Contacts of the helix formed by residues 504 - 528 (chain A) in PDB entry 1VDV
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 MET 504 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A SER* 5.3 5.6 - - - +
433A LYS* 3.3 39.7 - - - +
502A GLY 3.9 2.9 - - - +
503A GLY* 1.3 73.8 - - - +
505A ILE* 1.3 65.4 + - - +
506A GLU* 3.4 5.2 - - - -
507A PHE* 3.4 14.4 + - + -
508A ARG* 3.0 25.0 + - + +
1210A GLU* 3.9 7.6 - - - +
1212A HIS* 3.8 31.0 - - + +
1301A THR* 5.4 2.2 - - - +
1303A GLU* 3.3 55.0 - - + +
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Residues in contact with ILE 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A LEU* 3.9 37.0 - - + +
497A SER 3.6 20.4 - - - +
498A PRO* 3.9 22.0 - - + +
500A ALA* 4.3 8.3 - - + +
503A GLY* 3.4 27.8 - - - +
504A MET* 1.3 77.7 - - - +
506A GLU* 1.3 78.8 + - + +
508A ARG* 4.0 1.0 - - - +
509A ARG* 3.1 36.4 + - - +
1319A THR* 5.9 4.5 - - - +
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Residues in contact with GLU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A MET* 4.4 3.6 - - - -
505A ILE* 1.3 92.8 + - + +
507A PHE* 1.3 63.4 + - - +
509A ARG* 3.4 5.5 + - - +
510A THR* 3.0 30.0 + - - +
1303A GLU* 4.9 2.8 - - - +
1307A ASN* 4.1 19.9 + - - +
1317A CYS* 4.8 1.8 - - - +
1318A VAL 3.9 9.6 - - - +
1319A THR* 2.8 41.7 + - + +
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Residues in contact with PHE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLN* 4.0 6.5 - - + -
424A ALA 4.7 3.1 - - - -
433A LYS* 4.3 19.1 - - + -
504A MET* 3.4 22.5 + - + +
505A ILE 3.4 0.2 - - - -
506A GLU* 1.3 78.9 + - - +
508A ARG* 1.3 58.3 + - - +
510A THR* 3.3 3.6 + - - -
511A LEU* 3.0 52.4 + - + +
1168A THR 3.4 26.5 - - - -
1302A PRO* 3.6 16.2 - - + -
1303A GLU* 3.6 41.5 - - + -
1306A ARG* 3.4 29.2 - - + -
1307A ASN* 3.6 10.7 + - - +
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Residues in contact with ARG 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LYS* 3.5 29.6 - - + +
434A VAL* 3.5 19.7 - - + +
458A GLY 2.9 30.6 + - - -
459A MET* 3.8 10.8 - - - +
460A ALA 5.3 0.4 - - - +
496A LEU* 3.7 25.3 - - + +
500A ALA* 3.8 17.6 - - - +
501A PRO 3.1 26.3 + - - -
502A GLY* 4.8 2.6 - - - -
503A GLY 2.8 31.1 + - - +
504A MET* 3.0 15.4 + - + +
505A ILE* 4.0 3.3 - - - +
507A PHE* 1.3 75.3 - - + +
509A ARG* 1.3 65.7 + - - +
511A LEU* 3.3 3.8 + - - +
512A THR* 3.1 26.2 + - - +
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Residues in contact with ARG 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A MET* 4.3 1.1 - - + -
491A ALA* 2.5 47.8 + - - +
494A LEU 4.1 18.7 + - - +
495A SER* 4.6 5.3 - - - +
496A LEU* 4.3 18.8 - - + +
505A ILE* 3.1 32.2 + - - +
506A GLU* 3.9 4.3 - - - +
508A ARG* 1.3 76.0 - - - +
510A THR* 1.3 60.9 + - - +
512A THR* 2.5 29.6 + - - +
513A LEU* 3.3 4.2 + - - +
1316A LEU 4.6 1.4 + - - -
1317A CYS* 2.8 51.9 + - + +
1318A VAL 5.0 0.4 - - - -
1319A THR* 4.9 7.3 + - - +
1322A PRO* 5.7 4.8 - - - +
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Residues in contact with THR 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A GLU* 3.0 20.4 + - - +
507A PHE* 3.6 7.4 - - - -
509A ARG* 1.3 77.4 - - - +
511A LEU* 1.3 54.0 + - - +
513A LEU* 3.3 4.0 + - - +
514A SER* 2.7 36.3 + - - +
1306A ARG* 3.4 48.0 - - + +
1307A ASN* 4.8 2.9 + - - +
1313A PHE* 4.7 1.6 - - + -
1314A THR* 3.8 30.4 - - + +
1317A CYS* 3.6 13.1 - - - +
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Residues in contact with LEU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A GLN* 3.9 22.7 - - + -
433A LYS* 4.5 5.2 - - + -
434A VAL* 3.9 28.5 - - + -
507A PHE* 3.0 50.4 + - + +
508A ARG* 3.6 4.9 - - - +
509A ARG 3.2 0.2 - - - -
510A THR* 1.3 73.6 - - - +
512A THR* 1.3 60.7 + - - +
514A SER* 4.1 2.2 - - - -
515A PHE* 2.8 44.6 + - + +
1167A LEU 3.9 6.1 - - - +
1168A THR* 3.7 36.8 - - - +
1306A ARG* 4.8 1.8 - - + -
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Residues in contact with THR 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL* 4.3 3.4 - - + -
456A TYR* 2.8 42.6 + - + -
459A MET* 3.5 38.3 - - + +
490A LEU* 3.7 4.9 + - - +
494A LEU* 4.0 17.3 - - + +
508A ARG 3.1 16.5 + - - +
509A ARG* 2.5 21.0 + - - +
511A LEU* 1.3 77.5 - - - +
513A LEU* 1.3 70.9 + - - +
516A PHE 3.4 8.8 + - - -
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Residues in contact with LEU 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A CYS* 3.5 37.7 - - + +
490A LEU* 3.3 39.3 - - + -
491A ALA* 3.9 9.4 - - + +
509A ARG 3.3 10.4 + - - +
510A THR 3.8 4.7 - - - +
511A LEU 3.2 0.2 - - - -
512A THR* 1.3 87.8 + - - +
514A SER* 1.3 60.9 + - - +
516A PHE* 3.0 5.4 + - - +
517A PHE* 2.9 27.6 + - - +
1313A PHE* 4.2 21.1 - - + +
1316A LEU* 4.0 23.8 - - + -
1317A CYS* 3.8 13.0 - - - -
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Residues in contact with SER 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A THR* 2.7 26.5 + - - +
511A LEU* 3.8 5.8 - - - -
513A LEU* 1.3 72.7 - - - +
515A PHE* 1.3 62.2 + - - +
517A PHE* 3.2 10.5 + - - +
518A LYS* 3.0 29.5 + - - +
1167A LEU* 3.1 33.7 + - - +
1306A ARG* 3.0 27.4 + - - -
1313A PHE* 4.3 5.0 - - - +
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Residues in contact with PHE 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A PHE* 3.4 35.2 - - + -
422A LYS 4.0 1.8 - - - -
423A GLN* 3.6 32.1 - - + -
434A VAL* 3.5 38.8 - - + -
435A THR 4.4 0.4 - - - -
436A CYS* 3.6 19.1 - - + -
438A MET* 3.9 15.0 - - + -
456A TYR* 4.6 1.6 - + + -
511A LEU* 2.8 31.5 + - + +
512A THR 4.0 1.8 - - - +
514A SER* 1.3 73.3 - - - +
516A PHE* 1.3 58.3 + - - +
518A LYS* 3.2 21.7 + - + +
519A PHE* 2.9 24.9 + - - +
1168A THR* 3.9 23.6 - - + -
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Residues in contact with PHE 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A MET* 3.7 9.8 - - + +
452A LEU* 5.1 2.7 - - + -
454A LEU* 3.7 30.3 - - + -
478A TRP* 4.2 14.1 - + - -
482A LEU* 3.8 14.1 - - + -
483A LEU* 3.6 33.2 - - + -
486A VAL* 3.5 44.0 - - + -
487A CYS* 4.4 6.3 - - - -
490A LEU* 3.9 10.5 - - + -
512A THR 3.4 10.4 + - - +
513A LEU 3.0 8.7 + - - +
515A PHE* 1.3 77.8 - - - +
517A PHE* 1.3 53.8 + - - +
519A PHE* 3.1 20.6 + + - +
520A TYR* 2.6 36.8 + - + +
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Residues in contact with PHE 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 3.8 31.9 - - + -
513A LEU 2.9 11.0 + - - +
514A SER* 3.2 8.7 + - - +
516A PHE* 1.3 76.3 - - - +
518A LYS* 1.3 57.2 + - - +
520A TYR* 3.1 7.4 + + - +
521A LEU* 2.9 63.7 + - + +
542A TYR* 3.9 12.8 - + - -
993A TRP* 3.4 44.6 - + - -
1167A LEU* 3.8 19.5 - - + -
1312A LYS* 4.9 4.3 - - - -
1313A PHE* 3.3 35.7 - + + -
5002A GOL 5.1 1.8 - - - -
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Residues in contact with LYS 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A PHE* 3.7 34.1 - - + -
514A SER 3.0 24.8 + - - +
515A PHE* 3.4 30.1 - - + +
517A PHE* 1.3 78.0 - - - +
519A PHE* 1.3 52.9 + - - +
521A LEU* 3.4 6.5 + - - +
522A THR* 2.6 39.2 + - - +
545A ALA 3.7 25.7 + - - +
546A THR* 4.7 0.9 - - - +
547A LEU 5.2 6.1 + - - -
548A LEU* 5.7 1.0 - - - +
1165A ASP* 4.8 6.3 + - - -
1167A LEU* 3.8 23.6 - - + -
1168A THR* 4.2 18.8 - - + +
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Residues in contact with PHE 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PHE* 4.2 5.6 - - + -
418A PHE 4.2 1.6 - - - -
419A SER* 3.4 28.9 - - - -
421A PHE* 3.9 7.1 - - + -
438A MET* 3.5 61.9 - - + -
439A ARG 3.9 3.1 - - - -
440A VAL* 3.8 21.8 - - + -
452A LEU* 4.3 5.6 - - + -
454A LEU* 4.1 9.9 - - + -
478A TRP* 3.9 19.3 - + - -
515A PHE 2.9 6.6 + - - +
516A PHE* 3.4 23.6 - + - +
518A LYS* 1.3 75.9 - - - +
520A TYR* 1.3 57.7 + - - +
522A THR* 3.3 3.8 + - - -
523A VAL* 2.9 47.5 + - + +
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Residues in contact with TYR 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A TRP* 3.1 63.1 + + - +
479A ASN* 2.8 44.8 - - - -
480A GLU* 3.0 6.0 + - - +
482A LEU* 4.4 6.7 - - + -
483A LEU* 3.9 40.6 - - + -
516A PHE* 2.6 20.6 + + + +
517A PHE* 3.3 10.1 - + - +
519A PHE* 1.3 73.6 - - - +
521A LEU* 1.3 72.0 + - + +
524A LEU* 3.1 39.1 + - + +
5002A GOL 3.7 16.1 + - - -
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Residues in contact with LEU 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A PHE* 2.9 54.0 + - + +
518A LYS* 3.9 2.9 - - - +
520A TYR* 1.3 80.5 - - + +
522A THR* 1.3 66.7 + - - +
524A LEU* 3.2 7.3 + - + +
525A LYS* 3.1 22.0 + - - +
538A LEU* 3.9 16.4 - - + +
542A TYR* 3.9 15.7 - - + +
545A ALA* 3.8 25.1 - - + -
546A THR* 3.7 15.9 - - + +
5002A GOL 3.5 33.4 - - - +
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Residues in contact with THR 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A SER* 4.1 14.5 + - - +
421A PHE* 4.7 5.4 - - - -
518A LYS* 2.6 22.5 + - - +
519A PHE* 3.6 5.6 - - - -
521A LEU* 1.3 76.2 - - - +
523A VAL* 1.3 58.7 + - + +
525A LYS* 3.2 7.6 + - + +
526A LYS* 2.9 56.5 + - + +
546A THR* 3.6 33.8 + - - +
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Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PHE* 4.3 12.1 - - + -
440A VAL* 4.1 4.9 - - + -
442A PHE* 3.6 33.7 - - + -
478A TRP* 3.5 26.7 - - + +
519A PHE* 2.9 52.4 + - + +
522A THR* 1.3 77.1 - - + +
524A LEU* 1.3 60.0 + - - +
526A LYS* 3.2 7.2 + - + +
527A LEU* 2.8 34.7 + - + +
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Residues in contact with LEU 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A MET* 3.9 22.4 - - + -
478A TRP* 3.7 26.9 - - + +
520A TYR* 3.1 44.1 + - + +
521A LEU* 3.2 8.7 + - + +
523A VAL* 1.3 76.7 - - - +
525A LYS* 1.3 57.6 + - - +
527A LEU* 3.2 6.3 + - - +
528A GLY* 2.8 26.2 + - - -
538A LEU* 4.4 18.4 - - + -
5002A GOL 3.6 25.1 - - - +
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Residues in contact with LYS 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LEU 3.1 12.6 + - - +
522A THR* 3.3 12.3 - - + +
524A LEU* 1.3 77.1 - - - +
526A LYS* 1.3 63.2 + - + +
528A GLY* 3.1 10.4 + - - -
529A LYS 4.6 0.7 - - - +
530A ASP* 3.1 28.8 - - - +
537A LYS* 5.9 4.5 - - - +
538A LEU* 4.3 18.5 - - + +
543A THR* 4.6 11.1 - - - +
546A THR* 3.1 34.5 + - + +
547A LEU* 3.9 20.2 - - - +
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Residues in contact with LYS 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLU* 2.6 34.2 + - - +
328A ARG* 4.7 8.2 - - - +
417A PHE* 3.7 45.1 - - + +
418A PHE 3.0 20.2 + - - +
419A SER* 4.4 0.8 + - - -
519A PHE* 6.2 0.4 - - - -
522A THR* 2.9 42.3 + - + +
523A VAL* 3.8 4.7 - - + +
525A LYS* 1.3 78.3 - - + +
527A LEU* 1.3 62.3 + - - +
529A LYS* 3.4 15.5 + - - +
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Residues in contact with LEU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP* 6.0 2.0 - - - +
417A PHE* 3.8 25.8 - - + -
442A PHE* 3.8 15.5 - - + -
446A SER 4.0 19.3 - - - +
447A MET* 3.9 37.9 - - + -
478A TRP* 4.5 5.4 - - + -
523A VAL* 2.8 35.9 + - + +
524A LEU* 3.5 5.2 - - - +
526A LYS* 1.3 72.2 - - - +
528A GLY* 1.3 54.6 + - - +
529A LYS* 2.6 36.1 + - - +
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Residues in contact with GLY 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A LEU 2.8 14.0 + - - -
525A LYS* 3.1 9.2 + - - -
527A LEU* 1.3 74.2 - - - +
529A LYS* 1.3 64.5 + - - +
530A ASP* 2.8 24.3 + - - +
----------------------------------------------------------
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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