Contacts of the helix formed by residues 521 - 548 (chain I) 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 SER 521 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I LYS* 5.0 0.9 - - - -
477I GLN 3.2 19.4 + - - -
478I TYR* 3.5 18.4 - - - +
480I LYS* 6.0 0.7 - - - +
481I ASP 5.7 4.6 + - - -
482I GLU 4.8 2.1 + - - -
483I ASP* 5.1 3.1 - - - +
484I ASP* 3.8 23.6 + - - +
485I ASP 4.3 3.3 + - - -
486I LEU* 3.8 4.9 + - - +
520I LYS* 1.3 76.3 - - - +
522I LEU* 1.3 64.0 + - - +
523I HIS* 4.1 10.1 - - - -
524I PHE* 3.3 22.0 - - - +
525I VAL* 3.6 10.0 + - - +
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Residues in contact with LEU 522 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269I LEU* 3.8 27.8 - - + -
272I MET* 3.9 9.0 - - + -
352I LEU* 4.9 0.4 - - + -
396I PHE* 3.3 35.2 - - + +
399I LYS* 4.1 15.3 - - + +
400I ALA* 4.0 30.1 - - + +
403I LEU* 3.8 28.0 - - + -
478I TYR* 3.1 23.4 + - + +
479I LEU* 5.1 3.1 - - + -
521I SER* 1.3 71.2 - - - +
523I HIS* 1.3 65.8 + - - +
524I PHE 3.2 0.2 - - - -
525I VAL* 3.3 4.1 + - + +
526I LYS* 3.1 21.8 + - - +
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Residues in contact with HIS 523 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266I ASN* 6.0 1.4 + - - -
269I LEU* 3.5 41.0 - - + +
270I THR* 5.3 6.6 + - - -
273I CYS* 5.4 6.1 - - + -
478I TYR 4.0 2.2 + - - -
479I LEU* 3.7 21.9 + - + +
481I ASP* 3.7 31.1 - - + +
482I GLU 5.2 0.4 - - - +
521I SER* 3.4 6.0 - - - -
522I LEU* 1.3 76.9 - - - +
524I PHE* 1.3 64.1 + - - +
526I LYS* 3.6 9.8 + - + +
527I ARG* 3.1 60.2 + - - +
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Residues in contact with PHE 524 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482I GLU 5.8 0.2 + - - -
484I ASP* 3.7 28.7 - - + +
517I TYR* 4.9 6.3 - + + -
520I LYS* 3.6 53.6 - - + -
521I SER* 3.3 17.1 + - - +
522I LEU 3.2 0.8 - - - -
523I HIS* 1.3 77.1 - - - +
525I VAL* 1.3 70.9 + - + +
527I ARG* 3.1 25.3 + - + +
528I ARG* 3.2 51.7 + - + +
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Residues in contact with VAL 525 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392I ALA 4.6 1.3 - - - +
395I SER* 4.3 10.8 - - - +
396I PHE* 3.5 39.9 - - + +
399I LYS* 3.6 32.8 - - + -
517I TYR* 4.4 20.0 - - + -
520I LYS* 5.2 0.7 - - + -
521I SER 3.6 9.6 - - - +
522I LEU 3.3 5.7 + - - +
524I PHE* 1.3 83.2 - - + +
526I LYS* 1.3 60.5 + - - +
528I ARG* 3.4 7.0 - - + +
529I MET* 2.9 28.9 + - - +
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Residues in contact with LYS 526 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I ILE* 2.7 33.0 + - - -
266I ASN* 2.9 33.5 + - - +
269I LEU* 2.9 40.0 - - + +
396I PHE* 3.9 5.3 - - + -
522I LEU 3.1 16.1 + - - +
523I HIS* 3.8 13.7 - - + +
524I PHE 3.3 0.2 - - - -
525I VAL* 1.3 77.4 - - - +
527I ARG* 1.3 55.8 + - + +
529I MET* 3.1 23.3 + - + -
530I GLU* 2.8 49.7 + - + +
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Residues in contact with ARG 527 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481I ASP* 5.7 0.2 - - - +
482I GLU* 3.6 34.1 + - - +
484I ASP* 5.6 2.4 - - - +
523I HIS* 3.1 53.9 + - + +
524I PHE* 3.1 16.7 + - + +
526I LYS* 1.3 76.8 - - + +
528I ARG* 1.3 60.5 - - - +
530I GLU* 4.5 3.2 - - - +
531I ASN* 3.2 26.0 + - - +
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Residues in contact with ARG 528 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392I ALA* 4.7 3.6 - - + +
517I TYR* 3.1 51.3 + - - -
520I LYS* 5.3 2.2 - - - +
524I PHE* 3.2 43.1 + - + +
525I VAL* 3.4 11.2 - - + +
527I ARG* 1.3 77.1 - - - +
529I MET* 1.3 61.1 + - - +
531I ASN* 3.6 3.4 - - - +
532I ILE* 3.2 44.4 + - + +
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Residues in contact with MET 529 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I LEU* 4.8 0.7 - - + -
265I ILE* 3.9 32.3 - - + -
359I LEU* 4.6 2.5 - - - -
392I ALA* 3.7 18.1 - - + +
393I VAL* 4.1 21.3 - - + -
396I PHE* 3.4 49.4 - - + -
525I VAL 2.9 18.4 + - - +
526I LYS* 3.1 22.6 + - + +
528I ARG* 1.3 72.6 - - - +
530I GLU* 1.3 68.4 + - + +
532I ILE* 3.3 4.7 + - - +
533I ILE* 3.2 41.9 + - + +
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Residues in contact with GLU 530 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I LEU* 3.5 45.7 - - + +
265I ILE* 4.1 0.9 - - - +
266I ASN* 2.8 29.2 - - - +
526I LYS* 2.8 35.4 + - + +
527I ARG* 4.5 3.1 - - - +
529I MET* 1.3 75.1 - - + +
531I ASN* 1.3 56.7 + - - +
533I ILE* 3.3 9.0 + - - +
534I ASP* 2.9 41.8 + - - +
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Residues in contact with ASN 531 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527I ARG 3.2 20.6 + - - +
528I ARG* 3.6 6.3 - - - +
530I GLU* 1.3 77.9 - - - +
532I ILE* 1.3 67.3 + - - +
534I ASP* 3.4 8.9 + - - +
535I GLN* 3.3 41.9 + - - +
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Residues in contact with ILE 532 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I GLY* 4.4 2.2 - - - +
388I GLU* 3.8 24.9 - - + +
389I ALA* 3.6 26.5 - - + +
391I THR* 5.3 1.3 - - - +
392I ALA* 4.0 19.5 - - + -
528I ARG* 3.2 33.8 + - + +
529I MET 3.3 3.3 + - - +
531I ASN* 1.3 82.4 - - - +
533I ILE* 1.3 64.4 + - - +
535I GLN* 3.8 18.2 + - - +
536I CYS* 3.5 21.2 + - - +
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Residues in contact with ILE 533 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I PHE* 6.3 0.7 - - + -
258I ILE* 3.7 23.6 - - + -
262I LEU* 3.5 46.4 - - + -
359I LEU* 4.2 4.0 - - + -
363I LEU* 4.4 9.0 - - + -
389I ALA* 4.1 22.4 - - + +
393I VAL* 3.9 14.4 - - + -
529I MET* 3.2 31.0 + - + +
530I GLU 3.3 5.1 + - - +
532I ILE* 1.3 76.3 - - - +
534I ASP* 1.3 53.1 + - - +
536I CYS* 3.3 5.8 + - + +
537I LEU* 2.8 38.3 + - + +
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Residues in contact with ASP 534 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I LEU* 4.5 10.7 - - - +
530I GLU* 2.9 30.0 + - - +
531I ASN* 3.5 10.5 - - - +
532I ILE 3.4 0.2 - - - -
533I ILE* 1.3 74.0 - - - +
535I GLN* 1.3 55.6 + - + +
537I LEU* 3.1 11.3 + - - +
538I GLN* 2.7 48.4 + - + +
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Residues in contact with GLN 535 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531I ASN* 3.3 24.9 + - - +
532I ILE* 3.9 28.6 - - - +
533I ILE 3.4 0.2 - - - -
534I ASP* 1.3 76.4 - - + +
536I CYS* 1.3 61.2 + - - +
538I GLN* 3.7 6.0 + - - +
539I LYS* 3.2 28.4 + - - +
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Residues in contact with CYS 536 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I PHE* 4.2 10.4 - - + -
363I LEU* 6.1 0.7 - - + -
380I GLY 5.1 0.2 - - - +
381I LEU* 5.0 3.2 - - + +
382I ASP* 4.7 7.9 - - - -
385I GLY* 3.2 42.4 - - - -
386I ILE* 3.4 22.7 - - + -
389I ALA* 4.4 3.8 - - + -
532I ILE* 3.5 11.3 + - - +
533I ILE* 3.3 11.8 + - + +
534I ASP 3.2 0.4 - - - -
535I GLN* 1.3 80.9 - - - +
537I LEU* 1.3 56.3 + - - +
539I LYS* 3.9 5.0 - - - +
540I PRO* 2.8 26.0 - - - +
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Residues in contact with LEU 537 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I PHE* 3.6 35.7 - - + -
194I LYS* 4.8 3.4 - - + +
255I PHE* 3.8 27.3 - - + +
258I ILE* 4.1 20.6 - - + -
259I SER* 4.1 25.4 - - - +
262I LEU* 5.4 2.2 - - + -
533I ILE* 2.8 24.2 + - + +
534I ASP* 3.6 11.2 - - - +
536I CYS* 1.3 73.1 - - - +
538I GLN* 1.3 70.5 + - - +
540I PRO* 3.3 11.5 - - - +
541I ALA* 4.7 2.3 + - - +
----------------------------------------------------------
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Residues in contact with GLN 538 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I LYS* 4.0 29.4 + - - +
197I ARG* 4.5 6.2 + - - -
534I ASP* 2.7 32.3 + - + +
535I GLN* 4.0 6.3 - - - +
537I LEU* 1.3 79.8 - - - +
539I LYS* 1.3 64.9 + - - +
541I ALA* 3.2 18.4 + - - +
542I ASP* 3.3 25.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 539 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380I GLY* 3.6 7.4 - - - +
382I ASP* 3.3 38.1 + - - +
535I GLN 3.2 17.4 + - - +
536I CYS* 3.9 5.4 - - - +
538I GLN* 1.3 77.5 - - - +
540I PRO* 1.4 65.8 - - + +
542I ASP* 3.2 14.7 + - - +
543I VAL* 3.0 46.1 + - + +
546I LYS* 5.0 11.1 - - - +
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Residues in contact with PRO 540 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193I PHE* 5.1 7.4 - - + -
195I ILE* 5.3 1.8 - - + -
251I MET* 4.5 8.1 - - - -
255I PHE* 3.9 23.3 - - + -
379I LEU 3.4 24.7 - - - +
380I GLY 3.9 6.0 - - - +
381I LEU* 4.6 2.5 - - + -
536I CYS 2.8 29.2 - - - +
537I LEU 3.3 15.7 - - - +
538I GLN 3.4 0.4 - - - -
539I LYS* 1.4 83.4 - - + +
541I ALA* 1.3 56.5 + - - +
543I VAL* 3.2 1.0 + - - +
544I ILE* 2.9 43.6 + - + +
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Residues in contact with ALA 541 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194I LYS* 3.6 40.6 - - + +
195I ILE 3.7 12.7 + - - -
196I ALA* 3.7 12.5 - - - +
197I ARG* 3.3 16.8 + - + +
537I LEU 4.7 2.2 + - - +
538I GLN* 3.2 10.8 + - - +
540I PRO* 1.3 77.7 - - - +
542I ASP* 1.3 59.1 - - - +
545I GLY* 2.9 24.1 + - - -
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Residues in contact with ASP 542 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197I ARG* 4.4 21.6 + - - +
538I GLN* 3.3 27.2 + - - +
539I LYS* 3.2 18.1 + - - +
541I ALA* 1.3 76.7 - - - +
543I VAL* 1.3 53.4 + - + +
545I GLY* 3.2 2.3 + - - -
546I LYS* 2.9 61.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 543 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I LEU* 5.0 0.6 - - + +
377I GLU* 4.1 7.4 - - - +
378I PRO* 3.7 19.8 - - + +
380I GLY* 3.8 24.7 - - - +
539I LYS* 3.0 41.2 + - - +
540I PRO 3.9 1.3 - - - +
542I ASP* 1.3 72.0 - - + +
544I ILE* 1.3 64.4 + - - +
546I LYS* 3.5 16.8 + - + +
547I SER* 3.4 20.1 + - - -
----------------------------------------------------------
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Residues in contact with ILE 544 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I ILE* 3.3 41.7 - - + +
196I ALA* 3.8 12.3 - - + -
240I LEU* 5.1 9.8 - - + +
241I LEU* 3.9 17.5 - - + -
248I VAL* 5.3 0.4 - - + -
251I MET* 4.3 9.2 - - + -
378I PRO 4.5 4.0 - - - +
379I LEU* 4.1 32.5 - - + +
540I PRO* 2.9 25.4 + - + +
541I ALA 4.1 0.7 - - - +
543I VAL* 1.3 75.2 - - - +
545I GLY* 1.3 62.5 + - - +
547I SER* 3.3 19.0 + - - -
548I MET* 3.6 22.7 + - + +
----------------------------------------------------------
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Residues in contact with GLY 545 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196I ALA* 4.9 0.2 - - - -
197I ARG 2.9 32.9 - - - +
198I VAL* 4.3 10.1 - - - +
199I THR 5.3 0.5 + - - -
541I ALA 2.9 13.6 + - - -
542I ASP 3.5 1.3 - - - -
544I ILE* 1.3 79.3 - - - +
546I LYS* 1.3 60.8 + - - +
547I SER 3.4 0.3 + - - -
548I MET* 3.5 23.0 + - - +
----------------------------------------------------------
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Residues in contact with LYS 546 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539I LYS* 5.0 9.1 - - - +
542I ASP* 2.9 46.7 + - - +
543I VAL* 3.8 18.6 - - + +
544I ILE 3.3 0.2 - - - -
545I GLY* 1.3 76.3 - - - +
547I SER* 1.3 60.1 + - - +
548I MET 3.6 0.5 + - - -
549I ASN* 3.7 20.8 + - - +
----------------------------------------------------------
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Residues in contact with SER 547 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237I GLU 4.4 1.0 - - - +
239I ASN* 3.7 15.0 + - - +
240I LEU* 3.3 43.3 - - - +
543I VAL 3.4 10.4 + - - -
544I ILE 3.3 10.7 + - - -
545I GLY 3.2 0.4 - - - -
546I LYS* 1.3 76.0 - - - +
548I MET* 1.3 57.8 + - - +
549I ASN* 2.9 25.0 + - - +
----------------------------------------------------------
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Residues in contact with MET 548 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I LEU* 4.4 4.3 - - + -
196I ALA* 4.1 10.3 - - + -
198I VAL* 3.7 41.9 - - + +
217I LEU* 5.1 5.6 - - - -
236I LEU* 4.6 11.6 - - + +
237I GLU 3.7 16.4 - - - +
238I THR* 3.7 38.1 - - + -
240I LEU* 6.6 0.2 - - + -
241I LEU* 4.0 20.4 - - + +
544I ILE* 3.9 34.3 - - + +
545I GLY* 3.5 11.4 + - - +
546I LYS 3.4 0.8 - - - -
547I SER* 1.3 73.3 - - - +
549I ASN* 1.3 60.5 + - - +
550I GLN 3.4 6.3 + - - +
----------------------------------------------------------
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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