Contacts of the helix formed by residues 458 - 495 (chain A) in PDB entry 6ICV
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 SER 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLU* 2.8 27.4 + - - -
457A LEU* 1.3 77.3 - - - +
459A VAL* 1.3 64.8 + - - +
460A ARG* 3.5 3.3 + - - -
461A ALA* 2.9 19.6 + - - +
462A LYS* 2.9 24.2 + - - +
99B VAL* 4.1 14.3 - - - +
100B ASN* 3.3 27.1 - - - -
109B ARG* 4.6 1.0 - - - +
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Residues in contact with VAL 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASP* 3.9 22.2 - - - +
458A SER* 1.3 72.3 - - - +
460A ARG* 1.3 60.3 + - + +
462A LYS* 3.3 9.1 + - - +
463A MET* 2.9 40.9 + - + +
100B ASN 4.3 2.4 + - - +
102B LYS* 3.8 47.8 - - + +
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Residues in contact with ARG 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 4.9 8.1 - - - +
183A TYR 2.9 25.5 + - - +
184A ASP* 2.9 28.6 + - + +
188A TYR* 3.3 33.4 + - - +
189A PHE* 3.5 44.5 - - + -
190A GLU* 6.1 1.4 - - - +
193A GLU* 3.7 26.2 + - - +
458A SER* 3.3 2.5 + - - +
459A VAL* 1.3 78.0 - - + +
461A ALA* 1.3 62.3 + - - +
463A MET* 3.2 9.0 + - - +
464A ALA* 3.1 17.5 + - - +
74B LYS* 6.2 0.6 - - - +
76B GLU* 4.3 15.6 + - - -
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Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLU* 4.0 13.8 + - + -
196A TYR* 3.7 28.2 - - + +
457A LEU* 4.2 10.5 - - + -
458A SER* 2.9 28.3 + - - +
460A ARG* 1.3 76.7 - - - +
462A LYS* 1.3 58.4 + - - +
464A ALA* 3.2 4.7 + - - +
465A ILE* 3.0 34.1 + - - +
109B ARG* 5.7 1.8 - - - +
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Residues in contact with LYS 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452A LEU* 4.0 22.2 - - + -
457A LEU* 4.1 23.5 - - + +
458A SER 2.9 19.9 + - - +
459A VAL* 3.6 7.2 - - - +
461A ALA* 1.3 72.7 - - - +
463A MET* 1.3 60.7 + - - +
465A ILE 4.5 0.2 - - - +
466A LYS* 2.9 54.1 + - - +
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Residues in contact with MET 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASP* 3.6 31.9 - - - +
189A PHE* 3.9 6.5 - - + -
322A VAL* 3.7 29.9 - - + +
326A GLY 3.7 27.4 - - - +
327A PHE* 3.7 7.6 - - - +
328A PHE* 4.0 27.8 - - + +
459A VAL* 2.9 29.8 + - + +
460A ARG* 3.2 13.9 + - - +
462A LYS* 1.3 76.7 - - + +
464A ALA* 1.3 57.7 + - - +
466A LYS* 3.9 1.3 - - - +
467A LEU* 2.9 31.1 + - - +
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Residues in contact with ALA 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A PHE* 4.3 9.8 - - + -
193A GLU 3.5 25.1 - - - +
196A TYR* 4.0 8.1 - - + -
197A LEU* 3.3 31.9 - - + +
322A VAL* 6.0 0.7 - - - -
460A ARG 3.1 12.0 + - - +
461A ALA 3.2 8.5 + - - +
463A MET* 1.3 77.4 - - - +
465A ILE* 1.3 58.3 + - - +
467A LEU* 3.3 3.1 + - - -
468A ARG* 3.0 24.4 + - - +
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Residues in contact with ILE 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A TYR* 3.8 40.2 - - + -
448A ASP* 4.2 13.0 - - + +
451A VAL* 3.9 15.9 - - + -
452A LEU* 3.7 29.4 - - + -
457A LEU* 3.7 25.6 - - + -
461A ALA 3.0 21.6 + - - +
462A LYS 3.4 0.2 + - - -
464A ALA* 1.3 71.6 - - - +
466A LYS* 1.3 61.9 + - - +
468A ARG* 3.3 26.2 - - - +
469A LEU* 2.9 27.5 + - - +
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Residues in contact with LYS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PHE* 3.6 39.1 + - + +
330A ASP* 2.9 39.3 + - - +
452A LEU* 4.3 19.7 - - + -
462A LYS* 2.9 42.3 + - - +
463A MET 4.0 0.2 - - - +
465A ILE* 1.3 77.3 - - - +
467A LEU* 1.3 57.8 + - - +
469A LEU* 3.7 7.6 - - + +
470A GLY* 2.8 25.8 + - - -
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Residues in contact with LEU 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 4.1 15.9 - - + -
202A ALA* 3.6 28.0 - - + -
206A VAL* 5.9 0.4 - - + -
318A ASN* 3.9 11.9 - - + +
319A ALA* 3.7 34.1 - - + +
322A VAL* 4.0 29.2 - - + -
323A ILE* 5.3 1.8 - - + -
328A PHE* 3.7 9.6 - - + -
463A MET 2.9 18.5 + - - +
464A ALA* 3.5 5.6 - - - +
466A LYS* 1.3 77.4 - - - +
468A ARG* 1.3 60.9 + - - +
470A GLY* 3.3 1.6 + - - -
471A GLU* 3.1 29.1 + - + +
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Residues in contact with ARG 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A TYR* 2.9 50.5 + - - +
197A LEU* 4.3 3.5 - - + +
198A GLN 5.8 0.7 - - - -
200A THR* 3.6 30.1 - - + -
441A TYR* 4.5 1.2 - - - -
442A LYS* 5.6 4.6 - - - +
443A THR* 3.6 27.2 + - - +
448A ASP* 2.7 31.5 + - - +
451A VAL* 4.2 21.0 - - - +
464A ALA 3.0 11.4 + - - +
465A ILE* 3.3 28.3 - - - +
467A LEU* 1.3 73.2 - - - +
469A LEU* 1.3 67.2 + - - +
471A GLU* 3.6 5.6 + - - +
472A LYS* 2.9 30.6 + - - +
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A ILE* 3.6 46.4 - - + +
448A ASP* 3.4 18.8 - - + +
449A LYS* 4.2 15.0 - - + -
452A LEU* 3.9 24.5 - - + -
465A ILE 2.9 17.7 + - - +
466A LYS* 3.7 7.2 - - + +
468A ARG* 1.3 79.7 - - - +
470A GLY* 1.3 57.2 + - - +
472A LYS* 3.2 4.5 + - - +
473A GLU* 2.9 46.4 + - - +
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Residues in contact with GLY 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PHE* 5.2 5.8 - - - -
335A ASP* 4.9 9.6 - - - -
466A LYS 2.8 21.1 + - - -
467A LEU* 3.3 2.9 + - - -
469A LEU* 1.3 70.7 - - - +
471A GLU* 1.3 64.0 + - - +
473A GLU* 3.3 11.9 + - - +
474A ILE* 3.0 33.6 + - - +
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Residues in contact with GLU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A THR* 3.3 12.9 - - - -
201A GLN* 2.8 28.6 + - - +
202A ALA* 2.9 36.9 + - - +
319A ALA* 5.4 1.6 - - + +
337A VAL* 3.8 21.7 - - + +
441A TYR* 2.7 31.3 + - + +
467A LEU* 3.1 24.8 + - + +
468A ARG* 3.9 7.2 - - - +
469A LEU 3.3 0.2 - - - -
470A GLY* 1.3 75.3 - - - +
472A LYS* 1.3 64.2 + - - +
474A ILE* 3.3 3.3 + - - +
475A LEU* 3.1 27.1 + - - +
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Residues in contact with LYS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A LEU* 3.7 23.6 - - + +
441A TYR* 3.6 36.5 - - + +
443A THR* 3.2 33.4 + - - +
444A THR* 3.5 15.3 - - - -
445A ILE* 3.5 21.3 - - + +
448A ASP* 2.7 29.0 + - - -
468A ARG* 2.9 26.4 + - - +
469A LEU* 3.2 4.3 + - - +
471A GLU* 1.3 76.7 - - - +
473A GLU* 1.3 58.6 + - - +
475A LEU* 3.1 5.0 + - - +
476A GLU* 2.8 30.7 + - - +
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Residues in contact with GLU 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A PHE* 4.8 11.3 - - + -
445A ILE* 4.0 15.0 - - + +
449A LYS* 3.6 25.8 + - - -
469A LEU* 2.9 44.2 + - + +
470A GLY* 3.9 9.9 - - - +
472A LYS* 1.3 77.0 - - - +
474A ILE* 1.3 57.7 + - + +
476A GLU* 3.9 7.4 - - - +
477A LYS* 3.0 29.8 + - - +
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Residues in contact with ILE 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A ASP* 3.6 33.0 - - - +
336A ARG* 3.6 22.9 - - - +
337A VAL* 3.8 19.7 - - + -
370A LEU* 3.6 29.4 - - + +
371A HIS 4.2 10.2 - - - +
372A PHE* 4.0 22.9 - - + -
470A GLY 3.0 21.7 + - - +
471A GLU* 3.6 4.5 - - - +
473A GLU* 1.3 77.3 - - + +
475A LEU* 1.3 57.4 + - - +
477A LYS* 3.3 6.4 + - - +
478A ALA* 2.9 26.9 + - + +
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Residues in contact with LEU 475 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN* 5.5 3.6 - - - +
337A VAL* 4.0 14.6 - - + -
370A LEU* 3.9 25.6 - - + -
434A ALA* 3.9 8.7 - - - +
437A LEU* 4.0 33.4 - - + -
438A LEU* 4.0 18.8 - - + +
441A TYR* 3.6 37.2 - - + +
471A GLU 3.1 19.5 + - - +
472A LYS 3.1 5.8 + - - +
474A ILE* 1.3 75.7 - - - +
476A GLU* 1.3 57.5 + - - +
478A ALA* 3.1 6.0 + - - +
479A VAL* 2.9 32.9 + - - +
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Residues in contact with GLU 476 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A LEU* 4.2 17.9 - - + +
445A ILE* 3.6 28.0 - - + +
472A LYS 2.8 19.9 + - - +
473A GLU* 3.9 8.8 - - - +
475A LEU* 1.3 70.7 - - - +
477A LYS* 1.3 64.9 + - - +
479A VAL* 3.3 7.6 + - + +
480A LYS* 3.1 50.0 + - - +
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Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A PHE* 3.1 58.1 + - + +
373A THR* 4.7 1.0 - - - +
374A GLU* 4.0 23.2 + - - +
376A PRO* 5.7 0.9 - - - -
473A GLU 3.0 18.1 + - - +
474A ILE* 3.6 5.6 - - - +
476A GLU* 1.3 76.5 + - - +
478A ALA* 1.3 57.8 + - - +
480A LYS* 3.4 10.0 + - + +
481A SER* 3.0 38.9 + - - +
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Residues in contact with ALA 478 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU* 4.3 27.8 - - + -
371A HIS 5.7 0.9 - - - +
376A PRO* 4.3 26.1 - - + +
430A LEU* 5.2 4.9 - - + +
434A ALA* 4.3 7.9 - - + -
474A ILE* 2.9 13.6 + - + +
475A LEU 3.1 8.9 + - - +
477A LYS* 1.3 73.6 - - - +
479A VAL* 1.3 60.7 + - - +
481A SER* 3.3 1.1 + - - -
482A ALA* 2.9 33.9 + - - +
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Residues in contact with VAL 479 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLU* 3.8 24.3 - - + +
434A ALA* 3.5 9.6 - - + +
435A SER* 3.4 45.8 - - - +
438A LEU* 4.8 6.5 - - + -
475A LEU 2.9 17.5 + - - +
476A GLU* 3.3 12.8 + - + +
478A ALA* 1.3 76.8 - - - +
480A LYS* 1.3 67.7 + - + +
483A ALA* 3.0 22.8 + - + +
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Residues in contact with LYS 480 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476A GLU* 3.1 50.2 + - + +
477A LYS* 3.9 8.5 - - + +
479A VAL* 1.3 80.7 - - + +
481A SER* 1.3 59.0 + - - +
483A ALA* 3.3 6.6 + - - +
484A VAL* 3.0 35.1 + - + +
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Residues in contact with SER 481 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A GLU* 2.8 28.8 + - - -
376A PRO* 3.9 20.6 - - - +
477A LYS* 3.0 27.2 + - - +
478A ALA 3.9 3.4 - - - -
480A LYS* 1.3 77.2 - - - +
482A ALA* 1.3 56.8 + - - +
484A VAL* 3.4 6.9 + - - +
485A ASN* 3.0 35.0 + - - +
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Residues in contact with ALA 482 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A PRO* 5.3 0.2 - - - +
427A TRP* 3.6 47.1 - - + +
430A LEU* 4.2 8.1 - - + -
431A GLU* 3.7 19.1 - - + +
478A ALA 2.9 18.1 + - - +
481A SER* 1.3 74.0 - - - +
483A ALA* 1.3 60.2 + - - +
485A ASN 3.3 0.2 + - - -
486A ARG* 2.8 30.8 + - - +
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Residues in contact with ALA 483 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A GLU* 3.4 32.4 - - - +
479A VAL* 3.0 14.9 + - + +
480A LYS* 3.6 8.1 - - - +
482A ALA* 1.3 77.4 - - - +
484A VAL* 1.3 62.2 + - + +
486A ARG* 3.3 15.7 + - - +
487A GLU* 3.1 23.2 + - - +
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Residues in contact with VAL 484 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A LYS* 3.0 21.6 + - + +
481A SER* 3.6 7.2 - - - +
482A ALA 3.3 0.2 - - - -
483A ALA* 1.3 76.7 - - + +
485A ASN* 1.3 64.7 + - - +
487A GLU* 3.3 7.2 + - - +
488A TYR* 3.0 29.2 + - + +
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Residues in contact with ASN 485 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A GLU* 4.7 15.0 + - - +
376A PRO* 5.1 1.0 - - - +
427A TRP* 3.2 59.1 - - + +
481A SER* 3.0 24.2 + - - +
482A ALA 3.7 0.9 - - - +
484A VAL* 1.3 77.8 - - - +
486A ARG* 1.3 66.7 + - - +
488A TYR* 3.3 7.3 + - - +
489A TYR* 2.9 39.1 + - + -
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Residues in contact with ARG 486 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A VAL* 4.2 16.0 - - + +
427A TRP* 3.9 13.8 - - + +
428A THR* 3.2 31.0 - - - +
431A GLU* 2.9 38.2 + - - -
482A ALA 2.8 21.1 + - - +
483A ALA* 3.6 19.8 + - - +
485A ASN* 1.3 74.5 - - - +
487A GLU* 1.3 71.2 + - - +
489A TYR* 3.7 3.5 - - - +
490A ARG* 2.8 34.0 + - + +
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Residues in contact with GLU 487 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A ALA 3.1 11.6 + - - +
484A VAL* 3.7 8.3 - - - +
486A ARG* 1.3 91.7 - - - +
488A TYR* 1.3 66.4 + - - +
490A ARG* 3.3 12.1 + - - +
491A GLN* 2.9 24.3 + - - +
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Residues in contact with TYR 488 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A TRP* 5.2 2.7 - + - -
484A VAL* 3.0 17.3 + - + +
485A ASN* 3.6 9.9 - - - +
487A GLU* 1.3 76.9 - - - +
489A TYR* 1.3 96.1 + + - +
491A GLN* 3.3 14.3 + - - +
492A GLN* 3.2 55.5 + - + +
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Residues in contact with TYR 489 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A ARG* 5.4 0.2 + - - -
414A SER* 3.9 21.7 + - - -
417A PRO* 4.8 3.6 - - + -
420A TRP* 3.7 33.7 - + - +
423A GLU* 3.4 41.1 + - + -
424A VAL* 3.6 20.4 - - + +
427A TRP* 3.4 25.0 - + - -
485A ASN* 2.9 34.2 + - + +
486A ARG 4.1 0.2 - - - +
488A TYR* 1.3 100.0 - + - +
490A ARG* 1.3 61.5 + - - +
492A GLN* 3.4 5.5 + - + +
493A MET* 3.0 26.7 + - - +
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Residues in contact with ARG 490 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A VAL* 3.6 15.8 - - + +
486A ARG* 2.8 24.3 + - + +
487A GLU* 3.8 11.2 - - - +
489A TYR* 1.3 73.6 - - - +
491A GLN* 1.3 61.2 + - - +
493A MET* 3.3 15.1 + - + +
494A GLU* 2.9 50.1 + - + +
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Residues in contact with GLN 491 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A GLU 2.9 13.2 + - - +
488A TYR* 3.4 18.3 - - - +
489A TYR 3.2 0.2 - - - -
490A ARG* 1.3 74.1 - - - +
492A GLN* 1.3 78.2 + - - +
494A GLU* 3.3 6.5 + - - +
495A GLU* 2.9 57.5 + - + +
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Residues in contact with GLN 492 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A TRP* 3.6 39.7 - - + -
488A TYR* 3.2 57.9 + - + +
489A TYR* 3.7 4.5 - - - +
490A ARG 3.4 0.2 - - - -
491A GLN* 1.3 88.3 + - - +
493A MET* 1.3 61.1 + - - +
495A GLU* 3.7 6.6 + - - +
496A LYS* 3.1 2.8 + - - -
497A ALA* 2.9 51.5 + - - +
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Residues in contact with MET 493 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A TRP* 3.9 16.1 - - + -
421A ASP* 3.8 39.7 - - - +
424A VAL* 3.9 24.2 - - + -
489A TYR 3.0 12.4 + - - +
490A ARG* 3.5 19.5 - - + +
491A GLN 3.1 0.2 - - - -
492A GLN* 1.3 75.8 - - - +
494A GLU* 1.3 67.2 + - + +
496A LYS* 3.1 19.4 + - - +
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Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ARG* 2.9 44.4 + - + +
491A GLN* 3.3 5.8 + - - +
493A MET* 1.3 79.7 - - + +
495A GLU* 1.3 61.1 + - + +
496A LYS* 3.3 14.4 + - - +
----------------------------------------------------------
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Residues in contact with GLU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A GLN* 2.9 53.1 + - + +
492A GLN* 4.4 8.3 + - - +
494A GLU* 1.3 77.9 - - + +
496A LYS* 1.3 70.3 + - - +
497A ALA* 3.2 5.8 + - + +
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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