Contacts of the helix formed by residues 426 - 453 (chain B) in PDB entry 5NC5
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 PRO 426 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B GLY 3.6 4.5 - - - +
425B LEU* 1.3 101.9 - - + +
427B PRO* 1.4 77.4 - - + -
428B LYS 2.8 2.4 + - - +
429B GLU* 2.9 30.3 + - + +
430B ALA* 2.8 19.9 + - - -
499B PRO* 5.1 3.8 - - + -
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Residues in contact with PRO 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B VAL* 4.5 1.1 - - + +
420B MET* 3.7 18.4 - - - -
425B LEU 3.8 0.6 - - - -
426B PRO* 1.4 82.0 - - + -
428B LYS* 1.3 56.7 + - - +
430B ALA* 3.7 1.4 - - + +
431B THR* 2.7 36.9 + - - +
493B CYS 4.2 6.5 - - - +
494B ALA* 4.0 13.0 - - - +
497B LEU* 3.0 31.4 - - + +
499B PRO* 3.8 35.2 - - + -
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Residues in contact with LYS 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.9 18.1 - - + +
7B ASP* 3.6 11.8 + - - +
426B PRO* 2.8 4.8 + - - +
427B PRO* 1.3 78.9 - - - +
429B GLU* 1.3 70.7 + - - +
431B THR* 3.2 3.5 + - - -
432B ARG* 3.0 61.5 + - - +
494B ALA* 4.0 20.9 + - + +
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Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B LEU* 3.5 15.6 - - + +
426B PRO* 2.9 49.2 + - + +
428B LYS* 1.3 87.8 + - - +
430B ALA* 1.3 59.9 + - - +
432B ARG* 3.4 20.0 + - + +
433B LYS* 2.9 27.5 + - - +
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B VAL* 4.3 5.8 - - + +
419B VAL* 4.2 12.1 - - + +
420B MET* 3.5 32.5 - - + -
425B LEU* 3.9 17.1 - - + +
426B PRO 2.8 13.2 + - - +
427B PRO* 3.7 2.7 - - + +
429B GLU* 1.3 75.8 - - - +
431B THR* 1.3 61.5 + - - +
433B LYS* 3.7 5.9 - - - +
434B SER* 2.8 32.7 + - - -
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Residues in contact with THR 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.0 11.0 - - + -
416B VAL* 3.6 29.7 - - + +
427B PRO 2.7 25.6 + - - -
428B LYS 3.6 4.5 - - - -
430B ALA* 1.3 72.6 - - - +
432B ARG* 1.3 58.4 + - - +
435B MET* 2.8 36.2 + - + +
490B PRO* 3.5 29.6 - - + +
493B CYS* 3.7 7.0 - - + +
494B ALA* 3.6 18.6 + - - -
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Residues in contact with ARG 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASN* 3.8 38.5 + - - +
6B ILE* 4.0 18.1 - - + +
7B ASP* 3.1 27.3 + - - -
428B LYS* 3.0 55.1 + - - +
429B GLU* 3.5 24.9 + - + +
430B ALA 3.3 0.2 - - - -
431B THR* 1.3 76.7 - - - +
433B LYS* 1.3 61.7 + - - +
435B MET* 4.0 1.6 - - - +
436B GLY* 3.1 18.5 + - - -
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Residues in contact with LYS 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B VAL* 3.9 16.8 - - + -
423B GLU* 2.9 36.3 + - - +
425B LEU* 4.0 12.8 - - + -
429B GLU 2.9 18.0 + - - +
430B ALA* 3.3 6.9 + - - +
432B ARG* 1.3 75.2 - - - +
434B SER* 1.3 64.6 + - - +
436B GLY* 3.1 11.8 + - - -
437B GLN* 3.3 27.0 + - - +
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Residues in contact with SER 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ASN* 2.6 44.4 + - - +
416B VAL* 3.2 27.7 + - - +
419B VAL* 4.1 4.0 - - - +
430B ALA 2.8 21.4 + - - -
431B THR 3.7 0.2 - - - -
433B LYS* 1.3 73.5 - - - +
435B MET* 1.3 63.3 + - - +
437B GLN* 2.9 28.9 + - - +
438B ILE* 3.4 6.6 + - - +
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Residues in contact with MET 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B PRO* 4.0 28.9 - - + -
3B ASN* 4.9 3.1 - - - +
6B ILE* 4.6 1.6 - - + -
412B VAL* 3.4 49.4 - - + +
416B VAL* 4.7 3.1 - - + -
431B THR* 2.8 26.0 + - + +
432B ARG* 4.1 3.8 - - - +
434B SER* 1.3 80.0 - - - +
436B GLY* 1.3 57.4 + - - +
438B ILE* 3.7 19.5 - - + -
439B GLN* 3.0 38.1 + - - +
442B LEU* 5.3 3.6 - - - -
485B ALA 4.4 3.1 - - - +
486B LEU* 5.4 1.6 - - - -
490B PRO* 4.0 28.9 - - + -
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Residues in contact with GLY 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASN* 5.6 0.4 + - - -
432B ARG 3.1 11.2 + - - -
433B LYS 3.1 8.8 + - - -
434B SER 3.1 1.4 - - - -
435B MET* 1.3 79.9 - - - +
437B GLN* 1.3 60.7 + - - +
439B GLN* 4.0 17.2 + - - +
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Residues in contact with GLN 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ASN* 2.7 30.4 + - - +
418B ARG* 3.0 20.2 + - - +
419B VAL* 4.2 11.9 - - - +
423B GLU* 5.5 2.8 + - - -
433B LYS* 3.3 24.7 + - + +
434B SER* 2.9 7.2 + - - +
436B GLY* 1.3 78.1 - - - +
438B ILE* 1.3 65.7 + - + +
440B GLY 5.1 1.4 + - - -
441B ALA 5.1 0.7 + - - -
947B GLU* 4.2 21.5 - - - +
948B PHE* 4.0 13.2 - - + -
951B ASP* 5.2 17.8 - - - +
970B MET* 6.3 0.2 - - - -
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Residues in contact with ILE 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B VAL* 3.8 34.3 - - + +
412B VAL* 4.1 6.3 - - + -
415B ASN* 4.5 10.5 - - + +
434B SER 3.7 10.1 - - - +
435B MET* 3.7 26.7 - - + -
437B GLN* 1.3 86.0 - - + +
439B GLN* 1.3 67.9 + - - +
440B GLY 3.2 2.9 - - - -
441B ALA* 3.2 7.2 + - - +
442B LEU* 2.9 32.5 + - + +
944B LEU* 4.1 16.4 - - + -
948B PHE* 3.6 29.4 - - + -
971B ARG* 5.5 0.9 - - - +
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Residues in contact with GLN 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112A D12 5.7 8.5 - - + +
1B MET* 4.9 3.2 - - - +
2B PRO* 3.3 40.5 - - + +
3B ASN* 4.8 9.5 + - - +
435B MET* 3.0 28.0 + - + +
436B GLY* 4.0 14.3 - - - +
437B GLN 3.8 0.2 - - - -
438B ILE* 1.3 80.1 - - - +
440B GLY* 1.3 65.3 + - - +
442B LEU* 3.3 12.3 + - - +
443B VAL* 3.2 26.9 + - + +
486B LEU* 4.6 11.8 - - + +
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Residues in contact with GLY 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112A D12 4.1 29.2 - - - +
436B GLY 5.1 1.4 + - - -
437B GLN 5.1 1.6 + - - -
438B ILE 3.2 0.8 - - - +
439B GLN* 1.3 87.0 - - - +
441B ALA* 1.3 61.3 + - - +
443B VAL* 3.3 6.4 + - - +
444B GLY 3.0 17.0 + - - -
891B LEU* 3.6 13.0 - - - +
947B GLU* 6.2 0.7 - - - -
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B GLN 5.1 0.4 + - - -
438B ILE* 3.2 8.1 + - - +
440B GLY* 1.3 75.3 - - - +
442B LEU* 1.3 52.1 + - - +
444B GLY* 3.1 1.7 + - - -
445B ILE* 2.6 41.8 + - + +
891B LEU* 4.2 11.5 - - + +
943B ILE* 4.4 14.0 - - + +
944B LEU* 3.7 29.8 - - + -
947B GLU* 4.1 23.9 + - + +
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP* 3.6 24.7 - - - +
411B VAL* 4.5 18.6 - - + -
412B VAL* 4.3 14.6 - - + -
435B MET* 5.3 1.6 - - - -
438B ILE* 2.9 44.1 + - + +
439B GLN* 3.3 4.7 + - - +
441B ALA* 1.3 74.9 - - + +
443B VAL* 1.3 57.7 + - - +
445B ILE* 3.4 19.5 + - + +
446B ALA* 3.0 25.6 + - - +
482B VAL* 4.0 15.4 - - + +
485B ALA* 5.0 5.4 - - + -
486B LEU* 4.1 26.0 - - + -
940B LYS* 4.9 2.0 - - - -
944B LEU* 5.3 1.8 - - + -
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Residues in contact with VAL 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112A D12 4.2 22.2 - - + -
439B GLN* 3.2 16.8 + - + +
440B GLY* 3.7 7.4 - - - +
441B ALA 3.2 0.2 - - - -
442B LEU* 1.3 73.2 - - - +
444B GLY* 1.3 68.5 + - - +
446B ALA* 3.1 9.1 + - + +
447B MET* 3.0 29.3 + - + +
482B VAL* 5.0 4.0 - - + -
486B LEU* 4.3 21.1 - - + -
----------------------------------------------------------
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Residues in contact with GLY 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112A D12 4.2 17.4 - - - +
440B GLY 3.0 13.6 + - - -
441B ALA 3.4 3.6 - - - -
443B VAL* 1.3 78.1 - - - +
445B ILE* 1.3 62.7 + - - +
447B MET* 3.1 5.7 + - - +
448B VAL* 2.9 29.2 + - - +
887B CYS* 5.7 2.0 - - - -
891B LEU* 4.4 18.2 - - - -
943B ILE* 5.6 0.4 - - - -
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Residues in contact with ILE 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP* 5.6 0.2 - - - +
441B ALA* 2.6 32.9 + - + +
442B LEU* 3.6 20.0 - - + +
444B GLY* 1.3 73.0 - - - +
446B ALA* 1.3 57.5 + - - +
448B VAL* 3.2 6.5 + - - +
449B LEU* 2.8 60.8 + - + +
478B MET* 5.7 0.9 - - - -
482B VAL* 5.8 2.7 - - + -
891B LEU* 5.3 0.2 - - - +
940B LYS* 3.7 41.5 - - + +
943B ILE* 4.1 23.1 - - + -
944B LEU* 4.3 20.9 - - + -
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B LEU 3.0 14.2 + - - +
443B VAL* 3.4 10.8 - - + +
445B ILE* 1.3 76.9 - - - +
447B MET* 1.3 64.0 + - + +
450B SER* 2.6 33.8 + - - -
478B MET* 3.6 18.6 - - + +
479B ALA* 6.1 1.1 - - - -
482B VAL* 3.9 24.9 - - + +
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Residues in contact with MET 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111A LMT 5.4 1.0 - - - +
1112A D12 4.1 30.5 - - + -
1113A DD9 4.1 25.6 - - + +
443B VAL* 3.0 24.1 + - + +
444B GLY 3.1 5.6 + - - +
446B ALA* 1.3 86.3 - - + +
448B VAL* 1.3 61.7 + - - +
450B SER* 3.1 20.1 + - - +
451B ALA* 3.2 14.6 + - - +
883B VAL* 5.4 0.2 - - - +
887B CYS* 3.4 22.1 - - + -
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B GLY 2.9 19.9 + - - +
445B ILE* 3.7 6.1 - - - +
447B MET* 1.3 73.7 - - - +
449B LEU* 1.3 71.1 + - + +
451B ALA* 3.0 17.0 + - - +
452B VAL* 3.1 25.0 + - + +
884B VAL* 4.0 25.2 - - + +
887B CYS* 3.9 17.0 - - + -
888B LEU* 3.6 29.8 - - + -
939B ALA* 5.2 8.7 - - + -
943B ILE* 4.6 13.5 - - + -
1116B D10 5.4 1.3 - - + -
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU* 4.4 14.8 - - + -
445B ILE* 2.8 44.7 + - + +
448B VAL* 1.3 81.6 - - + +
450B SER* 1.3 56.3 + - - +
451B ALA 3.0 1.6 - - - -
452B VAL* 3.8 6.3 - - + -
453B PHE* 2.9 47.4 + - + +
475B VAL* 5.2 0.5 - - - +
478B MET* 3.8 35.7 - - + +
936B GLY* 3.8 34.5 - - - +
939B ALA* 5.4 3.1 - - + -
940B LYS* 4.7 12.6 - - + +
943B ILE* 6.4 0.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111A LMT 3.4 11.6 - - - +
1113A DD9 6.0 1.8 - - - -
446B ALA 2.6 21.8 + - - -
447B MET* 3.1 16.3 + - - +
449B LEU* 1.3 76.4 - - - +
451B ALA* 1.3 59.3 + - - +
453B PHE* 4.2 1.6 - - - -
454B VAL* 3.0 37.6 - - - +
475B VAL* 4.5 9.2 - - - +
478B MET* 3.3 15.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111A LMT 4.1 8.1 - - + -
447B MET 3.2 9.6 + - - +
448B VAL* 3.0 10.3 + - - +
450B SER* 1.3 79.7 - - - +
452B VAL* 1.3 61.6 + - - +
453B PHE 3.5 0.2 - - - -
455B PRO* 3.2 18.5 - - - +
880B SER* 2.8 21.3 + - - +
883B VAL* 3.8 34.3 - - + -
884B VAL* 4.1 12.6 - - + +
887B CYS* 5.5 0.2 - - - -
----------------------------------------------------------
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Residues in contact with VAL 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B VAL* 3.1 24.0 - - + +
449B LEU* 4.0 11.0 - - + +
451B ALA* 1.3 80.7 - - - +
453B PHE* 1.3 67.3 + - + +
455B PRO* 4.2 3.3 - - - +
456B MET* 4.6 1.0 + - - +
880B SER* 3.7 5.6 + - - -
884B VAL* 4.1 15.0 - - + -
932B LEU* 3.5 43.4 - - + +
935B ILE* 5.0 4.7 - - + -
936B GLY* 5.7 2.9 - - - +
1116B D10 3.9 46.9 - - + +
----------------------------------------------------------
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Residues in contact with PHE 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LEU* 4.5 10.8 - - + -
449B LEU* 2.9 44.3 + - + +
452B VAL* 1.3 85.0 - - + +
454B VAL* 1.3 69.0 + - - +
456B MET* 3.3 33.5 - - + +
471B SER* 3.0 18.1 + - - +
474B ILE* 3.8 40.2 - - + -
475B VAL* 3.7 17.5 - - + -
478B MET* 6.2 1.8 - - + -
929B VAL 5.0 0.2 - - - -
932B LEU* 3.4 43.7 - - + -
933B THR* 4.0 12.3 - - + -
936B GLY* 5.1 0.9 - - - -
----------------------------------------------------------
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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