Contacts of the helix formed by residues 438 - 461 (chain C) in PDB entry 6UZA
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 GLY 438 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C GLU* 3.8 14.8 - - - -
394C ASN* 4.9 4.0 - - - -
395C LEU* 6.3 1.8 - - - -
434C LYS 4.2 2.8 + - - -
435C ILE 3.2 14.0 + - - -
436C MET 4.3 0.2 - - - +
437C ARG* 1.3 81.7 - - - +
439C PRO* 1.3 75.7 - - - +
440C PHE 3.4 2.5 - - - -
441C MET 3.8 2.6 + - - -
442C LYS* 3.2 22.8 + - - +
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Residues in contact with PRO 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ARG* 4.6 7.0 - - - +
390C ILE 3.4 25.4 - - - +
391C TRP* 3.6 34.1 - - + +
393C GLU* 3.8 11.4 - - + +
437C ARG 4.4 1.3 - - - +
438C GLY* 1.3 85.7 - - - +
440C PHE* 1.3 55.7 + - - +
442C LYS* 3.4 4.6 + - + +
443C PHE* 2.9 27.5 + - - +
753C TYR* 3.9 25.7 - - + +
754C PHE* 3.6 21.3 - - + -
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Residues in contact with PHE 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C TRP* 3.4 48.3 + + - +
392C TYR* 3.7 19.1 - + + -
395C LEU* 3.6 25.6 - - + -
398C LEU* 4.1 25.1 - - + -
406C LYS* 4.2 28.7 - - + -
409C VAL* 5.6 1.1 - - + -
438C GLY 3.4 0.6 - - - -
439C PRO* 1.3 76.2 - - - +
441C MET* 1.3 62.9 + - - +
443C PHE* 3.3 9.7 + + - +
444C VAL* 2.9 48.5 + - + +
1005C Y01 3.6 24.5 - - + -
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Residues in contact with MET 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C LEU* 3.8 24.8 - - + +
398C LEU* 4.5 15.9 - - - -
409C VAL* 5.4 5.8 - - + -
413C VAL* 4.4 24.2 - - + -
420C LEU* 5.9 3.1 - - + -
432C MET* 6.2 3.1 - - + -
435C ILE* 3.5 39.5 - - + +
436C MET* 4.1 23.7 - - + +
438C GLY 3.8 2.7 + - - +
439C PRO 3.4 0.2 - - - -
440C PHE* 1.3 74.5 - - - +
442C LYS* 1.3 60.1 + - - +
444C VAL* 3.4 14.3 + - + +
445C ALA* 2.9 28.9 + - - +
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Residues in contact with LYS 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C MET 4.6 4.4 + - - +
437C ARG* 4.0 15.5 + - - +
438C GLY 3.2 22.2 + - - +
439C PRO* 3.5 5.4 - - - +
441C MET* 1.3 76.1 - - - +
443C PHE* 1.3 58.0 + - - +
445C ALA* 3.4 4.8 + - - +
446C HIS* 3.0 40.7 + - + -
753C TYR* 3.3 28.3 + - + -
754C PHE 5.1 0.2 - - - -
755C GLU 3.4 18.2 + - - -
756C GLU* 5.0 1.2 - - - +
757C GLY 4.8 6.1 - - - +
758C ARG 3.6 17.2 + - - +
759C THR* 4.1 28.5 + - + +
1002C R0G 3.5 24.6 + - - +
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Residues in contact with PHE 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C TRP* 3.7 24.9 - + + -
439C PRO 2.9 17.2 + - - +
440C PHE* 3.5 16.6 - + - +
442C LYS* 1.3 75.6 - - - +
444C VAL* 1.3 61.4 + - + +
446C HIS* 3.4 1.0 + - - +
447C ALA* 2.9 29.2 + - + +
612C TYR 4.6 2.9 - - - -
613C ILE* 3.8 42.2 - - + -
616C ALA* 3.7 28.7 - - + -
749C LEU* 4.6 3.6 - - + -
753C TYR* 3.5 35.1 - + + -
1002C R0G 5.9 0.2 - + - -
1005C Y01 4.3 31.6 - - + -
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Residues in contact with VAL 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C LYS 5.4 0.2 - - - +
409C VAL* 4.2 11.4 - - + +
410C VAL* 4.0 34.1 - - + +
413C VAL* 3.9 26.7 - - + -
440C PHE* 2.9 48.2 + - + +
441C MET* 3.7 15.7 - - + +
442C LYS 3.3 0.2 - - - -
443C PHE* 1.3 80.6 - - + +
445C ALA* 1.3 58.7 + - - +
447C ALA* 3.4 2.3 + - - +
448C ALA* 2.9 28.6 + - - +
1005C Y01 6.0 1.1 - - + -
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C VAL* 4.2 20.0 - - + -
417C LEU* 4.5 3.7 - - + +
441C MET* 2.9 17.8 + - + +
442C LYS* 3.7 7.0 - - - +
443C PHE 3.3 0.2 - - - -
444C VAL* 1.3 77.0 - - - +
446C HIS* 1.3 57.1 + - + +
448C ALA* 3.3 1.9 + - - +
449C SER* 3.0 30.0 + - - -
759C THR 4.9 5.4 - - - +
761C PRO* 3.7 24.3 - - + +
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Residues in contact with HIS 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C LYS* 3.0 38.0 + - + +
443C PHE 3.9 3.4 - - - +
445C ALA* 1.3 78.5 - - - +
447C ALA* 1.3 59.6 + - - +
449C SER* 3.9 3.5 + - - +
450C PHE* 3.7 14.0 + - - +
753C TYR* 4.5 4.9 - + - +
758C ARG* 3.5 26.2 + - + -
759C THR 4.4 5.2 + - - -
760C LEU 4.4 3.5 + - - -
761C PRO* 4.1 29.2 - - + +
762C VAL* 4.9 5.0 + - + +
1002C R0G 3.4 64.0 - + + -
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Residues in contact with ALA 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C VAL* 4.8 5.8 - - + -
443C PHE* 2.9 20.2 + - + +
444C VAL* 3.9 4.9 - - - +
446C HIS* 1.3 77.7 - - - +
448C ALA* 1.3 59.4 + - - +
450C PHE* 3.2 8.2 + - - +
451C THR* 3.0 30.7 + - - +
613C ILE* 4.2 22.7 - - + -
1002C R0G 4.5 0.6 - - - -
1005C Y01 4.1 26.7 - - + +
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Residues in contact with ALA 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C VAL* 3.6 25.2 - - - +
413C VAL* 3.9 10.5 - - + +
414C ALA* 3.6 18.5 - - - +
417C LEU* 4.8 1.8 - - + -
444C VAL 2.9 18.2 + - - +
445C ALA 3.3 4.9 + - - +
447C ALA* 1.3 76.3 - - - +
449C SER* 1.3 58.2 + - - +
451C THR* 3.3 8.9 + - - -
452C ILE* 3.0 34.9 + - - +
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Residues in contact with SER 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417C LEU* 4.1 15.6 - - - +
445C ALA 3.0 16.5 + - - -
446C HIS* 4.2 5.4 - - - -
447C ALA 3.3 0.2 - - - -
448C ALA* 1.3 75.6 - - - +
450C PHE* 1.3 56.2 + - - +
452C ILE* 4.1 5.8 - - - -
453C PHE* 3.8 6.1 + - - +
501C TRP* 3.1 21.0 + - - +
761C PRO* 3.6 17.9 - - - -
762C VAL* 3.4 12.2 - - - +
763C PRO* 3.3 24.6 - - - +
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Residues in contact with PHE 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C HIS 3.7 11.0 + - - +
447C ALA* 3.2 7.9 + - - +
448C ALA 3.1 0.6 - - - -
449C SER* 1.3 75.0 - - - +
451C THR* 1.3 62.1 + - - +
452C ILE 3.2 0.9 - - - -
453C PHE* 3.3 15.1 + + - +
454C LEU* 3.0 63.4 + - + +
505C MET* 6.2 1.8 - - + -
606C SER 3.5 25.8 - - - -
607C PHE* 4.7 0.4 - - - -
609C ARG* 3.7 33.7 - - + +
610C ILE* 3.7 28.9 - - + -
613C ILE* 4.5 17.7 - - + -
1002C R0G 4.5 12.6 - + + -
1005C Y01 5.1 5.6 - - + -
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Residues in contact with THR 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C VAL* 4.4 6.3 - - - +
411C LEU* 4.3 19.5 - - + -
414C ALA* 4.8 8.5 - - + -
447C ALA 3.0 14.8 + - - -
448C ALA* 3.6 12.4 - - - -
450C PHE* 1.3 77.8 - - - +
452C ILE* 1.3 57.0 + - - +
454C LEU* 3.5 6.9 + - - +
455C GLY* 2.9 25.5 + - - -
1005C Y01 3.5 47.8 - - + +
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Residues in contact with ILE 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C ALA* 3.3 36.3 - - + +
417C LEU* 3.8 29.4 - - + -
448C ALA 3.0 21.9 + - - +
449C SER* 4.4 2.7 - - - +
451C THR* 1.3 73.7 - - - +
453C PHE* 1.3 57.4 + - - +
455C GLY* 3.2 2.6 + - - +
456C LEU* 2.9 37.1 + - + +
501C TRP* 3.6 31.0 - - + -
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Residues in contact with PHE 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C SER 3.8 6.1 + - - +
450C PHE* 3.3 23.7 + + + +
452C ILE* 1.3 78.3 - - - +
454C LEU* 1.3 63.0 + - + +
456C LEU* 3.3 10.9 + - + +
457C LEU* 3.0 48.1 + - + +
498C ILE* 3.9 22.2 - - + -
501C TRP* 3.8 46.6 - + + +
502C VAL* 4.3 8.7 - - + -
505C MET* 4.3 20.2 - - + -
533C MET* 5.4 0.7 - - + -
537C PHE* 4.1 24.7 - + - -
606C SER* 4.2 15.3 - - - -
609C ARG* 6.3 1.3 - - - -
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Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C PHE* 3.0 58.0 + - + +
451C THR* 3.9 4.7 - - - +
453C PHE* 1.3 78.6 - - + +
455C GLY* 1.3 57.9 + - - +
457C LEU* 3.3 8.3 + - + +
458C VAL* 3.0 32.1 + - - +
606C SER* 4.3 11.2 - - - +
607C PHE* 3.9 41.8 - - + -
610C ILE* 4.8 3.8 - - + -
1005C Y01 3.9 39.5 - - + -
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Residues in contact with GLY 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C THR 2.9 15.3 + - - -
452C ILE* 3.2 4.4 + - - -
454C LEU* 1.3 76.5 - - - +
456C LEU* 1.3 59.0 + - - +
458C VAL* 3.4 2.5 + - - +
459C MET* 2.9 36.5 + - - +
1005C Y01 4.3 13.1 - - - +
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Residues in contact with LEU 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C ILE* 2.9 25.0 + - + +
453C PHE* 3.6 9.2 - - + +
455C GLY* 1.3 77.9 - - - +
457C LEU* 1.3 57.6 + - - +
459C MET* 3.7 0.6 - - + -
460C ASN* 2.9 33.1 + - - +
493C TRP* 6.1 2.9 - - + -
494C MET* 3.8 28.1 - - + +
497C LEU* 3.8 34.1 - - + -
498C ILE* 4.2 18.6 - - + +
501C TRP* 4.1 26.0 - - + -
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C PHE* 3.0 37.3 + - + +
454C LEU* 3.7 13.0 - - + +
456C LEU* 1.3 76.2 - - - +
458C VAL* 1.3 62.6 + - + +
460C ASN* 4.0 8.4 + - - +
461C ALA 4.6 1.2 + - - -
498C ILE* 4.1 15.3 - - + -
537C PHE* 4.2 12.1 - - + -
599C TYR* 3.3 26.1 + - + +
603C VAL* 3.8 29.2 - - + +
606C SER* 3.3 27.1 - - - +
607C PHE* 4.9 5.2 - - + -
650D ILE* 4.4 5.7 - - + +
654D ASN* 4.3 16.3 + - - +
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Residues in contact with VAL 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C LEU 3.0 20.1 + - - +
455C GLY* 3.8 6.5 - - - +
456C LEU 3.2 0.2 - - - -
457C LEU* 1.3 79.7 - - + +
459C MET* 1.3 74.4 + - + +
460C ASN 3.2 2.0 + - - -
461C ALA* 3.7 8.1 + - - +
465C PHE* 3.9 28.7 - - + -
607C PHE* 5.0 2.7 - - + -
1005C Y01 3.8 23.8 - - + -
650D ILE* 3.7 35.6 - - + +
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Residues in contact with MET 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C GLY* 2.9 20.8 + - - +
456C LEU* 4.9 0.7 - - + -
458C VAL* 1.3 84.5 - - + +
460C ASN* 1.3 64.0 + - - +
461C ALA 3.4 0.4 - - - -
462C ALA* 3.3 31.2 - - + +
465C PHE* 4.6 13.0 - - + -
494C MET* 3.3 28.2 - - + +
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Residues in contact with ASN 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456C LEU 2.9 18.2 + - - +
457C LEU 4.1 7.0 - - - +
458C VAL 3.2 1.2 - - - -
459C MET* 1.3 78.3 - - - +
461C ALA* 1.3 61.4 + - - +
462C ALA 3.2 4.6 + - - -
463C ASP* 4.9 1.4 + - - +
464C ARG* 5.1 1.6 + - - -
492C SER* 5.5 3.3 - - - -
494C MET* 3.7 21.1 - - - +
495C GLU* 4.5 14.1 + - - +
498C ILE* 4.1 16.6 - - + +
599C TYR* 3.1 29.2 + - - +
654D ASN* 6.2 0.2 - - - +
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Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C LEU 4.6 1.4 + - - +
458C VAL 3.7 5.7 + - - +
459C MET 3.4 0.4 - - - -
460C ASN* 1.3 78.6 - - + +
462C ALA* 1.3 57.3 + - - +
463C ASP 3.5 2.7 - - - +
464C ARG* 3.4 43.7 + - - +
465C PHE* 3.2 23.0 - - - -
653D PHE* 3.6 12.6 - - + -
654D ASN* 3.6 23.1 - - - +
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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