Contacts of the helix formed by residues 579 - 609 (chain D) in PDB entry 3RMD
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 ASP 579 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D HIS* 5.5 1.8 - - - -
427D PRO* 4.7 8.5 - - + +
430D ILE* 4.6 10.2 - - - +
570D LEU* 4.4 2.2 + - - +
577D TYR 3.6 4.6 + - - +
578D TYR* 1.3 87.1 - - - +
580D LEU* 1.3 66.9 + - - +
581D ARG* 2.8 34.9 + - - +
582D ASN* 2.8 46.2 + - + +
583D ALA* 2.9 11.8 + - - +
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Residues in contact with LEU 580 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D GLN* 4.9 25.1 - - + +
390D PRO 4.9 7.0 - - - +
391D TYR* 5.6 5.4 - - + -
392D PRO* 5.9 2.0 - - + -
578D TYR* 3.0 37.3 - - + +
579D ASP* 1.3 72.4 + - - +
581D ARG* 1.3 60.6 - - + +
583D ALA* 3.2 5.3 + - + +
584D THR* 2.7 48.0 + - - +
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Residues in contact with ARG 581 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D ILE* 4.0 13.1 - - + +
432D GLY* 5.9 0.4 - - - -
433D THR* 4.3 11.3 - - - +
459D ASN* 3.2 10.5 + - - +
461D MET* 3.1 48.8 - - - +
463D TYR* 4.2 0.8 + - - -
579D ASP* 2.8 27.6 + - - +
580D LEU* 1.3 83.1 - - + +
582D ASN* 1.3 60.9 + - - +
584D THR* 3.3 5.0 - - - -
585D ALA* 2.8 25.2 + - - +
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Residues in contact with ASN 582 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D ILE* 3.4 19.5 - - + +
426D SER* 3.2 34.4 + - - +
427D PRO* 3.3 12.5 - - - +
430D ILE* 4.0 5.7 - - - +
463D TYR* 2.7 28.0 + - - -
570D LEU* 6.1 4.0 - - + -
577D TYR 5.4 1.0 + - - +
579D ASP* 2.8 30.9 + - + +
581D ARG* 1.3 71.5 - - - +
583D ALA* 1.3 67.9 + - - +
584D THR 3.1 1.6 - - - -
585D ALA* 3.4 0.3 - - - +
586D ILE* 2.9 33.3 + - + +
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Residues in contact with ALA 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D TYR* 3.1 33.9 - - + +
567D TYR* 3.1 20.8 + - - -
570D LEU 4.5 4.6 + - - +
571D GLY* 4.5 2.9 - - - -
578D TYR* 4.4 12.6 - - + +
579D ASP 2.9 10.4 + - - +
580D LEU* 3.4 13.5 - - + +
582D ASN* 1.3 77.5 - - - +
584D THR* 1.3 62.6 + - - +
586D ILE* 3.4 7.2 + - - +
587D THR* 3.2 13.5 + - - +
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Residues in contact with THR 584 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D TYR* 4.5 1.0 - - - -
392D PRO* 4.4 22.9 - - + +
459D ASN* 3.3 19.7 - - + +
580D LEU* 2.7 30.5 + - - +
581D ARG* 3.3 11.6 - - - -
583D ALA* 1.3 75.3 - - - +
585D ALA* 1.3 65.9 + - - -
587D THR* 3.0 6.8 + - - -
588D THR* 2.8 39.3 + - - +
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Residues in contact with ALA 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D ILE* 3.4 20.0 - - + -
457D SER* 3.5 15.1 - - - +
459D ASN* 2.8 28.2 - - - +
461D MET* 4.3 0.4 - - + -
463D TYR* 3.6 13.2 - - + +
581D ARG 2.8 12.9 + - - +
582D ASN 3.4 5.8 - - - +
584D THR* 1.3 70.9 - - - +
586D ILE* 1.3 64.8 + - - +
588D THR* 3.8 0.9 - - - -
589D PHE* 2.9 26.0 + - - +
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Residues in contact with ILE 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D TYR* 3.0 41.1 - - + +
419D ILE* 3.7 12.6 - - + +
420D ILE* 3.6 29.4 - - + -
425D ILE* 3.4 25.8 - - + -
567D TYR* 3.8 22.0 - - + -
570D LEU* 4.0 13.0 - - + -
582D ASN* 2.9 18.5 + - + +
583D ALA* 3.5 7.4 - - - +
584D THR 3.2 0.2 - - - -
585D ALA* 1.3 77.4 - - - +
587D THR* 1.3 62.5 + - - +
589D PHE* 3.3 3.1 + - - +
590D GLY 3.1 16.5 + - - -
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Residues in contact with THR 587 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D TYR* 4.4 4.3 - - + -
392D PRO* 2.9 33.3 + - - +
393D GLY* 4.0 12.0 - - - +
394D ALA* 5.3 0.3 - - - -
416D TYR* 3.5 19.6 + - + +
567D TYR* 2.8 39.7 - - + +
583D ALA 3.2 5.3 + - - +
584D THR* 3.0 13.2 + - - -
586D ILE* 1.3 74.8 - - - +
588D THR* 1.3 71.7 + - - +
590D GLY* 3.1 2.9 + - - -
591D GLN* 3.0 23.6 + - - +
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Residues in contact with THR 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D PRO* 5.1 6.0 - - - +
439D LEU* 4.0 15.9 - - + +
458D PRO* 3.8 15.5 - - + -
459D ASN* 3.5 38.4 - - + +
584D THR* 2.8 27.5 + - - +
585D ALA 3.8 2.9 - - - -
587D THR* 1.3 76.8 + - - +
589D PHE* 1.3 69.4 + - - +
591D GLN* 2.9 19.3 + - - +
592D MET* 3.0 11.8 + - - +
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Residues in contact with PHE 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D ILE* 3.3 24.2 - - + -
422D GLN* 3.2 15.7 - - - -
423D VAL* 3.2 29.6 - - + -
456D CYS 3.5 16.4 - - - -
457D SER* 4.0 3.4 - - - -
458D PRO* 3.9 21.5 - - + +
585D ALA 2.9 19.4 + - - +
586D ILE 3.5 4.3 - - - +
588D THR* 1.3 75.0 - - - +
590D GLY* 1.3 64.3 + - - +
592D MET* 3.1 5.4 + - - +
593D ALA* 2.9 20.4 + - + -
670D MET* 3.7 27.8 - - + -
674D MET* 4.2 11.4 - - + -
676D ASN* 3.2 24.5 - - - -
681D MET* 4.1 9.4 - - - -
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Residues in contact with GLY 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415D LEU* 4.4 15.8 - - - +
416D TYR* 5.0 5.4 - - - -
419D ILE* 3.2 18.0 - - - +
586D ILE 3.1 11.8 + - - -
587D THR 3.1 3.8 + - - -
588D THR 3.1 0.4 - - - -
589D PHE* 1.3 77.4 - - - +
591D GLN* 1.3 62.9 + - - +
593D ALA* 3.1 6.1 + - - +
594D LEU* 2.9 25.7 + - - +
622D THR 5.5 1.3 - - - -
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Residues in contact with GLN 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393D GLY 3.9 19.8 + - - +
394D ALA* 4.3 4.3 + - - +
395D PHE* 2.6 59.6 - - - +
416D TYR* 5.6 0.2 + - - -
439D LEU* 4.0 20.0 - - + +
587D THR 3.0 8.9 + - - +
588D THR* 2.9 14.3 + - - +
590D GLY* 1.3 74.8 - - - +
592D MET* 1.3 65.0 + - - +
594D LEU* 3.6 4.7 + - - +
595D GLN* 3.3 31.1 + - - +
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Residues in contact with MET 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D LEU* 4.4 8.2 - - + +
442D TYR* 3.2 45.8 - - + +
443D ILE* 4.4 19.6 - - + +
458D PRO* 3.1 30.7 - - + -
588D THR 3.0 10.1 + - - +
589D PHE* 3.3 11.4 - - - +
591D GLN* 1.3 73.8 - - - +
593D ALA* 1.3 55.0 + - - +
595D GLN* 3.0 4.2 + - - +
596D TRP* 2.7 39.6 + - + +
670D MET* 4.0 25.4 - - + +
673D TYR* 4.6 6.7 - - + -
674D MET* 3.9 20.2 - - + -
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Residues in contact with ALA 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D LEU* 5.7 1.8 - - + -
415D LEU* 4.8 7.6 - - + -
589D PHE* 2.9 17.5 + - + +
590D GLY* 3.5 11.4 - - - +
592D MET* 1.3 72.9 - - - +
594D LEU* 1.3 63.4 + - - +
596D TRP* 3.4 0.7 - - - +
597D ILE* 3.0 27.2 + - - +
667D PHE* 3.9 10.8 - - + -
670D MET* 3.8 30.9 - - + -
681D MET* 4.5 14.4 - - - -
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Residues in contact with LEU 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D PHE* 3.9 30.1 - - + +
397D LYS 5.7 2.0 - - - +
412D LEU* 5.1 7.5 - - + +
590D GLY 2.9 15.4 + - - +
591D GLN* 3.7 4.5 - - - +
593D ALA* 1.3 75.9 - - - +
595D GLN* 1.3 72.0 + - + +
597D ILE* 3.2 10.7 - - - +
598D GLU* 3.0 50.5 + - - +
620D GLY 5.0 0.9 - - - -
621D ASP 3.6 23.1 - - - +
622D THR* 4.0 22.2 - - - +
623D ASP* 4.6 1.1 - - - +
624D SER 3.9 1.1 - - - +
625D ILE* 3.3 28.2 - - + +
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Residues in contact with GLN 595 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D PHE* 3.4 28.3 - - + -
439D LEU* 5.5 1.7 - - - +
440D HIS* 5.4 3.8 + - - -
443D ILE* 2.8 44.6 - - + +
591D GLN* 3.3 18.9 + - - +
592D MET 3.0 6.3 + - - +
594D LEU* 1.3 91.6 - - + +
596D TRP* 1.3 61.1 + - - +
598D GLU* 3.3 15.2 - - - +
599D ARG* 2.9 28.1 + - - +
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Residues in contact with TRP 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D TYR 3.2 22.7 - - - -
443D ILE* 3.0 30.5 - - - +
445D ALA* 3.5 26.5 - - + -
592D MET* 2.7 24.8 + - + +
593D ALA 3.4 4.7 - - - +
595D GLN* 1.3 72.5 - - - +
597D ILE* 1.3 62.1 + - - +
599D ARG* 2.9 17.3 + - - +
600D LYS* 2.8 37.7 + - + +
666D GLY 2.9 22.5 + - - -
667D PHE* 4.2 8.7 - + - -
669D GLU* 3.1 31.6 - - + -
670D MET* 3.3 48.1 - - + +
673D TYR* 3.8 18.4 - + - -
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Residues in contact with ILE 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D LEU* 5.3 1.3 - - + -
593D ALA 3.0 7.6 + - - +
594D LEU* 3.2 15.9 - - - +
596D TRP* 1.3 76.9 - - - +
598D GLU* 1.3 60.7 + - - +
600D LYS* 3.8 22.0 - - + -
601D VAL* 2.7 43.3 + - + +
625D ILE* 4.3 11.2 - - + -
663D ILE* 3.6 34.5 - - + +
666D GLY 4.7 0.2 - - - -
667D PHE* 3.5 30.5 - - + +
683D MET* 3.5 36.1 - - + -
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Residues in contact with GLU 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D LYS* 3.7 35.3 + - - +
594D LEU* 3.0 49.2 + - - +
595D GLN* 3.3 18.0 - - - +
596D TRP 3.1 0.2 - - - -
597D ILE* 1.3 76.7 - - - +
599D ARG* 1.3 65.3 + - - +
601D VAL* 3.5 5.4 - - - +
602D ASN* 3.0 29.2 + - - +
617D VAL* 3.9 14.2 - - + +
620D GLY* 4.4 7.4 - - - -
625D ILE* 4.1 22.2 - - + -
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Residues in contact with ARG 599 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D ILE* 3.1 26.1 + - + -
444D ASN* 3.0 49.5 + - - +
445D ALA* 4.1 2.8 - - - +
595D GLN 2.9 12.0 + - - +
596D TRP* 2.9 29.8 + - - +
598D GLU* 1.3 78.1 - - - +
600D LYS* 1.3 87.8 + - - +
602D ASN* 3.4 4.9 + - - +
603D GLU* 3.0 48.6 + - + +
669D GLU* 3.9 19.4 + - - -
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Residues in contact with LYS 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596D TRP* 2.8 36.0 + - + +
597D ILE* 3.6 17.7 - - + +
599D ARG* 1.3 94.0 - - - +
601D VAL* 1.3 64.4 + - - +
603D GLU* 2.9 20.9 + - - +
604D TYR* 2.9 23.5 + - - +
662D ALA 5.5 2.9 - - - +
663D ILE* 6.0 0.4 - - - -
666D GLY* 4.0 20.1 - - - -
669D GLU* 2.6 46.0 + - - -
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Residues in contact with VAL 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D PHE* 6.5 0.9 - - + -
597D ILE* 2.7 42.1 + - + +
598D GLU 3.5 3.8 - - - +
600D LYS* 1.3 72.1 - - - +
602D ASN* 1.3 65.3 + - - +
604D TYR* 3.1 8.5 + - - +
605D LEU* 3.0 45.2 + - + +
617D VAL* 3.5 26.2 - - + -
625D ILE* 5.5 4.0 - - + -
627D VAL* 4.3 5.2 - - + -
659D MET* 4.0 13.2 - - + -
663D ILE* 4.4 20.0 - - + -
683D MET* 4.9 4.0 - - + -
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Residues in contact with ASN 602 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D LYS* 5.3 1.0 + - - -
598D GLU 3.0 14.0 + - - +
599D ARG* 3.7 5.6 - - - +
601D VAL* 1.3 74.3 - - - +
603D GLU* 1.3 61.7 + - + +
606D ASN* 3.1 32.1 + - - +
614D GLU 4.3 5.4 - - - +
615D ALA* 3.6 12.1 - - - +
616D PHE* 3.4 25.2 + - - +
617D VAL* 3.1 47.3 - - - +
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Residues in contact with GLU 603 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599D ARG* 3.0 45.8 + - + +
600D LYS* 2.9 34.2 + - - +
602D ASN* 1.3 75.9 - - + +
604D TYR* 1.3 65.9 + - - +
606D ASN* 3.9 3.6 - - - +
607D GLU* 3.2 25.6 + - - +
----------------------------------------------------------
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Residues in contact with TYR 604 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600D LYS 2.9 11.5 + - - +
601D VAL* 3.4 10.1 - - - +
603D GLU* 1.3 73.5 - - - +
605D LEU* 1.3 86.6 + - + +
607D GLU* 3.1 5.5 + - - +
608D VAL* 2.9 50.8 + - + +
654D PHE* 4.6 2.7 - + - -
658D ARG* 3.1 54.9 + - + +
659D MET* 4.4 8.1 - - + -
662D ALA* 3.4 29.2 - - + -
665D ARG* 4.4 10.1 - - - -
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Residues in contact with LEU 605 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D VAL* 3.0 23.3 + - + +
602D ASN 4.4 0.2 - - - +
604D TYR* 1.3 85.2 - - + +
606D ASN* 1.3 53.0 + - - +
608D VAL* 3.2 2.9 + - - -
609D CYS* 2.7 42.1 + - - +
616D PHE* 3.2 49.1 - - + -
627D VAL* 4.7 7.2 - - + -
632D ILE* 4.3 9.6 - - + -
654D PHE* 3.8 29.6 - - + -
659D MET* 3.4 36.3 - - + -
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Residues in contact with ASN 606 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D ASN 3.1 21.1 + - - +
603D GLU* 3.9 4.3 - - - +
605D LEU* 1.3 76.0 - - - +
607D GLU* 1.3 59.3 + - + +
609D CYS 3.3 0.3 + - - -
610D GLY 2.8 8.0 + - - -
611D THR* 2.8 54.1 + - - +
612D GLU* 3.0 4.6 - - - +
613D GLY* 2.8 18.1 - - - +
614D GLU 2.5 50.5 - - - +
616D PHE* 3.0 16.0 - - - -
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Residues in contact with GLU 607 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902B ASP* 4.0 12.6 - - - +
603D GLU 3.2 14.8 + - - +
604D TYR* 3.1 6.2 + - - +
606D ASN* 1.3 80.0 - - + +
608D VAL* 1.3 61.9 + - + +
610D GLY* 3.1 17.1 + - - -
611D THR 5.0 1.6 - - - +
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Residues in contact with VAL 608 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B PHE* 3.3 40.9 - - + -
902B ASP* 2.9 34.9 + - - +
604D TYR* 2.9 55.3 + - + +
605D LEU* 3.9 5.8 - - - +
607D GLU* 1.3 77.9 - - + +
609D CYS* 1.3 59.5 + - - +
635D LYS* 4.3 0.2 - - - -
654D PHE* 4.6 12.1 - - + -
658D ARG* 5.5 5.4 - - + +
----------------------------------------------------------
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Residues in contact with CYS 609 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B PHE* 4.6 12.1 - - - -
902B ASP 5.6 0.4 - - - -
605D LEU* 2.7 25.8 + - - +
608D VAL* 1.3 82.1 - - - +
610D GLY* 1.3 63.8 + - - +
611D THR* 3.3 20.6 + - + +
616D PHE* 3.8 24.5 - - + -
631D LYS* 4.4 18.6 - - + +
632D ILE* 4.5 11.7 - - - -
635D LYS* 3.0 31.6 + - + +
654D PHE* 5.9 0.7 - - - -
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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