Contacts of the helix formed by residues 503 - 536 (chain B) in PDB entry 1WBB
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 ILE 503 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B LEU* 4.8 5.2 - - + -
454B GLU* 4.8 9.9 - - - -
475B ILE* 4.0 24.9 - - + -
488B ASN* 3.4 34.8 - - - +
489B TYR* 3.6 25.8 - - + -
490B MET* 5.2 0.7 - - - -
501B TYR* 5.9 0.2 - - + -
502B ILE* 1.3 83.5 - - - +
504B PRO* 1.3 73.8 - - + +
505B GLU* 3.9 27.6 - - + +
506B LEU* 3.1 29.9 + - + +
507B LYS* 3.3 6.7 + - - +
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Residues in contact with PRO 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B ASN* 5.3 6.5 - - + +
490B MET* 5.8 5.8 - - + -
503B ILE* 1.3 89.2 - - + +
505B GLU* 1.3 56.6 + - - +
507B LYS* 3.3 9.4 + - + +
508B GLU* 2.9 29.3 + - - +
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Residues in contact with GLU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B TYR* 2.7 28.3 + - - +
450B LEU* 3.6 23.5 - - + +
453B ARG* 3.1 13.8 + - - -
454B GLU* 4.6 7.1 - - - +
503B ILE* 3.2 19.4 - - + +
504B PRO* 1.3 77.9 - - + +
506B LEU* 1.3 66.3 + - - +
508B GLU* 3.3 17.4 + - - +
509B TYR* 3.3 32.1 + - + +
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 3.6 27.6 - - + +
450B LEU* 4.0 20.8 - - + +
465B VAL* 4.3 8.7 - - + -
473B TYR* 3.8 20.6 - - + +
474B TYR* 3.4 38.6 - - - -
475B ILE* 3.6 16.8 - - + +
501B TYR 3.9 6.3 - - - +
502B ILE* 4.4 4.9 - - - -
503B ILE* 3.1 16.6 + - + +
505B GLU* 1.3 79.8 - - - +
507B LYS* 1.3 67.6 + - + +
508B GLU 3.3 0.2 + - - -
509B TYR* 3.5 1.7 + - - +
510B GLU* 3.0 24.1 + - - +
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Residues in contact with LYS 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B HIS 3.7 12.0 + - - -
473B TYR* 3.2 20.8 + - - +
502B ILE* 3.9 37.8 - - + +
503B ILE 3.3 5.6 + - - +
504B PRO* 3.3 12.2 + - + +
506B LEU* 1.3 82.1 - - - +
508B GLU* 1.3 62.4 + - - +
510B GLU* 2.3 43.0 + - - +
511B ASP* 3.3 27.0 + - - +
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Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B PRO 2.9 17.3 + - - +
505B GLU* 3.6 10.4 - - - +
506B LEU 3.2 0.4 - - - -
507B LYS* 1.3 80.0 - - - +
509B TYR* 1.3 73.9 + - + +
511B ASP* 3.3 18.0 + - - +
512B LYS* 3.3 34.7 + - - +
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Residues in contact with TYR 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ALA* 4.1 10.3 - - - +
446B TYR* 3.1 71.4 + + + -
447B LEU* 3.7 25.4 - - + -
505B GLU* 3.3 21.3 + - + +
508B GLU* 1.3 91.2 + - + +
510B GLU* 1.3 65.6 + - - +
512B LYS* 3.0 49.1 + - + +
513B VAL* 3.1 18.3 + - - +
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Residues in contact with GLU 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B LEU* 4.5 0.8 - - - +
471B HIS 4.9 0.2 - - - +
472B GLY* 3.4 10.7 - - - -
473B TYR* 2.9 43.9 + - + -
506B LEU 3.0 17.3 + - - +
507B LYS* 2.3 44.2 + - - +
508B GLU 3.3 0.2 - - - -
509B TYR* 1.3 76.1 - - - +
511B ASP* 1.3 65.1 + - - +
513B VAL* 3.2 3.5 + - - +
514B LEU* 3.1 44.3 + - + +
----------------------------------------------------------
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Residues in contact with ASP 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LYS* 3.3 12.2 + - - +
508B GLU* 3.3 12.5 - - - +
509B TYR 3.1 0.2 - - - -
510B GLU* 1.3 82.0 - - - +
512B LYS* 1.3 55.1 + - + +
514B LEU* 4.3 3.3 - - - +
515B THR* 2.2 47.9 + - + +
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Residues in contact with LYS 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B LEU* 5.3 1.8 - - + +
443B ALA* 3.8 14.6 - - + +
508B GLU* 3.3 32.1 + - - +
509B TYR* 3.0 59.5 + - + +
511B ASP* 1.3 76.9 - - + +
513B VAL* 1.3 58.2 + - - +
515B THR* 3.3 4.6 + - - -
516B SER* 2.8 35.3 + - - +
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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
----------------------------------------------------------
440B ALA* 4.6 5.3 - - + +
443B ALA* 3.6 24.2 - - + -
444B THR* 3.9 13.9 - - - +
447B LEU* 4.0 21.5 - - + -
473B TYR* 3.8 18.8 - - + +
509B TYR 3.1 14.3 + - - +
510B GLU 3.2 6.3 + - - +
512B LYS* 1.3 74.9 - - - +
514B LEU* 1.3 71.2 + - + +
516B SER* 3.4 4.2 + - - -
517B LYS* 2.8 52.2 + - + +
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B PHE* 4.1 31.0 - - + -
472B GLY* 5.9 0.2 - - - -
473B TYR* 4.6 2.0 - - + -
510B GLU* 3.1 39.8 + - + +
511B ASP* 4.3 3.8 - - - +
513B VAL* 1.3 91.2 - - + +
515B THR* 1.3 62.0 + - + +
517B LYS* 3.9 9.8 - - + +
518B GLY* 3.0 24.3 + - - -
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Residues in contact with THR 515 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B ASP* 2.2 44.9 + - + +
512B LYS* 3.3 7.3 + - - -
514B LEU* 1.3 74.2 - - + +
516B SER* 1.3 60.1 + - - -
518B GLY* 3.3 1.1 + - - -
519B LYS* 3.0 56.5 + - - +
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Residues in contact with SER 516 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B TRP* 3.5 44.3 - - - +
439B LEU* 3.6 20.3 - - - +
440B ALA* 3.7 11.4 + - - -
512B LYS* 2.8 22.4 + - - +
513B VAL 3.7 2.7 - - - -
515B THR* 1.3 79.2 + - - +
517B LYS* 1.3 58.0 + - - +
519B LYS* 3.5 0.7 + - - +
520B ALA* 3.0 28.4 + - - +
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Residues in contact with LYS 517 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B ALA* 4.4 15.3 - - + -
444B THR* 5.1 5.1 + - - -
473B TYR* 4.8 5.7 + - - -
513B VAL* 2.8 42.0 + - + +
514B LEU* 4.0 9.8 - - + +
516B SER* 1.3 74.0 - - - +
518B GLY* 1.3 57.8 + - - +
520B ALA* 3.5 7.6 + - - +
521B LEU* 3.1 27.7 + - - +
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Residues in contact with GLY 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LEU 3.0 17.8 + - - -
515B THR* 3.8 0.9 - - - -
516B SER 3.2 0.2 - - - -
517B LYS* 1.3 76.3 - - - +
519B LYS* 1.3 63.0 + - - +
521B LEU* 3.5 9.6 + - - +
522B ALA* 3.1 24.3 + - - +
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Residues in contact with LYS 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B TRP* 3.6 57.8 - - + +
515B THR* 3.0 45.1 + - - +
516B SER 3.9 3.8 - - - +
518B GLY* 1.3 74.6 - - - +
520B ALA* 1.3 63.6 + - - +
522B ALA* 3.5 6.2 + - - +
523B LEU* 3.1 24.3 + - - +
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 3.2 29.1 - - + +
436B TRP* 4.2 13.6 - - + +
437B ARG* 4.5 16.8 - - + +
516B SER 3.0 18.2 + - - +
517B LYS* 3.7 8.3 - - - +
518B GLY 3.3 0.2 - - - -
519B LYS* 1.3 77.9 - - - +
521B LEU* 1.3 56.0 + - - +
523B LEU* 3.4 1.1 + - - -
524B GLU* 3.0 30.0 + - - +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B VAL 4.7 1.3 - - - +
420B ARG 3.6 9.4 - - - +
421B ASP* 3.5 34.8 - - - +
422B GLY* 3.6 9.2 - - - +
517B LYS 3.1 17.0 + - - +
518B GLY* 3.8 7.6 - - - +
519B LYS 3.3 0.2 - - - -
520B ALA* 1.3 74.2 - - - +
522B ALA* 1.3 64.4 + - - +
523B LEU 3.1 1.6 - - - -
524B GLU* 3.4 7.6 + - + +
525B LYS* 3.2 49.3 + - + +
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Residues in contact with ALA 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B GLY 3.1 17.7 + - - +
519B LYS* 3.9 6.5 - - - +
521B LEU* 1.3 78.1 - - - +
523B LEU* 1.3 57.3 + - - +
524B GLU 3.5 0.2 - - - -
525B LYS* 3.8 10.1 + - - +
526B GLN* 3.2 31.4 + - - +
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ASN* 3.6 7.4 - - - +
432B GLU* 3.6 27.8 - - + +
433B LEU* 3.4 37.2 - - + +
436B TRP* 4.5 6.7 - - + -
519B LYS 3.1 15.8 + - - +
520B ALA 3.7 4.7 - - - +
521B LEU 3.1 0.8 - - - -
522B ALA* 1.3 77.7 - - - +
524B GLU* 1.3 64.3 + - - +
525B LYS 3.3 0.2 - - - -
526B GLN* 4.4 8.3 - - + +
527B LEU* 2.9 46.5 + - + +
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B VAL* 5.9 0.9 - - - +
422B GLY* 3.5 12.4 - - - -
423B GLY 2.9 16.7 + - - -
424B VAL* 2.8 34.1 + - + +
425B ILE* 3.2 24.7 + - + +
433B LEU* 3.9 6.2 - - + +
437B ARG* 3.0 30.8 + - - +
520B ALA* 3.0 23.8 + - - +
521B LEU* 3.4 8.2 + - - +
523B LEU* 1.3 76.3 - - - +
525B LYS* 1.3 57.8 + - + +
527B LEU* 3.3 4.0 + - - +
528B TYR* 2.9 31.6 + - - +
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Residues in contact with LYS 525 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B VAL* 4.8 20.9 - - + +
420B ARG* 3.2 39.6 + - - +
521B LEU* 3.2 39.6 + - + +
522B ALA* 3.9 8.7 - - - +
524B GLU* 1.3 79.7 - - + +
526B GLN* 1.3 62.4 + - + +
528B TYR* 3.2 7.9 + - - +
529B GLU* 3.0 29.5 + - + +
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Residues in contact with GLN 526 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B ALA 3.2 18.7 + - - +
523B LEU* 3.4 12.5 + - + +
524B GLU 3.3 0.2 - - - -
525B LYS* 1.3 80.2 - - + +
527B LEU* 1.3 59.2 + - + +
529B GLU* 3.4 14.0 + - - +
530B GLU* 3.0 26.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE* 4.2 10.5 - - + -
429B TYR* 4.0 26.1 + - + -
430B ASN* 3.7 43.1 - - + +
433B LEU* 4.1 20.0 - - + -
523B LEU* 2.9 36.4 + - + +
524B GLU 3.6 4.0 - - - +
526B GLN* 1.3 76.5 - - + +
528B TYR* 1.3 60.3 + - - +
530B GLU* 3.4 26.3 - - - +
531B LEU* 3.3 24.3 + - - +
----------------------------------------------------------
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Residues in contact with TYR 528 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ALA 2.7 23.1 + - - -
361B ARG* 3.0 19.6 + - - -
362B PRO* 3.6 12.1 - - + +
365B LEU* 3.4 30.2 - - + +
411B ILE* 4.6 2.5 - - + -
419B VAL* 3.5 38.1 - - + -
424B VAL* 4.0 15.5 - - + -
425B ILE* 4.7 3.8 - - + -
524B GLU 2.9 17.0 + - - +
525B LYS* 3.5 8.1 - - - +
526B GLN 3.2 0.4 - - - -
527B LEU* 1.3 74.1 - - - +
529B GLU* 1.3 72.1 + - - +
530B GLU 3.0 1.1 - - - -
531B LEU* 3.0 30.4 + - + +
532B PHE* 3.5 30.0 + + - -
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Residues in contact with GLU 529 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ARG* 3.2 34.0 + - - +
525B LYS* 3.0 21.2 + - + +
526B GLN* 3.7 15.3 - - - +
528B TYR* 1.3 82.5 - - - +
530B GLU* 1.3 59.4 + - - +
532B PHE* 3.4 21.1 + - - -
533B ASP* 3.2 19.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B TYR* 2.7 31.8 + - - -
526B GLN 3.0 14.3 + - - +
527B LEU* 3.4 26.0 - - - +
528B TYR 3.0 0.2 - - - -
529B GLU* 1.3 77.3 - - - +
531B LEU* 1.3 63.0 + - - +
533B ASP* 3.3 16.8 + - + +
534B LEU* 3.2 33.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B LEU* 4.0 17.3 - - + -
406B LEU* 4.1 20.9 - - + -
407B LEU* 4.2 4.9 - - + -
410B ALA* 3.6 29.2 - - + -
411B ILE* 3.7 31.9 - - + -
425B ILE* 4.8 3.6 - - + -
429B TYR* 3.8 17.3 - - + +
527B LEU 3.3 13.5 + - - +
528B TYR* 3.0 18.4 + - + +
530B GLU* 1.3 74.8 - - - +
532B PHE* 1.3 64.7 + - - +
534B LEU* 3.1 6.2 + - + +
535B LEU* 3.0 33.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 3.6 35.2 - - + -
358B ARG* 3.3 46.0 - - + +
360B ALA* 3.3 50.5 - - + -
365B LEU* 4.8 6.7 - - + -
528B TYR* 3.5 38.3 + + - -
529B GLU* 3.4 18.7 + - - +
530B GLU 3.3 0.2 - - - -
531B LEU* 1.3 78.8 - - + +
533B ASP* 1.3 59.5 + - - +
535B LEU* 4.7 3.6 - - + -
536B LEU* 3.1 35.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B ARG* 3.3 21.5 + - - -
529B GLU 3.2 16.9 - - - +
530B GLU* 3.3 17.9 + - + +
531B LEU 3.2 0.6 - - - -
532B PHE* 1.3 77.2 - - - +
534B LEU* 1.3 60.5 + - + +
536B LEU* 4.8 2.9 - - - +
537B PRO* 3.2 22.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LEU* 4.5 3.7 - - + +
406B LEU* 3.7 39.5 - - + -
429B TYR* 4.6 1.1 - - - +
530B GLU* 3.2 33.3 + - + +
531B LEU* 3.1 8.5 + - - +
533B ASP* 1.3 79.1 - - + +
535B LEU* 1.3 65.2 + - - +
537B PRO* 3.4 9.0 - - - +
538B HIS* 3.4 18.2 + - - -
----------------------------------------------------------
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Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 3.8 35.4 - - + -
365B LEU* 4.0 18.4 - - + -
368B MET* 4.5 15.3 - - - -
403B LEU* 4.4 23.6 - - + -
406B LEU* 3.5 29.8 - - + -
407B LEU* 4.3 17.3 - - + -
531B LEU* 3.0 23.3 + - + +
532B PHE* 4.1 0.9 - - + +
534B LEU* 1.3 75.8 - - - +
536B LEU* 1.3 57.9 + - - +
537B PRO* 3.2 4.5 - - - -
538B HIS* 3.0 29.5 + - - +
539B LEU 3.8 2.8 + - - -
542B LEU* 3.9 6.4 - - + +
----------------------------------------------------------
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Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B PRO* 5.3 4.5 - - + -
355B LEU* 3.5 40.8 - - + +
356B ALA* 4.1 11.0 - - - +
358B ARG* 4.3 28.0 - - + +
532B PHE* 3.1 25.9 + - + +
533B ASP* 4.8 2.2 - - - +
535B LEU* 1.3 70.9 - - - +
537B PRO* 1.3 70.1 - - + +
538B HIS 3.1 3.0 + - - -
539B LEU* 3.3 32.4 + - + +
----------------------------------------------------------
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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