Contacts of the helix formed by residues 451 - 478 (chain F) in PDB entry 5G04
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 ALA 451 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452F PHE* 1.3 68.2 + - - +
453F ASN* 3.3 4.3 - - - +
454F LEU* 3.4 13.1 + - - +
455F GLN* 3.4 23.5 + - - +
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Residues in contact with PHE 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451F ALA* 1.3 78.9 - - - +
453F ASN* 1.3 62.2 + - - +
455F GLN* 3.7 5.7 + - - +
456F LYS* 3.2 25.9 + - - +
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Residues in contact with ASN 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451F ALA 3.3 3.0 - - - +
452F PHE* 1.3 76.0 - - - +
454F LEU* 1.3 60.3 + - - +
456F LYS* 3.6 5.8 + - - +
457F ALA* 3.1 30.5 + - - +
460F GLU* 5.1 0.3 - - - +
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Residues in contact with LEU 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451F ALA* 3.4 14.1 + - - +
453F ASN* 1.3 80.1 - - - +
455F GLN* 1.3 61.7 + - - +
457F ALA* 3.8 14.3 + - - +
458F ALA* 4.1 6.2 + - - +
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Residues in contact with GLN 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451F ALA* 3.4 14.3 + - - +
452F PHE* 4.1 6.1 - - - +
454F LEU* 1.3 77.8 - - - +
456F LYS* 1.3 65.5 + - - +
457F ALA 3.4 0.5 + - - -
458F ALA* 3.8 8.3 + - - +
459F ALA 3.9 1.4 + - - -
5H GLN* 4.1 30.5 + - - +
7H PRO* 3.6 42.9 - - + +
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Residues in contact with LYS 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170F PHE 5.0 15.7 - - - +
452F PHE 3.2 19.4 + - - +
453F ASN* 3.8 6.7 - - - +
455F GLN* 1.3 77.1 - - - +
457F ALA* 1.3 57.0 + - - +
459F ALA* 3.3 8.6 + - - +
460F GLU* 2.9 48.1 + - + +
463F MET* 5.6 2.0 - - - +
7H PRO* 5.4 0.4 - - - -
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Residues in contact with ALA 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453F ASN 3.1 18.6 + - - +
454F LEU* 3.8 9.2 - - - +
455F GLN 3.3 0.6 - - - -
456F LYS* 1.3 74.6 - - - +
458F ALA* 1.3 61.7 + - - +
460F GLU* 3.3 30.9 + - - +
461F GLY 3.9 2.9 + - - -
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Residues in contact with ALA 458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454F LEU 4.1 5.7 + - - +
455F GLN 3.8 7.2 + - - +
456F LYS 3.5 0.2 - - - -
457F ALA* 1.3 77.6 - - - +
459F ALA* 1.3 61.0 + - - +
460F GLU 3.6 0.2 + - - -
461F GLY* 3.8 9.4 + - - -
462F LEU 4.7 1.0 + - - -
5H GLN* 5.4 13.2 - - + -
6H GLU 5.4 1.1 - - - +
7H PRO* 5.3 5.8 - - + -
34H GLU* 5.7 0.3 - - - +
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Residues in contact with ALA 459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PHE* 4.0 20.7 - - + -
455F GLN 3.9 1.6 + - - +
456F LYS* 3.3 9.5 + - - +
458F ALA* 1.3 75.0 - - - +
460F GLU* 1.3 58.0 + - - +
461F GLY 3.1 2.9 - - - -
462F LEU* 2.9 24.7 + - - +
463F MET* 3.0 17.2 + - + +
7H PRO* 3.5 34.2 - - + +
8H VAL* 4.4 8.9 - - + +
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Residues in contact with GLU 460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F PHE 5.6 1.8 - - - +
170F PHE 5.7 2.8 - - - -
453F ASN 5.1 0.3 - - - +
456F LYS* 2.9 39.0 + - + +
457F ALA* 3.3 20.8 + - - +
459F ALA* 1.3 72.8 - - - +
461F GLY* 1.3 59.4 + - - +
463F MET* 3.6 20.5 - - + +
464F SER* 2.8 35.9 + - - +
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Residues in contact with GLY 461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457F ALA 3.9 3.4 + - - -
458F ALA 3.8 8.0 + - - -
459F ALA 3.1 1.6 - - - -
460F GLU* 1.3 79.6 - - - +
462F LEU* 1.3 60.3 + - - +
464F SER* 3.4 16.4 - - - -
465F LEU* 3.5 7.4 + - - +
34H GLU* 4.3 6.3 - - - -
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Residues in contact with LEU 462 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PHE* 4.7 2.7 - - + -
458F ALA 4.7 1.2 + - - -
459F ALA* 2.9 13.1 + - - +
461F GLY* 1.3 71.6 - - - +
463F MET* 1.3 60.9 + - - +
465F LEU* 3.1 32.5 + - + +
466F LEU* 2.9 40.6 + - + +
495F HIS* 4.4 3.6 - - + -
8H VAL* 3.6 42.0 - - + -
27H LEU* 4.1 14.6 - - + +
30H ARG* 4.3 19.3 - - + +
31H LEU* 5.0 2.5 - - + +
34H GLU* 3.6 31.6 + - + +
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Residues in contact with MET 463 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F ASN 5.2 2.2 - - - +
146F PRO* 5.5 1.6 - - + -
147F PHE* 3.7 41.2 - - + +
167F THR 3.1 23.6 - - - +
168F PHE 3.2 23.6 - - - +
169F LYS 3.8 13.7 - - - +
170F PHE 3.8 24.2 - - - +
456F LYS* 5.6 1.6 - - - +
459F ALA* 3.0 17.4 + - + +
460F GLU* 3.6 21.3 - - + +
462F LEU* 1.3 76.2 - - - +
464F SER* 1.3 62.1 + - - +
466F LEU* 3.2 16.5 + - + +
467F ARG* 3.0 26.0 + - - +
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Residues in contact with SER 464 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460F GLU* 2.8 16.2 + - - +
461F GLY* 3.4 12.7 - - - -
462F LEU 3.2 0.2 - - - -
463F MET* 1.3 75.6 - - - +
465F LEU* 1.3 62.5 + - - +
467F ARG* 3.2 39.7 + - - +
468F GLU* 3.2 23.4 + - - +
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Residues in contact with LEU 465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461F GLY 3.5 7.2 + - - +
462F LEU* 3.1 27.3 + - + +
464F SER* 1.3 76.2 - - - +
466F LEU* 1.3 66.9 + - + +
468F GLU* 3.4 9.3 + - - +
469F MET* 3.0 38.6 + - + +
491F LEU* 3.7 24.0 - - + -
492F PRO* 4.0 14.1 - - + -
495F HIS* 3.3 55.6 - - + +
30H ARG* 4.9 4.5 - - + -
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Residues in contact with LEU 466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F PHE* 4.9 25.6 - - + +
148F LEU 6.4 0.2 - - - -
149F TRP* 3.9 34.0 - - + -
167F THR* 4.3 20.0 + - + +
462F LEU* 2.9 40.2 + - + +
463F MET* 3.2 18.4 + - + +
465F LEU* 1.3 79.8 - - + +
467F ARG* 1.3 52.7 + - - +
469F MET* 3.2 8.8 + - - +
470F GLY* 2.8 33.6 + - - -
26H PHE* 4.2 16.6 - - + -
27H LEU* 5.6 5.4 - - + -
30H ARG* 5.8 3.6 - - + -
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Residues in contact with ARG 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F PRO* 3.8 25.4 - - + +
165F ASP* 4.6 4.5 - - - +
167F THR* 4.0 11.6 + - - +
168F PHE* 3.3 42.4 + - + +
463F MET* 3.0 7.9 + - - +
464F SER* 3.2 39.7 + - - +
466F LEU* 1.3 74.5 - - - +
468F GLU* 1.3 80.6 + - - +
470F GLY* 3.2 1.6 + - - -
471F LYS* 3.1 30.9 + - - +
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Residues in contact with GLU 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464F SER* 3.2 21.6 + - - +
465F LEU* 3.7 8.7 - - + +
466F LEU 3.3 0.2 - - - -
467F ARG* 1.3 94.9 + - - +
469F MET* 1.3 61.7 + - - +
471F LYS* 3.4 37.7 + - - +
487F ILE* 3.5 18.4 - - + +
490F HIS* 6.3 2.5 - - + -
491F LEU* 4.4 16.2 - - + +
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Residues in contact with MET 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F TRP* 4.4 4.0 - - + -
465F LEU* 3.0 36.3 + - + +
466F LEU* 3.4 12.3 - - - +
468F GLU* 1.3 73.9 - - - +
470F GLY* 1.3 60.2 + - - +
472F GLY* 3.1 5.2 + - - -
473F TYR* 3.0 26.2 + - - +
488F LEU* 4.6 8.3 - - + +
491F LEU* 3.7 36.3 - - + +
495F HIS* 4.5 0.4 - - + -
500F TRP* 3.5 31.8 - - + -
501F VAL* 4.0 9.9 - - + -
26H PHE* 3.6 21.5 - - - -
30H ARG* 3.8 23.1 - - - +
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Residues in contact with GLY 470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F TRP* 3.5 21.1 - - - -
152F PHE* 3.8 17.9 - - - -
164F PRO* 5.0 2.2 - - - -
167F THR* 5.2 2.2 - - - -
466F LEU 2.8 20.8 + - - -
467F ARG 3.2 2.4 + - - -
469F MET* 1.3 71.6 - - - +
471F LYS* 1.3 62.7 + - - +
473F TYR* 3.3 0.5 + - - -
474F LEU* 3.0 25.8 + - - +
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Residues in contact with LYS 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F PRO* 3.3 34.9 - - + +
467F ARG* 3.1 24.0 + - - +
468F GLU* 3.4 30.0 + - - +
470F GLY* 1.3 74.0 - - - +
472F GLY* 1.3 58.2 + - - +
474F LEU* 3.4 10.1 + - + +
475F ALA* 3.0 29.6 + - - +
487F ILE* 3.9 20.9 - - + -
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Residues in contact with GLY 472 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468F GLU 3.6 2.8 + - - -
469F MET 3.1 7.6 + - - -
471F LYS* 1.3 77.6 - - - +
473F TYR* 1.3 57.4 + - - +
475F ALA* 3.2 6.2 + - - +
476F LEU* 2.8 31.2 + - - +
484F ALA* 3.7 13.1 - - - +
487F ILE* 3.6 20.3 - - - +
488F LEU* 4.7 11.2 - - - -
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Residues in contact with TYR 473 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F TRP* 3.8 22.9 - + + -
152F PHE* 4.9 0.7 - - + -
153F GLU* 3.7 33.5 + - + +
156F CYS* 3.8 25.6 - - - -
157F GLU* 3.5 18.6 + - + -
469F MET 3.0 10.7 + - - +
470F GLY 3.9 4.5 - - - +
472F GLY* 1.3 75.2 - - - +
474F LEU* 1.3 57.9 + - - +
476F LEU* 3.1 12.1 + - + +
477F CYS* 2.9 42.7 + - + +
488F LEU* 5.4 2.1 - - + +
500F TRP* 3.6 27.1 - + + -
504F GLN* 3.6 26.2 - - + -
22H ARG* 6.0 0.2 + - - -
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Residues in contact with LEU 474 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F PHE* 4.5 8.9 - - + -
156F CYS* 4.3 15.5 - - + +
161F LYS* 3.7 39.7 - - + -
162F PRO* 3.5 28.3 - - + +
163F ASP* 5.1 0.2 - - - -
164F PRO* 4.0 22.2 - - + -
470F GLY 3.0 14.5 + - - +
471F LYS* 3.6 9.4 - - + +
473F TYR* 1.3 76.0 - - - +
475F ALA* 1.3 59.6 + - + +
477F CYS* 3.4 2.6 + - - +
478F SER* 3.0 30.6 + - - -
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Residues in contact with ALA 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471F LYS 3.0 17.7 + - - +
472F GLY* 3.5 6.3 - - - +
474F LEU* 1.3 77.1 - - - +
476F LEU* 1.3 63.1 + - - +
478F SER* 3.2 9.2 + - - -
479F TYR 3.1 5.4 + - - -
480F ASN* 2.9 44.1 + - + +
483F GLU* 4.9 9.0 - - + +
484F ALA* 4.1 11.7 - - + +
487F ILE* 6.2 1.6 - - + -
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Residues in contact with LEU 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472F GLY 2.8 13.9 + - - +
473F TYR* 3.4 17.9 - - + +
475F ALA* 1.3 76.1 - - - +
477F CYS* 1.3 60.5 + - + +
479F TYR* 2.9 26.9 + - - -
480F ASN 4.8 2.5 - - - +
481F CYS* 5.0 4.6 - - - +
484F ALA* 3.9 10.5 - - + +
488F LEU* 4.9 6.5 - - + -
504F GLN* 3.3 50.7 - - + +
507F ARG* 3.8 31.6 - - - +
508F ALA* 3.8 28.0 - - + +
511F GLU* 5.3 3.6 - - + -
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Residues in contact with CYS 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F CYS* 4.4 11.0 - - - +
157F GLU* 3.5 45.3 - - - -
473F TYR* 2.9 30.4 + - + +
474F LEU* 3.8 5.6 - - - +
476F LEU* 1.3 81.0 - - - +
478F SER* 1.3 58.8 + - - +
479F TYR* 3.1 24.7 + - - -
507F ARG* 5.6 8.3 - - - +
633F ARG* 3.6 14.0 + - - -
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Residues in contact with SER 478 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F LYS* 3.6 32.0 + - - +
474F LEU* 3.0 18.3 + - - -
475F ALA* 3.4 10.7 + - - -
477F CYS* 1.3 74.0 - - - +
479F TYR* 1.3 68.7 + - - +
480F ASN* 4.5 8.7 + - - +
633F ARG* 4.2 12.2 + - - +
664F ILE 4.0 6.2 - - - +
666F PRO* 4.3 8.5 - - - +
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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