Contacts of the helix formed by residues 491 - 517 (chain C) in PDB entry 3G4G
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 491 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C TRP* 4.9 6.5 - - + +
269C GLY* 3.8 29.4 - - - +
489C THR 4.5 1.3 - - - +
490C LYS* 1.3 87.0 - - + +
492C LEU* 1.3 55.6 - - - +
493C GLN* 3.2 19.7 - - + +
494C LEU* 2.7 35.3 + - + +
495C TYR 3.0 9.2 + - - -
564C THR* 4.3 8.3 - - + -
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Residues in contact with LEU 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 5.0 3.8 - - + -
496B ARG* 3.8 17.0 - - - +
571B TRP* 3.5 33.0 - - + +
490C LYS 3.2 4.6 + - - -
491C PRO* 1.3 70.6 - - - +
493C GLN* 1.3 64.8 + - - +
495C TYR* 4.1 15.5 - - + -
496C ARG* 3.0 27.5 + - + +
564C THR* 5.2 0.2 - - - +
568C ASN* 3.5 35.7 + - + +
571C TRP* 3.7 39.5 - - + -
572C TYR* 4.8 2.2 - - + -
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Residues in contact with GLN 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B PRO* 5.0 5.4 - - - +
492B LEU* 4.0 44.0 + - + +
493B GLN 5.6 0.3 + - - -
568B ASN* 5.4 0.9 - - - +
571B TRP* 4.3 10.4 - - + -
269C GLY 5.6 0.8 + - - -
271C HIS* 3.3 36.9 + - - -
491C PRO* 4.1 16.6 - - + +
492C LEU* 1.3 74.6 - - - +
494C LEU* 1.3 81.6 + - - +
496C ARG* 4.0 3.3 + - - +
497C GLN* 3.4 31.3 + - - +
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Residues in contact with LEU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C CA 3.9 14.8 - - - -
269C GLY* 3.9 24.5 - - - +
270C LEU 3.5 25.8 - - - +
271C HIS* 4.5 2.0 - - - -
272C VAL* 4.5 3.1 - - + +
273C PHE* 3.7 28.6 - - + -
490C LYS* 4.3 13.7 - - + -
491C PRO* 2.7 27.6 + - + +
493C GLN* 1.3 89.7 - - - +
495C TYR* 1.3 64.0 + - - +
497C GLN* 3.0 19.0 + - - +
498C TRP* 3.2 25.7 + - - +
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Residues in contact with TYR 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C ASN* 3.3 29.8 + - + +
488C PRO* 3.5 31.9 - - + +
490C LYS 4.1 4.5 - - - +
491C PRO 3.0 11.3 + - - +
492C LEU* 3.9 9.9 - - + +
494C LEU* 1.3 77.3 - - - +
496C ARG* 1.3 59.6 + - - +
498C TRP* 3.3 6.1 + - - +
499C THR* 2.8 43.9 + - - -
535C GLN* 2.4 37.1 + - - +
539C ILE* 3.7 14.2 - - + +
568C ASN* 3.7 27.1 - - + -
572C TYR* 3.5 25.6 - + - -
903C D71 4.0 4.7 - + - -
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Residues in contact with ARG 496 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B GLU* 4.9 7.7 + - - +
571B TRP* 3.5 30.3 - - - +
574B SER* 3.3 39.7 + - - -
575B THR* 4.4 5.8 - - - -
492C LEU* 3.0 19.7 + - + +
493C GLN 4.2 2.8 + - - +
495C TYR* 1.3 77.5 - - - +
497C GLN* 1.3 78.3 + - - +
499C THR* 3.4 3.5 + - - -
500C ASP* 2.9 64.3 + - - +
571C TRP* 4.8 13.5 - - + -
572C TYR* 4.0 20.4 - - + +
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Residues in contact with GLN 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PHE* 3.9 40.9 - - + +
493C GLN* 3.4 25.0 + - - +
494C LEU* 3.0 11.8 + - - +
496C ARG* 1.3 92.9 - - - +
498C TRP* 1.3 63.8 + - - +
500C ASP* 3.5 9.6 + - - +
501C ARG* 3.1 34.1 + - - +
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Residues in contact with TRP 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 3.8 17.9 - - + +
273C PHE* 3.4 38.9 - + - -
325C TYR* 3.6 25.8 - + - -
327C ASN* 5.4 1.1 - - - -
329C ILE* 3.9 9.2 - - + -
330C HIS* 3.8 39.0 - - + -
333C ASP* 3.7 18.5 + - - -
487C ASN* 3.3 47.1 - - + +
490C LYS* 5.4 4.7 - - + +
494C LEU* 3.2 29.7 + - + +
495C TYR* 3.6 7.4 - - - +
497C GLN* 1.3 76.7 - - - +
499C THR* 1.3 58.2 + - - +
501C ARG* 3.2 12.7 + - - +
502C ILE* 2.8 31.7 + - - +
903C D71 4.3 2.7 - - + -
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Residues in contact with THR 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C TYR* 2.8 36.0 + - - -
496C ARG 3.5 9.0 - - - -
497C GLN 3.2 0.2 - - - -
498C TRP* 1.3 74.7 - - - +
500C ASP* 1.3 66.2 + - - +
502C ILE* 3.2 2.1 - - - +
503C MET* 3.0 28.7 + - + +
531C VAL* 3.9 25.4 - - + -
535C GLN* 4.1 10.1 - - - +
572C TYR* 3.4 17.9 + - - +
903C D71 3.4 20.1 - - + -
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Residues in contact with ASP 500 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C ARG* 2.9 48.6 + - - +
497C GLN* 3.6 11.7 - - - +
498C TRP 3.4 0.2 - - - -
499C THR* 1.3 78.0 - - - +
501C ARG* 1.3 59.6 + - + +
503C MET* 3.9 4.6 - - - +
504C GLU* 3.0 30.7 + - - +
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Residues in contact with ARG 501 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C PHE* 3.5 36.1 - - - -
324C ALA* 3.3 45.7 + - + +
325C TYR* 3.9 8.7 - - + +
327C ASN* 4.0 13.7 + - - +
329C ILE* 4.0 17.5 - - - +
497C GLN* 3.1 21.9 + - - +
498C TRP* 3.5 18.3 - - - +
500C ASP* 1.3 82.3 - - + +
502C ILE* 1.3 56.9 + - - +
504C GLU* 3.4 9.0 + - - +
505C GLU* 3.0 24.9 + - - +
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Residues in contact with ILE 502 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325C TYR* 3.4 39.6 - - + -
326C HIS* 4.4 3.6 - - + -
498C TRP 2.8 15.4 + - - +
499C THR* 3.2 13.9 - - + +
501C ARG* 1.3 69.1 - - - +
503C MET* 1.3 67.5 + - - +
505C GLU* 3.2 4.8 + - + +
506C PHE* 2.8 62.7 + - + -
903C D71 3.6 64.2 - - + +
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Residues in contact with MET 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499C THR* 3.0 28.9 + - + +
500C ASP* 3.9 4.5 - - - +
502C ILE* 1.3 78.7 - - - +
504C GLU* 1.3 58.5 + - - +
506C PHE* 3.3 5.2 + - + +
507C PHE* 2.8 67.0 + - + -
523C MET* 3.1 35.7 - - + +
529C ALA* 4.9 3.1 - - + -
531C VAL* 3.7 28.9 - - + -
534C SER* 5.0 3.8 - - - -
535C GLN* 5.4 0.2 - - - -
903C D71 3.9 28.3 - - - -
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Residues in contact with GLU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ALA* 4.0 8.6 - - + +
500C ASP 3.0 17.6 + - - +
501C ARG* 3.5 10.7 - - - +
502C ILE 3.3 0.2 - - - -
503C MET* 1.3 74.2 - - - +
505C GLU* 1.3 65.9 + - - +
507C PHE* 3.5 9.9 + - + +
508C ARG* 3.1 59.5 + - + +
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Residues in contact with GLU 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C VAL* 2.9 21.9 - - + +
324C ALA* 3.8 10.0 - - + +
325C TYR* 2.9 33.3 + - + +
326C HIS* 2.3 38.5 + - - -
370C HIS* 4.0 0.5 - - - -
372C GLY* 3.4 29.9 - - - +
501C ARG 3.0 13.5 + - - +
502C ILE* 3.2 7.6 + - + +
504C GLU* 1.3 74.9 - - - +
506C PHE* 1.3 71.2 + - + +
508C ARG* 3.3 9.7 + - - +
509C GLN* 3.2 19.8 + - - +
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Residues in contact with PHE 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C PHE* 3.5 37.9 - + - -
326C HIS* 5.6 1.1 - + - -
374C SER* 6.4 1.8 - - - -
502C ILE* 2.8 42.1 + - + +
503C MET* 3.6 13.0 - - + +
505C GLU* 1.3 85.3 - - + +
507C PHE* 1.3 56.7 + - - +
509C GLN* 3.2 15.6 + - - +
510C GLY 2.9 23.0 + - - -
523C MET* 3.6 30.5 - - + +
524C CYS* 3.5 21.8 - - - +
903C D71 3.7 38.1 - + - -
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Residues in contact with PHE 507 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C MET* 2.8 62.3 + - + +
504C GLU* 3.9 7.6 - - - +
505C GLU 3.3 0.4 - - - -
506C PHE* 1.3 72.9 - - - +
508C ARG* 1.3 57.4 + - + +
510C GLY* 3.3 1.0 + - - -
511C ASP* 2.9 36.7 + - - +
523C MET 3.8 4.9 - - - -
524C CYS 3.6 11.4 - - - +
525C ASP 3.7 8.5 - - - -
526C LYS* 3.7 46.4 - - + -
529C ALA* 3.7 17.5 - - + -
531C VAL* 5.0 4.5 - - + -
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Residues in contact with ARG 508 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C ASP* 2.7 37.8 + - - +
323C VAL* 4.1 2.4 - - - +
324C ALA* 3.9 18.2 - - - +
372C GLY 6.0 0.7 - - - +
504C GLU* 3.1 51.9 + - + +
505C GLU* 3.8 7.8 - - - +
506C PHE 3.3 0.2 - - - -
507C PHE* 1.3 73.7 - - + +
509C GLN* 1.3 64.3 + - - +
511C ASP* 3.4 12.9 + - - +
512C ARG* 3.2 27.4 + - - +
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Residues in contact with GLN 509 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C GLY 4.4 2.7 + - - +
373C VAL* 3.5 23.2 - - + +
374C SER* 3.1 41.9 + - - +
377C PHE* 3.9 21.8 - - + +
505C GLU 3.2 11.2 + - - +
506C PHE* 3.2 18.6 + - - +
508C ARG* 1.3 76.0 - - - +
510C GLY* 1.3 54.3 + - - +
512C ARG* 2.9 11.7 + - - +
513C GLU* 2.8 54.5 + - - +
521C SER* 3.5 8.7 + - - -
524C CYS* 4.1 11.5 - - - -
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Residues in contact with GLY 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C PHE 2.9 9.5 + - - -
507C PHE 3.3 0.9 + - - -
509C GLN* 1.3 79.3 - - - +
511C ASP* 1.3 56.0 + - - +
513C GLU* 3.3 18.3 + - - +
514C ARG* 3.0 29.5 + - - +
520C ILE* 3.8 8.3 - - - +
524C CYS* 3.2 27.1 - - - +
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Residues in contact with ASP 511 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507C PHE* 2.9 25.8 + - - +
508C ARG* 3.7 16.2 - - - +
509C GLN 3.1 0.4 - - - -
510C GLY* 1.3 73.8 - - - +
512C ARG* 1.3 65.3 + - + +
514C ARG* 2.6 36.9 + - - +
515C GLU* 3.1 31.4 + - + +
526C LYS* 3.2 29.0 + - - +
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Residues in contact with ARG 512 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C PRO* 4.8 9.3 + - - +
373C VAL* 3.8 29.0 - - - +
377C PHE* 4.2 28.8 - - + -
508C ARG* 3.2 14.0 + - - +
509C GLN* 2.9 9.3 + - - +
511C ASP* 1.3 75.9 - - - +
513C GLU* 1.3 63.6 + - - +
515C GLU* 3.4 12.2 + - - +
516C ARG* 3.1 38.6 + - + +
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Residues in contact with GLU 513 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C PHE* 3.8 21.7 - - + +
380C ASN* 6.0 0.2 + - - -
509C GLN* 2.8 32.7 + - - +
510C GLY* 3.4 16.0 - - - +
511C ASP 3.3 0.2 - - - -
512C ARG* 1.3 76.1 - - - +
514C ARG* 1.3 60.8 + - - +
516C ARG* 3.3 1.4 + - - +
517C GLY 3.1 3.5 + - - -
518C MET* 2.9 49.8 + - + +
519C GLU 4.0 16.3 - - - +
520C ILE* 3.3 7.1 - - - -
521C SER* 2.4 46.1 + - - -
524C CYS* 4.1 0.3 - - - +
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Residues in contact with ARG 514 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C GLY 3.0 13.5 + - - +
511C ASP* 2.6 40.2 + - - +
512C ARG 3.2 0.2 - - - -
513C GLU* 1.3 78.6 - - - +
515C GLU* 1.3 61.0 + - + +
517C GLY* 3.2 13.2 + - - -
518C MET 4.5 5.8 - - - -
520C ILE* 2.9 39.3 - - + +
524C CYS 5.2 0.8 + - - -
525C ASP* 3.4 18.4 + - - -
526C LYS* 3.6 19.0 - - - +
527C HIS* 3.6 18.5 + - - -
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Residues in contact with GLU 515 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C ASP* 3.1 20.1 + - + +
512C ARG* 3.8 12.4 - - - +
513C GLU 3.3 0.4 - - - -
514C ARG* 1.3 77.8 - - + +
516C ARG* 1.3 61.5 + - + +
517C GLY 3.4 0.5 + - - -
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Residues in contact with ARG 516 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C PHE* 4.4 12.2 - - + -
381C THR* 3.4 35.9 + - - +
512C ARG* 3.1 29.4 + - + +
513C GLU 3.7 4.7 - - - +
514C ARG 3.3 0.2 - - - -
515C GLU* 1.3 76.6 - - + +
517C GLY* 1.3 60.7 + - - +
518C MET* 3.6 26.5 + - + +
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Residues in contact with GLY 517 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C GLU 3.1 2.6 + - - -
514C ARG 3.2 12.7 + - - -
515C GLU 3.2 1.4 - - - -
516C ARG* 1.3 79.2 - - - +
518C MET* 1.3 62.9 + - - +
519C GLU* 4.4 6.6 - - - +
----------------------------------------------------------
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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