Contacts of the helix formed by residues 474 - 506 (chain D) in PDB entry 1O1F
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 474 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D PHE* 3.8 23.1 + - - -
473D ASN* 1.3 76.1 - - - +
475D PHE* 1.3 55.9 + - - +
476D GLU* 3.2 17.5 + - - -
477D GLN* 2.6 42.6 + - - +
478D LEU 3.3 4.0 + - - -
590D TYR* 4.1 1.6 - - - -
591D ASN* 3.2 6.5 + - - -
593D SER 4.7 1.0 + - - -
595D TRP* 2.8 34.5 + - - -
598D MLY 4.2 10.9 + - - -
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Residues in contact with PHE 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D LEU* 6.5 0.7 - - + -
474D SER* 1.3 77.7 + - - +
476D GLU* 1.3 75.7 + - + +
478D LEU* 3.1 13.7 + - + +
479D CYS* 3.2 36.1 + - - -
533D PHE* 4.3 11.4 - + - -
536D LEU* 4.2 15.3 - - + -
595D TRP* 3.0 51.0 - + + +
598D MLY 3.9 27.6 - - + -
599D ASN* 3.6 24.9 - - + -
649D VAL* 3.8 26.2 - - + -
650D SER* 4.3 1.8 - - - -
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Residues in contact with GLU 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D LEU* 5.5 8.2 - - + +
474D SER* 3.9 7.6 - - - -
475D PHE* 1.3 89.2 + - + +
477D GLN* 1.3 81.0 + - - +
479D CYS* 3.3 7.0 + - - +
480D ILE* 3.1 27.4 + - + +
598D MLY 2.7 50.6 + - + +
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Residues in contact with GLN 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468D GLU 4.9 3.8 - - - +
470D PHE* 3.8 38.3 - - + -
472D PHE* 3.6 5.4 - - - +
473D ASN* 3.4 19.7 - - + +
474D SER* 2.6 50.9 + - - +
476D GLU* 1.3 88.8 + - - +
478D LEU* 1.3 58.5 + - - +
480D ILE* 4.5 3.4 - - + +
481D ASN* 2.7 45.5 + - - +
590D TYR* 4.0 3.1 - - + -
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Residues in contact with LEU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D SER 3.3 1.8 + - - +
475D PHE* 3.1 11.8 + - + +
477D GLN* 1.3 79.4 - - - +
479D CYS* 1.3 58.5 + - - +
482D PHE* 2.7 34.3 + - - +
526D ILE* 4.2 23.8 - - + -
532D ILE* 4.4 15.3 - - + -
533D PHE* 3.5 35.0 - - + -
536D LEU* 5.8 0.2 - - + -
579D PHE* 5.2 3.6 - - + -
581D LEU* 4.6 5.6 - - + -
583D HIS* 4.9 0.7 - - + -
590D TYR* 3.4 39.3 - - + +
595D TRP* 4.0 24.2 - - + -
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Residues in contact with CYS 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D LEU* 4.4 16.4 - - + -
475D PHE* 3.2 45.2 + - - -
476D GLU* 3.9 6.7 - - - +
477D GLN 3.2 0.2 - - - -
478D LEU* 1.3 80.5 - - - +
480D ILE* 1.3 54.4 + - - +
482D PHE* 3.5 2.7 - - - +
483D THR* 2.5 33.0 + - - -
533D PHE* 4.3 8.7 - - - -
649D VAL 5.8 0.2 - - - -
650D SER* 5.7 0.9 - - - -
653D PHE* 3.2 42.3 - - + -
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Residues in contact with ILE 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D LEU* 3.9 29.8 - - + -
464D ILE* 4.6 12.1 - - + -
465D ALA* 4.4 27.4 - - + +
466D GLY 4.5 9.2 - - - +
468D GLU* 5.1 1.8 - - + +
476D GLU* 3.1 17.3 + - + +
477D GLN* 3.9 2.7 - - + +
479D CYS* 1.3 75.7 - - - +
481D ASN* 1.3 79.0 + - - +
483D THR* 2.8 22.7 + - - +
484D ASN* 2.9 23.5 + - - +
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Residues in contact with ASN 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D PHE* 3.9 30.8 - - + +
468D GLU 3.7 21.8 + - - +
477D GLN* 2.7 28.0 + - - +
478D LEU 3.8 0.7 - - - +
480D ILE* 1.3 86.6 - - - +
482D PHE* 1.3 52.3 - - - +
484D ASN* 3.0 4.9 + - - +
485D GLU* 2.7 35.7 + - - +
583D HIS* 3.6 12.8 - - + -
588D VAL* 4.2 6.9 - - - +
590D TYR* 3.1 27.5 + - - +
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Residues in contact with PHE 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D LEU 2.7 19.0 + - - +
479D CYS* 3.5 3.1 - - - +
481D ASN* 1.3 78.3 - - - +
483D THR* 1.3 64.4 + - - +
485D GLU* 3.4 6.5 + - + +
486D MLY 3.4 34.1 + - + +
523D ILE* 4.2 19.1 - - + -
526D ILE* 3.7 41.3 - - + -
527D GLU* 3.5 33.4 - - + -
533D PHE* 4.0 23.3 - + + -
583D HIS* 4.6 1.2 - - - -
653D PHE* 4.2 6.1 - + - -
654D ARG* 4.7 9.4 - - + -
657D LEU* 3.5 30.1 - - + -
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Residues in contact with THR 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269D LEU* 5.1 1.2 - - - +
464D ILE* 4.4 22.0 - - + -
479D CYS 2.5 23.6 + - - -
480D ILE* 2.8 14.2 + - - +
482D PHE* 1.3 77.5 - - - +
484D ASN* 1.3 66.4 + - - +
486D MLY 3.2 5.0 + - - +
487D LEU* 3.1 39.8 + - + +
653D PHE* 3.3 16.2 - - + -
657D LEU* 3.9 27.8 - - + -
660D LEU* 5.2 1.6 - - + -
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Residues in contact with ASN 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D THR* 4.0 10.6 + - - +
465D ALA 2.5 30.5 + - - +
466D GLY* 2.9 5.7 - - - -
467D PHE* 2.8 40.7 - - + +
480D ILE* 2.9 19.8 + - - +
481D ASN 3.7 5.8 - - - +
483D THR* 1.3 76.2 - - - +
485D GLU* 1.3 63.4 + - - +
486D MLY 2.8 6.3 + - - -
487D LEU* 3.0 17.9 + - - +
488D GLN* 2.9 24.4 + - - +
584D TYR* 3.9 8.5 + - - +
673D ARG* 5.4 2.9 + - - -
697D CYS 6.0 0.4 - - - -
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Residues in contact with GLU 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D PHE* 4.1 1.8 - - + -
481D ASN 2.7 18.7 + - - +
482D PHE* 4.1 7.4 - - + +
484D ASN* 1.3 72.2 - - - +
486D MLY 1.3 60.2 + - - +
488D GLN 4.0 0.2 - - - -
489D GLN* 3.5 14.2 + - - +
519D LEU* 3.7 19.1 - - + +
522D CYS* 4.0 16.8 - - + +
523D ILE* 4.0 18.0 - - + +
526D ILE* 6.3 0.9 - - + -
582D VAL 4.3 0.2 - - - +
583D HIS* 2.5 44.0 + - - +
584D TYR* 2.5 52.4 + - + +
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Residues in contact with MLY 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D PHE* 3.4 26.7 + - + +
483D THR* 3.2 11.4 + - - +
484D ASN 2.9 0.2 - - - -
485D GLU* 1.3 79.3 + - - +
487D LEU* 1.3 65.4 + - - +
489D GLN* 3.1 9.1 + - - +
490D PHE* 3.0 20.9 + - - +
523D ILE* 4.4 20.0 - - + -
527D GLU* 2.8 44.9 - - - -
657D LEU* 4.3 20.6 - - + -
658D ASN* 3.1 37.0 - - - -
661D MET* 4.2 30.6 - - + +
665D ARG* 4.8 16.6 + - - -
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Residues in contact with LEU 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LEU* 4.6 15.7 - - + -
178D THR* 5.4 4.3 - - - +
462D LEU* 4.6 12.6 - - + -
464D ILE* 5.2 7.0 - - + -
465D ALA 5.6 1.1 - - - +
483D THR* 3.1 36.8 + - + +
484D ASN* 3.4 23.6 - - - +
486D MLY 1.3 77.5 + - - +
488D GLN* 1.3 57.7 + - - +
490D PHE* 2.8 28.3 - - + +
491D PHE* 3.1 8.8 + - - +
657D LEU* 6.0 0.2 - - + -
660D LEU* 5.5 3.6 - - + -
661D MET* 3.6 25.1 - - + -
664D LEU* 3.9 15.0 - - + -
671D PHE* 4.8 2.5 - - + -
673D ARG* 5.1 13.5 - - - +
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Residues in contact with GLN 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D PHE* 5.6 0.7 - - - -
484D ASN 2.9 6.7 + - - +
485D GLU 3.8 3.4 - - - +
487D LEU* 1.3 72.1 - - - +
489D GLN* 1.3 57.4 + - - +
490D PHE 2.9 4.5 - - - -
491D PHE* 2.9 40.7 + - - +
492D ASN* 2.7 45.1 + - - +
519D LEU* 4.1 6.3 - - + -
584D TYR* 3.4 49.0 + - + +
673D ARG* 4.6 8.6 + - - +
698D ASN 3.9 6.4 - - - +
699D GLY* 3.5 29.4 + - - -
702D GLU* 4.9 9.5 - - + +
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Residues in contact with GLN 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D GLU 3.5 9.9 + - - +
486D MLY 3.1 11.5 + - - +
488D GLN* 1.3 77.9 - - - +
490D PHE* 1.3 62.1 + - - +
492D ASN* 3.8 5.5 - - - +
493D HIS* 3.1 24.9 + - + +
516D GLY* 3.2 37.1 + - - +
517D MET* 4.1 0.8 - - - +
519D LEU* 3.9 13.4 - - + +
520D ALA* 3.4 31.1 - - - +
523D ILE* 3.7 15.9 - - + +
665D ARG* 5.8 2.1 + - - -
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Residues in contact with PHE 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D SER* 5.1 0.4 - - - -
176D LEU* 4.5 12.1 - - + -
486D MLY 3.0 8.7 + - - +
487D LEU* 2.8 22.9 - - - +
489D GLN* 1.3 80.5 - - - +
491D PHE* 1.3 60.7 + - - +
493D HIS* 3.9 5.4 - + + +
494D HIS* 3.4 18.3 + - + +
661D MET* 4.1 19.5 - - + -
664D LEU* 3.3 48.0 - - + -
665D ARG* 4.3 18.2 - - + -
667D THR 4.9 0.4 - - - -
669D PRO* 3.5 37.9 - - + -
671D PHE* 4.1 10.8 - + - -
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Residues in contact with PHE 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 4.0 26.0 - - + -
122D PHE* 3.3 40.4 - + - -
487D LEU 3.8 5.2 - - - +
488D GLN* 2.9 30.7 + - - +
490D PHE* 1.3 77.8 - - - +
492D ASN* 1.3 71.4 + - - +
493D HIS 2.7 5.5 + - - -
494D HIS* 2.6 27.1 + + - +
495D MET* 2.8 28.5 + - + +
671D PHE* 3.2 51.4 - + + -
673D ARG* 5.9 2.0 - - - +
699D GLY 4.7 0.7 - - - -
703D GLY* 4.3 16.6 - - - -
706D ILE* 5.0 3.1 - - + -
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Residues in contact with ASN 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D GLN* 2.7 44.4 + - - +
489D GLN* 3.8 4.9 - - - +
491D PHE* 1.3 77.4 - - - +
493D HIS* 1.3 59.6 + - - +
495D MET* 3.9 5.0 - - - +
496D PHE* 3.3 12.8 + - - +
515D PHE* 3.4 48.1 + - + +
516D GLY* 3.7 4.3 - - - +
518D ASP* 5.6 0.4 - - - +
519D LEU* 3.7 12.7 - - - +
702D GLU* 3.7 26.5 + - - +
706D ILE* 4.1 13.5 - - - +
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Residues in contact with HIS 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D GLN* 3.1 18.2 + - + +
490D PHE* 3.9 6.3 - + + +
491D PHE 2.7 5.1 + - - -
492D ASN* 1.3 71.9 - - - +
494D HIS* 1.3 54.7 + - - +
495D MET 2.9 4.0 - - - -
496D PHE* 2.5 27.7 + + - +
497D VAL* 2.7 41.9 + - + +
514D ASP* 2.4 39.9 + - - +
516D GLY* 4.9 0.7 - - - -
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Residues in contact with HIS 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 4.2 23.4 - - + +
490D PHE* 3.4 12.6 + - + +
491D PHE* 2.6 14.3 + + - +
493D HIS* 1.3 80.0 - - - +
495D MET* 1.3 58.8 + - - +
497D VAL* 3.5 9.7 + - - +
498D LEU* 2.9 52.7 + - + +
668D HIS* 3.6 31.8 + + - -
669D PRO* 3.6 29.1 + - + +
671D PHE* 4.2 18.4 - + - -
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Residues in contact with MET 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLY* 5.2 5.6 - - - -
121D LEU* 3.5 38.4 - - + +
491D PHE* 2.8 32.2 + - + +
492D ASN* 4.0 9.0 - - - +
494D HIS* 1.3 78.3 - - - +
496D PHE* 1.3 59.7 + - - +
498D LEU* 3.5 7.4 - - + +
499D GLU* 2.7 43.2 + - + +
515D PHE* 4.5 0.9 - - - -
703D GLY* 4.3 8.5 - - - +
706D ILE* 3.7 30.1 - - + -
707D CYS* 4.0 24.0 - - - -
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Residues in contact with PHE 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492D ASN 3.3 12.8 + - - +
493D HIS* 2.5 16.4 + + - +
495D MET* 1.3 74.8 - - - +
497D VAL* 1.2 81.5 + - + +
499D GLU* 3.8 1.0 - - - +
500D GLN* 3.3 45.3 + - - +
512D PHE* 3.0 41.5 - + - -
513D ILE* 3.3 7.0 - - - -
514D ASP* 2.9 50.9 - - + -
515D PHE* 3.4 18.6 - + + +
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Residues in contact with VAL 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D HIS* 2.7 44.3 + - + +
494D HIS* 3.5 11.9 - - + +
496D PHE* 1.2 92.9 - - + +
498D LEU* 1.3 66.3 + - + +
500D GLN* 3.6 9.7 + - - +
501D GLU* 3.5 24.4 + - - +
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Residues in contact with LEU 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 4.1 33.9 - - + -
494D HIS* 2.9 39.6 + - + +
495D MET* 3.5 6.7 - - + +
497D VAL* 1.3 79.7 - - + +
499D GLU* 1.3 68.1 + - - +
501D GLU* 3.0 31.8 + - - +
502D GLU* 3.6 3.3 + - - +
668D HIS* 5.3 3.4 - - - +
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Residues in contact with GLU 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D MET* 2.7 36.1 + - + +
496D PHE 3.8 0.4 - - - +
498D LEU* 1.3 71.8 - - - +
500D GLN* 1.3 55.0 + - - +
502D GLU* 2.8 39.5 + - - +
503D TYR* 3.0 36.9 + - - -
512D PHE* 3.6 20.6 - - + -
515D PHE* 4.7 8.3 - - + -
706D ILE* 4.9 10.3 - - + +
707D CYS* 5.2 9.9 - - - +
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Residues in contact with GLN 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496D PHE* 3.3 38.3 + - - +
497D VAL* 3.9 8.3 - - - +
498D LEU 3.3 0.6 - - - -
499D GLU* 1.3 78.3 - - - +
501D GLU* 1.3 60.6 + - - +
503D TYR* 3.9 6.7 + - - +
504D MLY 3.2 22.1 + - + +
510D TRP 5.8 1.0 + - - -
512D PHE* 3.3 35.2 + - + +
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Residues in contact with GLU 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D VAL* 3.5 20.4 + - - +
498D LEU* 3.0 23.2 + - - +
499D GLU 2.8 0.8 + - - -
500D GLN* 1.3 75.1 - - - +
502D GLU* 1.3 56.1 + - - +
504D MLY 2.9 9.7 + - + +
505D MLY 2.6 69.0 + - - +
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Residues in contact with GLU 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498D LEU 3.6 2.7 + - - +
499D GLU* 2.8 16.1 + - - +
501D GLU* 1.3 74.5 - - - +
503D TYR* 1.3 62.1 + - + +
504D MLY 2.6 15.6 + - - -
505D MLY 2.7 32.5 + - - +
506D GLU* 2.7 44.8 + - + +
508D ILE* 6.1 0.9 - - + -
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Residues in contact with TYR 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499D GLU* 3.0 36.3 + - - -
500D GLN* 4.1 5.6 - - - +
501D GLU 3.4 0.2 - - - -
502D GLU* 1.3 85.3 - - + +
504D MLY 1.3 56.1 + - - +
507D GLY* 3.1 5.1 + - - -
508D ILE* 2.9 73.9 + - + +
510D TRP* 3.3 48.8 + + + +
512D PHE* 3.6 22.4 - + - -
707D CYS 5.5 2.3 + - - -
709D LYS 5.9 2.8 - - - -
710D GLY* 6.0 2.1 - - - -
714D ARG* 5.3 11.3 + - - -
762D HIS* 4.8 0.5 - - - -
766D PHE* 4.6 7.2 - + - -
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Residues in contact with MLY 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500D GLN* 3.2 16.9 + - + +
501D GLU* 2.9 14.3 + - + +
502D GLU 2.6 5.3 + - - -
503D TYR* 1.3 74.9 + - - +
505D MLY 1.3 63.2 + - - +
507D GLY* 3.8 4.4 + - - -
762D HIS* 3.8 17.3 + - + -
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Residues in contact with MLY 505 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501D GLU* 2.6 57.7 + - - +
502D GLU* 3.3 29.2 + - - +
504D MLY 1.3 77.3 + - - +
506D GLU* 1.3 73.1 + - - +
762D HIS* 4.5 3.1 + - - +
763D THR* 4.8 1.0 + - - -
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Residues in contact with GLU 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502D GLU* 2.7 37.5 + - + +
505D MLY 1.3 87.7 + - - +
507D GLY* 1.3 60.5 + - - +
508D ILE* 3.9 22.0 - - + -
762D HIS* 2.9 16.5 - - - +
763D THR* 3.0 26.8 + - - +
764D MLY 3.0 52.4 - - + -
766D PHE* 5.1 0.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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