Contacts of the helix formed by residues 496 - 522 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 4.6 9.4 - - + -
400A MET* 5.0 0.7 - - + -
461B ALA* 4.3 22.0 - - + +
464B ILE* 4.2 13.2 - - + -
465B GLN* 3.5 32.5 - - + +
492B LEU* 3.4 39.2 + - + +
493B SER* 4.9 3.8 - - - -
494B TYR 3.2 0.6 - - - -
495B ILE* 1.3 82.1 - - + +
497B PHE* 1.3 60.0 + - - -
498B LEU 3.6 0.9 - - - -
499B VAL* 3.9 17.9 - - + -
500B ASN* 2.7 42.8 + - - +
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Residues in contact with PHE 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.5 46.7 - + + -
97A LEU* 4.3 19.3 - - + -
98A PHE* 4.5 6.1 - + + -
132A PRO* 5.2 2.5 - - + -
281A VAL* 4.5 20.6 - - + -
401A GLY* 6.4 1.1 - - - -
403A THR* 3.7 27.6 - - - -
404A SER* 4.0 13.6 - - - -
407A ALA* 6.4 0.4 - - + -
493B SER 4.6 6.7 - - - +
494B TYR* 3.5 17.6 + - + +
495B ILE 3.2 4.4 + - - -
496B LEU* 1.3 75.7 - - - +
498B LEU* 1.3 89.5 + - + +
499B VAL 3.4 0.3 + - - -
500B ASN* 3.4 12.0 + - - +
501B VAL* 3.5 19.3 + - + +
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Residues in contact with LEU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 3.4 29.6 - - + +
98A PHE* 4.5 2.2 - - + -
101A LEU* 3.9 36.0 - - + +
104A MET* 6.5 1.1 - - - -
127A ALA 4.9 1.1 - - - +
128A LEU* 3.8 44.5 + - + +
131A TYR* 4.3 15.5 - - + -
132A PRO* 4.2 17.4 - - + +
495B ILE 4.7 2.4 + - - -
497B PHE* 1.3 96.8 - - + +
499B VAL* 1.3 65.6 + - - +
501B VAL* 3.6 16.0 + - + +
502B MET* 3.8 5.9 + - - +
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Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.1 28.3 - - + +
129A LEU* 4.2 24.2 - - + -
457B THR* 4.7 6.7 - - - +
458B LEU* 4.4 7.4 - - + +
461B ALA* 3.7 28.3 - - + -
465B GLN* 6.3 0.2 - - - +
495B ILE 4.9 0.7 - - - +
496B LEU* 3.7 19.2 + - + +
497B PHE 3.2 0.8 - - - -
498B LEU* 1.3 78.8 - - - +
500B ASN* 1.3 59.6 + - - +
502B MET* 2.9 23.0 + - - +
503B ILE* 3.1 17.6 + - + +
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Residues in contact with ASN 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A MET 3.9 15.1 + - - +
401A GLY* 4.0 7.8 - - - +
404A SER* 3.1 29.0 + - - +
405A TYR* 3.9 10.4 + - + -
465B GLN* 3.0 35.1 + - - +
493B SER* 5.7 3.0 + - - +
496B LEU* 2.7 25.2 + - - +
497B PHE* 3.9 1.9 - - - +
498B LEU 3.4 0.2 - - - -
499B VAL* 1.3 73.5 - - - +
501B VAL* 1.3 60.3 + - - +
503B ILE* 3.5 23.6 - - + +
504B GLY* 3.0 21.5 + - - -
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Residues in contact with VAL 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 4.7 16.2 - - + -
101A LEU* 3.7 26.5 - - + -
404A SER* 3.8 22.2 - - - +
407A ALA* 5.8 1.6 - - + -
408A ALA* 3.9 16.2 - - + +
497B PHE* 3.5 23.5 + - + +
498B LEU* 3.8 16.4 - - + +
499B VAL 3.1 1.0 - - - -
500B ASN* 1.3 78.8 - - - +
502B MET* 1.3 64.1 + - + +
504B GLY* 2.9 16.5 + - - -
505B VAL* 3.2 15.3 + - + +
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Residues in contact with MET 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LEU* 4.6 15.9 - - + -
105A VAL* 5.7 7.6 - - + -
128A LEU* 4.5 20.2 - - + -
454B PHE* 4.5 19.5 - - + -
458B LEU* 3.8 31.2 - - + +
498B LEU 4.3 9.0 - - - +
499B VAL* 2.9 10.7 + - - +
501B VAL* 1.3 85.8 - - + +
503B ILE* 1.3 64.2 + - - +
505B VAL* 3.8 26.3 + - + +
506B VAL* 4.0 7.4 + - - +
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Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR* 3.8 19.3 - - + +
458B LEU* 3.7 38.4 - - + +
461B ALA* 4.9 1.6 - - + -
462B ALA* 4.2 22.0 - - + +
465B GLN* 5.1 2.2 - - - +
499B VAL* 3.1 15.4 + - + +
500B ASN* 3.5 29.4 - - - +
501B VAL 3.2 0.2 - - - -
502B MET* 1.3 75.3 - - - +
504B GLY* 1.3 58.1 + - - +
505B VAL 3.1 6.8 + - - -
506B VAL* 3.1 18.3 + - + +
507B LEU* 3.2 17.7 + - + +
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Residues in contact with GLY 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR* 3.6 26.9 - - - -
408A ALA* 3.3 21.3 - - - +
409A PHE* 3.4 10.4 - - - -
412A LEU* 5.1 0.2 - - - +
500B ASN 3.0 9.1 + - - -
501B VAL 2.9 11.9 + - - -
503B ILE* 1.3 75.7 - - - +
505B VAL* 1.3 55.8 + - - +
507B LEU* 4.6 2.0 - - - -
508B GLY* 3.3 15.4 + - - -
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Residues in contact with VAL 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA* 4.6 10.5 - - + +
412A LEU* 4.6 18.6 - - + -
501B VAL* 3.2 16.1 + - + +
502B MET* 4.2 26.0 - - + +
503B ILE 3.1 1.0 - - - -
504B GLY* 1.3 76.9 - - - +
506B VAL* 1.3 64.0 + - + +
507B LEU 3.3 0.4 - - - -
508B GLY* 2.9 15.3 + - - +
509B ILE* 3.0 22.4 + - + +
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Residues in contact with VAL 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B TRP* 5.8 3.4 - - + +
458B LEU* 4.2 17.5 - - + -
502B MET 4.0 12.8 - - - +
503B ILE* 3.1 11.1 + - + +
505B VAL* 1.3 78.8 - - + +
507B LEU* 1.3 65.6 + - + +
509B ILE* 3.5 16.2 - - + +
510B TRP* 3.4 19.9 + - - +
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Residues in contact with LEU 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR* 3.7 39.0 - - + +
409A PHE* 3.7 19.1 - - + -
540A PRO* 4.1 24.7 - - + +
544A CYS* 4.7 10.3 - - - -
503B ILE* 3.2 18.1 + - + +
504B GLY* 4.6 1.6 - - - +
506B VAL* 1.3 80.5 - - + +
508B GLY* 1.3 64.0 + - - +
510B TRP* 3.7 10.4 - - + +
511B ARG* 3.2 23.0 + - - +
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Residues in contact with GLY 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 3.5 18.8 - - - -
412A LEU* 3.6 22.0 - - - +
504B GLY 3.3 7.9 + - - -
505B VAL 2.9 9.3 + - - -
507B LEU* 1.3 78.6 - - - +
509B ILE* 1.3 60.4 + - - +
510B TRP 3.4 0.2 + - - -
511B ARG* 3.5 5.7 + - - +
512B VAL* 3.5 23.0 + - - +
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Residues in contact with ILE 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 4.5 13.7 - - + -
505B VAL* 3.0 19.6 + - + +
506B VAL* 3.5 19.7 - - + +
508B GLY* 1.3 76.3 - - - +
510B TRP* 1.3 62.1 + - + +
512B VAL* 3.5 7.6 + - + +
513B VAL* 3.0 36.6 + - + +
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Residues in contact with TRP 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PHE 4.6 6.7 + - - -
540A PRO* 3.6 25.8 - - + -
506B VAL 3.4 13.8 + - - +
507B LEU* 3.8 13.2 - - + +
508B GLY 3.2 0.8 - - - -
509B ILE* 1.3 82.3 - - + +
511B ARG* 1.3 59.6 + - - +
513B VAL* 4.4 16.8 - - + +
514B ILE* 2.9 63.9 + - + +
517B LEU* 6.4 0.9 - - + -
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Residues in contact with ARG 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 3.8 22.8 - - + -
522A HIS 3.9 7.9 + - - -
523A LEU* 3.6 22.2 + - + +
525A ARG 3.0 24.4 + - - -
528A ILE 3.4 16.2 + - - -
530A LEU* 3.5 29.8 - - + +
539A ASP* 2.6 43.7 + - - +
540A PRO* 4.3 14.1 - - + +
541A GLY* 3.5 15.5 - - - -
542A TYR 3.8 2.2 - - - +
507B LEU 3.2 17.0 + - - +
508B GLY 3.8 5.4 - - - +
509B ILE 3.3 0.4 - - - -
510B TRP* 1.3 78.5 - - - +
512B VAL* 1.3 49.8 + - + +
514B ILE* 4.1 2.2 - - - +
515B THR* 2.7 40.2 + - - +
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Residues in contact with VAL 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A LEU* 6.0 4.0 - - + -
416A ILE* 3.9 25.6 - - + -
523A LEU* 4.2 24.0 - - + -
701A CLR 3.4 37.0 - - + +
508B GLY 3.5 12.8 + - - +
509B ILE* 3.8 10.5 - - + +
510B TRP 3.2 0.4 - - - -
511B ARG* 1.3 77.9 - - + +
513B VAL* 1.3 66.8 + - + +
515B THR* 2.8 15.4 + - - -
516B ALA* 3.4 10.9 + - - +
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Residues in contact with VAL 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B ILE* 3.0 26.5 + - + +
510B TRP* 4.0 21.5 - - + +
512B VAL* 1.3 77.7 - - + +
514B ILE* 1.3 59.1 + - + +
515B THR 3.1 3.6 - - - -
516B ALA* 2.8 27.6 + - - +
517B LEU* 3.0 29.4 + - + +
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Residues in contact with ILE 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 3.8 20.3 - - + +
538A PHE* 4.7 9.0 - - + +
539A ASP* 4.9 1.6 - - - +
540A PRO* 4.6 9.2 - - + -
510B TRP* 2.9 59.0 + - + +
511B ARG* 4.1 9.9 - - - +
513B VAL* 1.3 76.9 - - + +
515B THR* 1.3 63.8 - - + +
517B LEU* 4.2 19.3 - - + +
518B PHE* 3.4 24.3 + - - +
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Residues in contact with THR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ASN* 3.8 4.5 - - - +
523A LEU* 5.9 0.5 - - - +
530A LEU* 3.7 36.8 - - + +
531A LEU* 4.0 18.6 - - + -
539A ASP* 4.5 7.6 - - - +
701A CLR 3.2 20.0 + - - -
511B ARG 2.7 25.8 + - - +
512B VAL* 2.8 15.2 + - - -
514B ILE* 1.3 80.4 - - + +
516B ALA* 1.3 57.6 + - - +
518B PHE 3.9 0.4 - - - -
519B ASN* 2.9 37.8 + - - +
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Residues in contact with ALA 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A CLR 4.6 15.3 - - + -
512B VAL 3.6 10.5 - - - +
513B VAL* 2.8 12.4 + - + +
515B THR* 1.3 79.3 + - - +
517B LEU* 1.3 66.2 + - + +
519B ASN* 3.2 10.0 + - - +
520B ILE* 3.3 22.2 + - + +
701B CLR 4.6 35.7 - - + -
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Residues in contact with LEU 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B VAL* 6.1 1.3 - - + -
421B PHE* 4.8 11.0 - - + -
424B CYS* 6.2 4.0 - - - -
510B TRP* 6.4 0.9 - - + -
513B VAL* 3.0 31.3 + - + +
514B ILE* 4.6 18.2 - - + +
516B ALA* 1.3 77.6 - - + +
518B PHE* 1.3 57.5 + - - +
520B ILE* 3.2 18.9 - - + +
521B VAL* 3.0 37.5 + - + +
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Residues in contact with PHE 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A LEU* 3.9 22.7 - - + -
532A ASN* 4.0 26.0 - - + -
535A VAL* 3.7 30.7 - - + -
514B ILE 3.4 19.0 + - - +
515B THR 4.1 1.3 - - - +
516B ALA 3.2 0.8 - - - -
517B LEU* 1.3 80.4 - - - +
519B ASN* 1.3 67.7 + - - +
521B VAL* 4.8 1.1 - - - -
522B HIS* 3.4 58.5 + + + +
528B ILE* 4.1 15.3 - - + -
529B SER 5.7 0.2 - - - -
530B LEU* 4.6 9.9 - - + +
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Residues in contact with ASN 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A THR* 3.9 16.5 - - - +
519A ASN* 4.3 14.4 + - - +
530A LEU 5.3 3.8 + - - -
531A LEU* 5.2 2.4 - - - +
515B THR* 2.9 26.1 + - - +
516B ALA 3.2 1.5 + - - +
518B PHE* 1.3 91.6 + - - +
520B ILE* 1.3 59.3 + - - +
522B HIS 4.2 0.4 - - - -
523B LEU* 3.1 32.1 - - - +
530B LEU* 4.3 23.9 + - + +
701B CLR 2.5 40.4 + - + +
----------------------------------------------------------
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Residues in contact with ILE 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ILE* 4.1 13.5 - - + -
417B GLN* 2.6 39.0 + - + +
420B VAL* 3.8 24.0 - - + -
421B PHE* 3.7 32.8 - - + -
516B ALA 3.3 14.3 + - - +
517B LEU* 3.2 24.5 - - + +
519B ASN* 1.3 80.1 - - - +
521B VAL* 1.3 61.0 + - + +
522B HIS 3.3 0.2 - - - -
523B LEU* 3.3 15.5 + - + +
701B CLR 3.6 31.0 - - + -
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B VAL* 4.0 23.3 - - + +
356B ASN* 4.4 1.4 - - - +
359B MET* 4.0 25.6 - - + +
417B GLN* 3.4 14.7 + - - +
421B PHE* 5.1 11.2 - - + -
517B LEU* 3.0 25.0 + - + +
518B PHE* 4.8 0.4 - - - -
520B ILE* 1.3 83.2 - - + +
522B HIS* 1.3 80.9 + - + +
523B LEU 3.2 2.8 + - - -
524B GLY 4.4 2.6 + - - -
525B ARG* 5.6 0.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A ARG* 4.0 5.7 + - - -
359B MET* 3.9 11.5 - - + +
518B PHE* 3.4 50.4 + + + +
519B ASN 4.2 3.4 - - - -
520B ILE 3.3 0.2 - - - -
521B VAL* 1.3 92.1 - - + +
523B LEU* 1.3 62.1 + - - +
524B GLY 3.4 2.0 - - - -
525B ARG* 3.2 47.8 + - - +
528B ILE* 4.0 22.5 - - + +
530B LEU* 3.8 21.2 - - + +
----------------------------------------------------------
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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