Contacts of the helix formed by residues 496 - 522 (chain A) in PDB entry 5SY1
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 LEU 496 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ALA* 4.3 21.8 - - + +
464A ILE* 4.2 12.8 - - + -
465A GLN* 3.5 32.8 - - + +
492A LEU* 3.4 40.1 + - + +
493A SER* 4.9 2.9 - - - -
494A TYR 3.2 1.2 - - - -
495A ILE* 1.3 81.9 - - + +
497A PHE* 1.3 60.2 + - - -
498A LEU 3.6 1.1 - - - -
499A VAL* 3.9 19.1 - - + -
500A ASN* 2.7 42.8 + - - +
129B LEU* 4.7 7.6 - - + -
400B MET* 5.1 0.2 - - + -
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Residues in contact with PHE 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER 4.6 8.3 - - - +
494A TYR* 3.5 17.4 + - + +
495A ILE 3.2 4.0 + - - -
496A LEU* 1.3 75.0 - - - +
498A LEU* 1.3 89.2 + - + +
499A VAL 3.4 0.5 + - - -
500A ASN* 3.4 13.1 + - - +
501A VAL* 3.5 19.2 + - + +
94B TYR* 3.6 41.5 - + + -
97B LEU* 4.3 19.5 - - + -
98B PHE* 4.7 9.4 - + + -
132B PRO* 5.2 2.9 - - + -
281B VAL* 4.7 19.1 - - + -
401B GLY* 6.2 2.5 - - - -
403B THR* 3.7 26.5 - - - -
404B SER* 4.0 16.1 - - - -
407B ALA* 6.5 0.2 - - + -
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Residues in contact with LEU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ILE 4.7 2.0 + - - -
497A PHE* 1.3 97.3 - - + +
499A VAL* 1.3 65.3 + - - +
501A VAL* 3.6 16.9 + - + +
502A MET* 3.8 5.7 + - - +
97B LEU* 3.6 27.6 - - + +
98B PHE* 4.8 2.5 - - + -
100B LYS 5.8 0.2 - - - -
101B LEU* 4.0 33.7 - - + +
104B MET* 6.5 0.9 - - - -
127B ALA 4.7 1.6 - - - +
128B LEU* 3.7 49.3 - - + +
131B TYR* 4.3 13.9 - - + -
132B PRO* 4.1 17.8 - - + +
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Residues in contact with VAL 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A THR* 4.7 6.5 - - - +
458A LEU* 4.8 6.7 - - + -
461A ALA* 3.7 29.4 - - + -
495A ILE 4.9 0.7 - - - +
496A LEU* 3.7 20.8 + - + +
497A PHE 3.2 0.6 - - - -
498A LEU* 1.3 78.7 - - - +
500A ASN* 1.3 58.2 + - - +
502A MET* 2.9 22.5 + - - +
503A ILE* 3.1 17.1 + - + +
128B LEU* 4.2 23.6 - - + +
129B LEU* 4.2 27.1 - - + -
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Residues in contact with ASN 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A GLN* 3.0 34.8 + - - +
493A SER* 5.7 3.0 + - - +
496A LEU* 2.7 25.0 + - - +
497A PHE* 3.4 1.9 + - - +
498A LEU 3.4 0.2 - - - -
499A VAL* 1.3 73.6 - - - +
501A VAL* 1.3 59.9 + - - +
503A ILE* 3.5 24.2 - - + +
504A GLY* 3.0 20.6 + - - -
400B MET* 3.9 16.8 + - - +
401B GLY* 4.1 6.1 - - - +
404B SER* 3.3 28.9 + - - +
405B TYR* 3.8 11.5 + - + -
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Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A PHE* 3.5 23.1 + - + +
498A LEU* 3.8 15.9 - - + +
499A VAL 3.1 1.0 - - - -
500A ASN* 1.3 78.1 - - - +
502A MET* 1.3 64.2 + - + +
504A GLY* 2.9 16.3 + - - -
505A VAL* 3.2 15.0 + - + +
98B PHE* 4.8 15.0 - - + -
101B LEU* 3.8 25.8 - - + -
404B SER* 3.7 22.7 - - - +
407B ALA* 6.0 1.3 - - + -
408B ALA* 4.1 16.1 - - + +
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Residues in contact with MET 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A PHE* 4.5 20.6 - - + -
458A LEU* 3.8 30.3 - - + +
498A LEU 4.3 9.2 - - - +
499A VAL* 2.9 10.9 + - - +
501A VAL* 1.3 85.8 - - + +
503A ILE* 1.3 63.5 + - - +
505A VAL* 3.8 27.4 + - + +
506A VAL* 4.0 7.8 + - - +
101B LEU* 4.8 14.1 - - + -
105B VAL* 5.8 6.7 - - + -
128B LEU* 4.5 20.4 - - + -
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A LEU* 3.7 36.8 - - + +
461A ALA* 4.9 1.6 - - + -
462A ALA* 4.2 22.2 - - + +
465A GLN* 5.1 2.5 - - - +
499A VAL* 3.1 16.4 + - + +
500A ASN* 3.5 29.2 - - - +
501A VAL 3.2 0.2 - - - -
502A MET* 1.3 76.2 - - - +
504A GLY* 1.3 58.6 + - - +
505A VAL 3.1 6.2 + - - -
506A VAL* 3.1 18.6 + - + +
507A LEU* 3.2 18.7 + - + +
405B TYR* 3.9 18.8 - - + +
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Residues in contact with GLY 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ASN 3.0 8.7 + - - -
501A VAL 2.9 11.5 + - - -
503A ILE* 1.3 76.0 - - - +
505A VAL* 1.3 56.3 + - - +
507A LEU* 4.6 2.2 - - - -
508A GLY* 3.3 15.4 + - - -
405B TYR* 3.6 26.9 - - - -
408B ALA* 3.5 17.0 - - - +
409B PHE* 3.4 14.2 - - - -
412B LEU* 5.1 0.2 - - - +
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Residues in contact with VAL 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A VAL* 3.2 15.9 + - + +
502A MET* 3.8 26.2 + - + +
503A ILE 3.1 1.2 - - - -
504A GLY* 1.3 77.9 - - - +
506A VAL* 1.3 64.1 + - + +
507A LEU 3.3 0.2 - - - -
508A GLY* 2.9 15.6 + - - +
509A ILE* 3.0 22.4 + - + +
408B ALA* 4.7 9.6 - - + +
412B LEU* 4.6 18.8 - - + -
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Residues in contact with VAL 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A TRP* 5.8 3.6 - - - +
458A LEU* 4.2 17.7 - - + -
502A MET 4.0 13.0 - - - +
503A ILE* 3.1 11.3 + - + +
505A VAL* 1.3 79.4 - - + +
507A LEU* 1.3 65.6 + - + +
509A ILE* 3.5 16.5 - - + +
510A TRP* 3.4 20.1 + - - +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ILE* 3.2 17.4 + - + +
504A GLY* 4.6 1.8 - - - +
506A VAL* 1.3 80.7 - - + +
508A GLY* 1.3 64.2 + - - +
510A TRP* 3.4 10.5 + - + +
511A ARG* 3.2 22.7 + - - +
405B TYR* 3.8 37.5 - - + +
409B PHE* 3.8 18.1 - - + -
540B PRO* 4.1 26.1 - - + +
544B CYS* 4.7 10.3 - - - -
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Residues in contact with GLY 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A GLY 3.3 7.7 + - - -
505A VAL 2.9 9.0 + - - -
507A LEU* 1.3 79.5 - - - +
509A ILE* 1.3 60.6 + - - +
510A TRP 3.4 0.3 + - - -
511A ARG* 3.5 6.0 + - - +
512A VAL* 3.5 22.0 + - - +
409B PHE* 3.5 18.6 - - - -
412B LEU* 3.7 22.9 - - - +
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Residues in contact with ILE 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A VAL* 3.0 19.3 + - + +
506A VAL* 3.5 20.0 - - + +
508A GLY* 1.3 76.3 - - - +
510A TRP* 1.3 63.1 + - + +
512A VAL* 3.5 7.8 + - - +
513A VAL* 3.0 36.6 + - + +
412B LEU* 4.6 13.2 - - + -
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Residues in contact with TRP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A VAL 3.4 14.2 + - - +
507A LEU* 3.8 13.9 - - + +
508A GLY 3.2 0.8 - - - -
509A ILE* 1.3 81.9 - - + +
511A ARG* 1.3 60.0 + - - +
513A VAL* 4.4 15.9 - - + -
514A ILE* 2.9 63.5 + - + +
517A LEU* 6.4 0.4 - - + -
538B PHE 4.5 6.5 + - - -
540B PRO* 3.7 26.0 - - + -
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Residues in contact with ARG 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A LEU 3.2 16.2 + - - +
508A GLY* 3.8 7.2 - - - +
509A ILE 3.3 0.2 - - - -
510A TRP* 1.3 78.9 - - - +
512A VAL* 1.3 50.5 + - - +
514A ILE* 4.1 1.5 - - - +
515A THR* 2.7 40.0 + - - +
409B PHE* 3.8 22.6 - - - -
522B HIS 4.0 7.1 + - - -
523B LEU* 3.7 22.4 + - + +
525B ARG 3.1 25.2 + - - -
528B ILE* 3.4 16.8 + - - +
530B LEU* 3.5 30.7 - - + +
539B ASP* 2.5 44.3 + - - +
540B PRO* 4.3 13.9 - - + -
541B GLY* 3.4 16.2 - - - -
542B TYR 3.8 1.8 - - - +
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLY 3.5 12.6 + - - +
509A ILE* 3.5 10.3 + - - +
510A TRP 3.2 0.4 - - - -
511A ARG* 1.3 77.3 - - + +
513A VAL* 1.3 67.7 + - + +
515A THR* 2.9 15.7 + - - -
516A ALA* 3.4 11.1 + - - +
412B LEU* 6.1 3.8 - - + -
416B ILE* 4.0 24.7 - - + -
523B LEU* 4.2 25.1 - - + -
701B CLR 3.7 35.0 - - + +
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Residues in contact with VAL 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A ILE* 3.0 25.0 + - + +
510A TRP* 3.4 21.5 + - + +
511A ARG 3.4 0.2 - - - -
512A VAL* 1.3 78.1 - - + +
514A ILE* 1.3 58.7 + - + +
515A THR 3.1 3.4 - - - -
516A ALA* 2.7 27.9 + - + +
517A LEU* 3.0 29.6 + - + +
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Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A TRP* 2.9 59.4 + - + +
511A ARG* 4.1 9.2 - - - +
513A VAL* 1.3 77.5 - - + +
515A THR* 1.3 63.8 + - + +
517A LEU* 4.2 20.1 - - + +
518A PHE* 3.4 24.4 + - - +
531B LEU* 3.8 20.1 - - + +
538B PHE* 4.7 8.7 - - + +
539B ASP* 5.0 1.1 - - - -
540B PRO* 4.6 8.7 - - + -
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Residues in contact with THR 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ARG 2.7 25.4 + - - +
512A VAL* 2.9 15.8 + - - -
514A ILE* 1.3 80.2 - - + +
516A ALA* 1.3 56.7 + - - +
518A PHE 3.9 0.4 - - - -
519A ASN* 3.1 36.6 + - - +
519B ASN* 3.9 4.3 - - - +
523B LEU* 5.9 0.9 - - - +
530B LEU* 3.7 36.3 - - + +
531B LEU* 3.9 20.9 - - + -
539B ASP* 4.5 5.8 - - - +
701B CLR 3.4 19.2 + - - -
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Residues in contact with ALA 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A VAL* 3.6 10.5 - - + +
513A VAL* 2.7 12.6 + - + +
515A THR* 1.3 79.5 + - - +
517A LEU* 1.3 68.2 + - + +
519A ASN* 3.2 12.0 + - - +
520A ILE* 3.3 21.9 + - + +
701A CLR 4.7 32.0 - - + +
701B CLR 4.7 15.9 + - + -
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Residues in contact with LEU 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A VAL* 6.1 1.1 - - + -
421A PHE* 4.8 11.2 - - + -
424A CYS* 6.2 4.0 - - - -
510A TRP* 6.4 0.9 - - + -
513A VAL* 3.0 30.4 + - + +
514A ILE* 4.6 18.8 - - + +
516A ALA* 1.3 76.2 - - + +
518A PHE* 1.3 58.2 + - - +
520A ILE* 3.2 20.0 - - + +
521A VAL* 3.0 38.1 + - + +
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Residues in contact with PHE 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A ILE 3.4 19.0 + - - +
515A THR 4.2 1.3 - - - +
516A ALA 3.2 0.6 - - - -
517A LEU* 1.3 78.3 - - - +
519A ASN* 1.3 68.2 + - - +
521A VAL* 4.2 1.6 - - - -
522A HIS* 3.4 58.6 + + + +
528A ILE* 4.1 14.8 - - + -
530A LEU* 4.6 11.2 - - + +
531B LEU* 3.9 22.4 - - + -
532B ASN* 4.0 26.5 - - + -
535B VAL* 3.7 29.6 - - + -
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Residues in contact with ASN 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A THR* 3.1 26.9 + - - +
516A ALA 3.2 1.1 + - - +
518A PHE* 1.3 92.2 + - - +
520A ILE* 1.3 58.4 + - - +
522A HIS 4.3 0.6 - - - -
523A LEU* 3.1 32.8 - - - +
530A LEU* 4.3 25.7 + - - +
701A CLR 2.5 40.6 + - + +
515B THR* 3.8 16.1 - - - +
519B ASN* 4.3 15.4 + - - +
530B LEU 5.3 4.6 + - - -
531B LEU* 5.3 1.4 - - - +
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Residues in contact with ILE 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 4.0 14.6 - - + -
417A GLN* 2.6 40.8 + - + +
420A VAL* 3.8 23.8 - - + -
421A PHE* 3.7 33.4 - - + -
516A ALA 3.3 12.8 + - - +
517A LEU* 3.2 24.2 - - + +
519A ASN* 1.3 80.3 - - - +
521A VAL* 1.3 59.8 + - + +
522A HIS 3.3 0.2 - - - -
523A LEU* 3.3 15.0 + - + +
701A CLR 3.6 31.2 - - + -
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Residues in contact with VAL 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A VAL* 4.0 23.7 - - + +
356A ASN* 4.4 1.9 - - - +
359A MET* 4.0 26.4 - - + +
417A GLN* 3.4 13.7 + - - +
421A PHE* 5.1 10.8 - - + -
517A LEU* 3.0 23.5 + - + +
518A PHE* 4.8 1.1 - - - -
520A ILE* 1.3 83.6 - - + +
522A HIS* 1.3 81.5 + - + +
523A LEU 3.2 2.6 + - - -
524A GLY 4.4 2.4 + - - -
525A ARG* 5.5 0.5 - - - +
----------------------------------------------------------
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Residues in contact with HIS 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A MET* 3.9 12.1 - - + +
518A PHE* 3.4 50.3 + + + +
519A ASN 4.3 2.7 - - - -
520A ILE 3.3 0.2 - - - -
521A VAL* 1.3 92.4 - - + +
523A LEU* 1.3 61.3 + - - +
524A GLY 3.4 2.4 + - - -
525A ARG* 3.2 48.5 + - - +
528A ILE* 4.0 23.4 - - + +
530A LEU* 3.8 21.0 - - + +
511B ARG* 3.9 5.5 + - - -
----------------------------------------------------------
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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