Contacts of the helix formed by residues 482 - 505 (chain D) in PDB entry 1JLH
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 THR 482 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556C VAL* 4.4 19.6 - - + +
47D HIS* 4.7 5.2 + - - +
170D LEU* 4.1 3.1 - - - -
173D TYR* 3.5 15.3 - - + +
480D LYS* 3.0 30.8 + - + +
481D LEU* 1.3 76.9 - - - +
483D PRO* 1.3 76.7 - - - +
484D PHE* 3.6 7.6 + - - +
485D MET* 3.1 21.4 + - - +
486D LEU* 2.9 22.7 + - - +
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Residues in contact with PRO 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D LEU* 3.9 30.5 - - + -
173D TYR* 3.6 27.6 - - + -
291D ASN* 3.6 45.8 - - + +
294D GLN* 3.8 8.3 - - + -
295D LEU* 3.4 17.0 - - - +
482D THR* 1.3 90.1 - - - +
484D PHE* 1.3 62.2 + - - +
486D LEU 3.4 0.2 + - - -
487D GLY 3.1 17.3 + - - -
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Residues in contact with PHE 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 3.5 30.7 - - + -
47D HIS* 3.5 43.7 - + + -
294D GLN* 3.3 39.7 + - - +
297D SER* 3.5 24.7 - - - -
298D GLY* 3.2 37.1 - - - -
301D TRP* 3.8 23.1 - + + -
482D THR* 3.2 7.1 + - - +
483D PRO* 1.3 80.7 - - - +
485D MET* 1.3 68.3 + - + +
487D GLY 3.2 9.5 + - - -
488D ALA* 3.2 5.6 + - + +
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Residues in contact with MET 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 4.4 5.6 - - + +
47D HIS 4.3 5.8 - - - +
48D GLY* 3.8 31.6 - - - +
49D HIS 3.9 5.6 - - - +
50D ILE* 3.5 42.4 - - + -
478D PHE* 3.8 24.7 - - + -
479D THR 4.8 1.3 - - - +
480D LYS 3.2 28.7 - - - +
481D LEU* 4.5 1.3 - - - -
482D THR* 3.1 13.5 + - - +
484D PHE* 1.3 83.2 - - + +
486D LEU* 1.3 63.6 + - - +
488D ALA* 3.1 6.4 + - - +
489D LEU* 3.0 28.7 + - + +
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Residues in contact with LEU 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D MET* 4.5 11.7 - - - -
166D VAL* 4.0 24.0 - - + -
169D ALA* 4.0 11.4 - - + -
170D LEU* 3.8 27.8 - - + -
295D LEU* 4.1 8.1 - - + -
344D LEU* 4.6 9.9 - - + -
347D PHE* 4.5 10.5 - - + -
481D LEU* 4.2 23.7 - - + +
482D THR 2.9 16.3 + - - +
483D PRO 3.8 4.3 - - - +
485D MET* 1.3 75.8 - - - +
487D GLY* 1.3 64.1 + - - +
489D LEU* 3.3 5.5 + - + +
490D VAL* 3.0 46.2 + - + +
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Residues in contact with GLY 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D TRP* 3.6 7.7 - - - -
295D LEU* 3.4 34.0 - - - +
299D ALA* 3.3 11.0 - - - +
483D PRO 3.1 10.9 + - - -
484D PHE 3.2 2.2 + - - -
486D LEU* 1.3 78.0 - - - +
488D ALA* 1.3 60.3 + - - +
490D VAL 3.6 0.2 + - - -
491D ALA* 3.1 26.0 + - - +
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Residues in contact with ALA 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 5.2 0.4 - - + -
50D ILE* 4.2 21.3 - - + -
298D GLY* 3.3 20.3 - - - +
301D TRP* 5.1 3.8 - - + -
302D MET* 3.3 22.5 - - + +
484D PHE* 3.2 15.4 + - + +
485D MET* 3.1 13.8 + - - +
487D GLY* 1.3 77.4 - - - +
489D LEU* 1.3 57.7 + - - +
491D ALA 3.5 0.3 + - - -
492D MET* 2.9 25.3 + - - +
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Residues in contact with LEU 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ILE* 4.6 16.6 - - + -
344D LEU* 5.7 2.7 - - + -
347D PHE* 4.7 15.0 - - + -
406D LEU* 5.1 6.3 - - + -
476D ILE* 4.2 9.4 - - + -
478D PHE* 3.6 46.9 - - + -
481D LEU* 4.0 17.0 - - + -
485D MET* 3.0 17.5 + - + +
486D LEU* 3.7 8.1 - - + +
488D ALA* 1.3 73.7 - - - +
490D VAL* 1.3 66.7 + - - +
492D MET* 3.2 32.2 + - + +
493D TYR* 3.2 21.4 + - + -
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Residues in contact with VAL 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D MET* 4.1 15.5 - - + -
166D VAL* 5.7 1.1 - - + -
275D LEU* 4.6 5.4 - - + -
276D TRP* 3.6 28.3 - - + -
295D LEU* 5.7 0.7 - - + -
347D PHE* 4.3 6.7 - - + -
350D TYR* 4.0 18.4 - - + +
351D PHE* 3.5 22.9 - - + -
486D LEU* 3.0 38.4 + - + +
487D GLY* 4.8 0.2 - - - -
489D LEU* 1.3 74.2 - - - +
491D ALA* 1.3 58.2 + - - +
493D TYR 3.3 2.6 + - - -
494D GLU* 3.0 35.9 + - - +
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Residues in contact with ALA 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ARG* 3.9 10.1 - - - +
276D TRP* 4.4 0.6 - - - -
299D ALA* 3.7 26.7 - - + +
302D MET* 3.8 11.9 - - + -
303D ASP* 4.3 2.0 - - - +
487D GLY 3.1 19.6 + - - +
488D ALA 3.7 3.6 - - - +
490D VAL* 1.3 74.3 - - - +
492D MET* 1.3 66.9 + - - +
494D GLU* 3.2 14.5 + - - +
495D HIS* 3.0 27.4 + - + -
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Residues in contact with MET 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 5.8 0.2 - - - -
50D ILE* 5.2 3.1 - - - -
52D VAL* 4.4 10.5 - - - -
302D MET* 3.5 23.7 - - + +
315D ALA* 4.2 14.8 - - - -
316D PRO* 3.6 22.7 - - + +
319D LEU* 3.8 31.0 - - + -
476D ILE* 4.3 17.0 - - + -
488D ALA 2.9 15.3 + - - +
489D LEU* 3.2 26.9 + - + +
491D ALA* 1.3 78.2 - - - +
493D TYR* 1.3 80.6 + - + +
495D HIS 3.3 0.5 + - - -
496D LYS* 3.0 23.2 + - - +
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Residues in contact with TYR 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D LEU* 4.7 9.2 - - + +
337D MET* 3.5 34.9 - - + +
347D PHE* 4.1 12.6 - + - -
351D PHE* 3.3 25.1 - + + -
404D ASP* 2.7 40.1 + - - +
406D LEU* 3.8 22.5 - - + +
476D ILE* 4.5 5.5 - - - +
489D LEU* 3.2 19.6 + - + -
490D VAL 3.3 0.2 + - - -
492D MET* 1.3 96.8 - - + +
494D GLU* 1.3 66.6 + - - +
496D LYS* 3.0 28.9 + - + +
497D ILE* 2.9 32.4 + - + +
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Residues in contact with GLU 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D HIS* 3.7 7.7 + - + -
103D ARG* 2.8 36.8 + - - -
272D ARG 5.7 0.4 - - - +
273D TYR* 3.5 43.1 + - + -
276D TRP* 2.9 30.1 + - - -
350D TYR* 4.4 7.7 + - + +
351D PHE* 4.2 6.0 - - + -
490D VAL* 3.0 21.1 + - + +
491D ALA* 3.2 9.3 + - - +
493D TYR* 1.3 77.6 - - - +
495D HIS* 1.3 60.9 + - + +
497D ILE* 3.4 12.9 + - + +
498D PHE* 3.0 24.3 + - - +
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Residues in contact with HIS 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D MET* 4.7 10.5 - - - -
84D PHE* 4.3 2.3 - + - -
99D HIS* 4.7 5.0 - + - -
100D VAL* 3.8 17.7 - - + +
103D ARG* 3.9 7.8 + - - -
302D MET* 4.3 5.4 + - - +
303D ASP* 2.8 39.3 + - - -
306D PHE* 3.3 45.2 - + + +
316D PRO* 3.7 20.0 - - + -
491D ALA 3.0 16.5 + - - +
494D GLU* 1.3 79.1 - - + +
496D LYS* 1.3 61.5 + - - +
498D PHE* 3.4 7.1 - - + +
499D VAL* 2.8 34.5 + - - +
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Residues in contact with LYS 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D PRO* 3.5 19.7 - - + +
319D LEU* 3.8 24.8 + - + +
320D ALA* 3.5 19.6 - - - +
323D GLY* 5.3 2.7 - - - -
335D HIS* 3.4 39.8 + - - -
337D MET* 6.0 0.4 - - - -
355D ASP* 4.6 9.5 + - - +
404D ASP* 4.5 0.8 + - - -
492D MET 3.0 13.8 + - - +
493D TYR* 3.4 32.7 - - + +
495D HIS* 1.3 74.9 - - - +
497D ILE* 1.3 66.9 + - + +
499D VAL* 3.0 4.7 + - - +
500D GLN* 2.9 49.9 + - - +
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Residues in contact with ILE 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D TYR* 3.8 10.8 - - + +
351D PHE* 4.0 20.6 - - + -
354D GLY* 3.6 9.0 - - - +
355D ASP* 3.6 40.4 - - + +
358D SER* 3.6 25.8 - - - -
359D ASN* 3.1 27.9 + - - +
493D TYR* 2.9 20.3 + - + +
494D GLU* 3.4 10.1 - - - +
496D LYS* 1.3 82.8 - - + +
498D PHE* 1.3 61.6 + - - +
500D GLN* 4.5 3.4 - - - +
501D GLY 3.1 17.5 + - - -
508D SER* 3.8 4.1 + - - +
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Residues in contact with PHE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 4.9 2.7 - - + -
79D ALA* 3.7 24.0 - - + -
80D ARG* 3.7 22.7 - - + -
83D MET* 3.4 36.8 - - + -
89D ILE* 3.9 12.8 - - + -
99D HIS* 6.3 0.9 - - + -
273D TYR* 5.7 0.2 - - - -
306D PHE* 3.7 28.5 - + - -
494D GLU 3.0 15.1 + - - +
495D HIS* 3.4 10.8 - - + +
496D LYS 3.1 0.2 - - - -
497D ILE* 1.3 77.9 - - - +
499D VAL* 1.3 64.5 + - + +
501D GLY* 3.3 2.6 + - - -
502D ILE* 3.1 54.9 + - + +
508D SER* 4.6 4.4 + - - -
509D PHE* 3.5 21.5 - + + -
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Residues in contact with VAL 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 4.1 20.4 - - + -
306D PHE* 3.8 28.3 - - + -
317D VAL* 4.0 23.8 - - + +
320D ALA* 3.5 19.5 - - + -
321D LEU* 4.6 2.9 - - + -
495D HIS 2.8 20.0 + - - +
496D LYS 3.0 6.7 + - - +
498D PHE* 1.3 77.5 - - + +
500D GLN* 1.3 61.6 + - - +
502D ILE* 3.2 8.3 + - - +
503D ILE* 3.1 37.5 + - + +
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Residues in contact with GLN 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320D ALA* 3.1 37.3 + - + +
323D GLY* 3.5 22.6 - - - -
324D ILE* 3.9 10.2 - - + +
327D ILE* 4.6 4.4 - - - +
355D ASP* 4.5 10.2 - - - +
359D ASN* 3.9 9.2 + - - +
376D PRO* 4.9 4.0 - - - +
496D LYS* 2.9 38.1 + - - +
497D ILE* 4.5 2.9 - - - -
499D VAL* 1.3 76.0 - - - +
501D GLY* 1.3 62.9 + - - +
503D ILE* 3.3 4.6 + - - +
504D TRP* 3.0 59.8 + - + -
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Residues in contact with GLY 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D ASN* 3.7 5.1 - - - +
497D ILE 3.1 10.5 + - - -
498D PHE 3.3 0.9 + - - -
499D VAL 3.2 0.2 - - - -
500D GLN* 1.3 77.4 - - - +
502D ILE* 1.3 62.6 + - - +
504D TRP* 3.2 1.5 + - - -
505D ASP 2.9 18.2 + - - -
506D ILE* 3.1 28.8 + - - +
508D SER* 3.4 23.8 - - - -
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Residues in contact with ILE 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ARG* 3.4 32.4 + - - +
76D VAL* 4.1 17.3 - - + -
79D ALA* 3.7 27.1 - - + -
82D ARG* 5.3 4.0 - - - +
89D ILE* 5.9 2.0 - - + -
498D PHE* 3.1 48.6 + - + +
499D VAL* 3.6 9.6 - - - +
501D GLY* 1.3 77.1 - - - +
503D ILE* 1.3 63.6 + - - +
505D ASP* 3.1 12.2 + - - +
506D ILE 5.2 4.9 - - - +
509D PHE* 6.0 0.9 - - + -
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Residues in contact with ILE 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 3.7 20.1 - - + +
70D LEU* 4.0 25.4 - - + -
71D ALA* 4.7 4.5 - - - -
74D ARG* 2.9 38.1 + - + +
76D VAL* 4.0 16.6 - - + -
321D LEU* 3.6 31.0 - - + -
324D ILE* 4.1 27.4 - - + -
499D VAL* 3.1 23.4 + - + +
500D GLN* 3.6 7.0 - - - +
502D ILE* 1.3 76.6 - - - +
504D TRP* 1.3 59.7 + - - +
505D ASP 3.1 0.2 - - - -
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Residues in contact with TRP 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D ALA* 5.7 0.2 - - - +
3D LEU* 3.6 22.4 + - + -
324D ILE* 3.4 21.2 - - + +
327D ILE* 3.9 20.2 - - + -
328D ASN* 2.7 22.0 + - - -
359D ASN* 3.5 27.6 - - + -
364D THR* 4.1 4.3 - - - +
372D HIS* 3.7 29.1 + + + -
373D GLN 3.4 5.7 + - - -
374D THR* 3.5 34.5 - - + -
375D GLY* 3.5 19.7 - - - -
376D PRO* 4.2 0.4 - - + -
500D GLN* 3.0 43.3 + - + +
501D GLY 3.8 3.1 - - - +
503D ILE* 1.3 73.7 - - - +
505D ASP* 1.3 70.8 + - - +
506D ILE* 3.4 24.9 + - + +
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Residues in contact with ASP 505 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ALA* 3.8 21.3 + - + +
3D LEU 5.1 0.7 - - - +
74D ARG* 3.0 24.1 + - - +
91D TYR* 3.6 1.8 + - - -
364D THR* 3.2 23.4 + - + -
365D LYS* 2.9 55.4 + - - +
366D SER* 4.3 5.0 + - - -
501D GLY 2.9 4.4 + - - -
502D ILE* 3.1 11.3 + - - +
503D ILE 3.1 0.2 - - - -
504D TRP* 1.3 81.7 - - - +
506D ILE* 1.3 60.1 + - - +
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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