ILE 3.2 3.6 + - - -
416B ILE* 1.3 78.2 - - - +
418B LEU* 1.3 53.0 + - - +
420B LEU* 3.2 10.3 + - - +
421B THR* 2.6 37.6 + - - -
437B ILE* 4.3 4.8 - - - +
438B SER* 3.6 24.0 - - - -
441B PHE* 5.1 5.2 - - - -
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 4.9 2.5 - - + +
85B LEU* 3.4 50.3 - - + +
86B PHE* 4.1 20.4 - - + -
89B VAL* 4.0 19.1 - - + -
381B LEU* 5.1 2.5 - - + -
389B TYR* 3.7 30.3 - - + +
414B ILE* 2.9 13.6 + - + +
415B LEU* 3.4 11.9 - - + +
417B GLY* 1.3 75.7 - - - +
419B CYS* 1.3 57.3 + - - +
421B THR* 3.2 11.4 - - - -
422B LEU* 2.9 29.5 + - + +
435B LEU* 6.0 1.3 - - + -
438B SER* 3.7 4.5 - - - -
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Residues in contact with CYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 4.7 11.2 - - + +
86B PHE* 4.3 14.1 - - + -
415B LEU 2.9 12.6 + - - +
416B ILE* 3.3 24.7 - - + +
418B LEU* 1.3 76.9 - - - +
420B LEU* 1.3 72.2 + - - +
422B LEU* 3.2 8.8 + - - +
423B LEU* 2.9 38.6 + - - +
33C ILE* 5.3 14.4 - - + -
36C VAL* 5.9 0.2 - - + -
37C ALA* 6.3 2.5 - - - -
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Residues in contact with LEU 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ILE* 2.9 19.8 + - + +
417B GLY* 3.2 12.5 + - - +
419B CYS* 1.3 86.0 - - - +
421B THR* 1.3 53.3 + - - +
423B LEU* 3.2 9.0 + - + +
424B LEU* 2.8 36.4 + - - +
437B ILE* 4.6 23.1 - - + -
441B PHE* 5.1 13.9 - - + -
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Residues in contact with THR 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B TYR* 5.7 0.2 - - - -
417B GLY 2.6 20.1 + - - -
418B LEU* 3.2 12.2 - - + -
420B LEU* 1.3 72.3 - - - +
422B LEU* 1.3 58.5 + - - +
424B LEU* 3.2 5.1 + - - +
425B LEU* 2.7 40.6 + - + +
432B LEU* 5.4 3.6 - - + -
433B PRO* 4.8 7.0 - - + -
434B ALA* 2.6 59.5 + - + +
435B LEU* 4.2 11.4 - - + +
437B ILE* 4.1 0.5 - - - +
438B SER* 3.8 1.0 + - - -
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY 5.3 2.0 - - - +
81B HIS* 5.1 7.2 - - + +
82B VAL* 3.6 45.3 - - + +
85B LEU* 3.2 36.8 - - + -
379B VAL* 4.3 14.8 - - + -
418B LEU* 2.9 13.6 + - + +
419B CYS 3.2 9.2 + - - +
421B THR* 1.3 75.3 - - + +
423B LEU* 1.3 61.8 - - + +
425B LEU* 3.2 14.4 + - + +
426B ALA* 2.9 33.6 + - + +
429B LYS* 5.7 5.4 - - - +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY 5.9 1.1 - - - +
82B VAL* 5.1 9.9 - - + -
419B CYS* 2.9 24.4 + - - +
420B LEU* 3.8 9.9 - - + +
422B LEU* 1.3 84.6 - - + +
424B LEU* 1.3 58.4 + - - +
426B ALA* 3.2 8.9 + - + +
427B ILE* 2.9 44.5 + - + +
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LEU 2.8 16.5 + - - +
421B THR* 3.4 8.1 - - - +
423B LEU* 1.3 77.5 - - - +
425B LEU* 1.3 66.1 + - - +
427B ILE* 3.2 10.8 + - + +
428B PHE* 3.1 52.0 + - + +
430B LYS* 6.1 0.9 - - + -
433B PRO* 3.7 31.4 - - + -
434B ALA* 5.1 8.1 - - + -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B VAL* 4.8 9.4 - - + -
380B LYS 5.0 0.2 - - - +
421B THR* 2.7 24.8 + - + +
422B LEU* 3.4 21.3 - - + +
424B LEU* 1.3 79.1 - - + +
426B ALA* 1.3 59.3 + - - +
428B PHE* 5.4 0.4 - - - -
429B LYS* 2.6 59.6 + - + +
430B LYS 4.2 17.0 - - - +
431B ALA* 4.4 0.9 - - - +
432B LEU* 3.7 47.1 - - + +
433B PRO* 3.9 11.2 - - + -
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B LEU* 2.9 20.0 + - + +
423B LEU* 3.3 17.0 - - + +
425B LEU* 1.3 79.6 - - - +
427B ILE* 1.3 67.6 + - + +
428B PHE 3.4 0.9 + - - -
429B LYS* 4.3 22.4 - - - +
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 2.9 31.5 + - + +
424B LEU* 3.2 11.9 + - + +
426B ALA* 1.3 82.8 - - + +
428B PHE* 1.3 94.0 + - + +
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Residues in contact with PHE 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LEU* 3.1 46.6 + - + +
425B LEU 3.4 0.4 - - - -
426B ALA 4.4 0.4 - - - +
427B ILE* 1.3 97.5 - - + +
429B LYS* 1.3 68.1 + - - +
430B LYS* 4.3 23.1 - - + +
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Residues in contact with LYS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B VAL* 5.1 9.7 - - - +
422B LEU* 5.7 4.8 - - - +
425B LEU* 2.6 53.7 + - + +
426B ALA* 4.3 19.2 - - - +
428B PHE* 1.3 76.5 - - - +
430B LYS* 1.3 67.0 + - - +
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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