Contacts of the helix formed by residues 553 - 583 (chain B) in PDB entry 1XSK
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 553 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG* 5.8 2.4 + - - -
549B TRP* 5.8 3.9 - - - +
552B ASP* 1.3 72.7 - - - +
554B GLU* 1.3 68.1 + - - +
555B SER 3.0 1.8 - - - -
556B CYS* 2.8 27.4 + - - +
557B ASP* 3.4 9.1 + - - +
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Residues in contact with GLU 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LYS* 2.7 33.2 + - - +
552B ASP* 2.8 12.3 + - - +
553B ASP* 1.3 75.1 - - - +
555B SER* 1.3 62.3 + - - +
557B ASP* 2.9 30.2 + - + +
558B VAL* 3.0 18.4 + - + +
656B PHE* 3.3 24.4 + - + +
657B LEU* 5.6 2.7 - - + -
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Residues in contact with SER 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B TYR* 3.8 16.1 - - - -
525B LYS* 3.5 20.5 - - - +
548B PRO* 3.4 16.2 - - - -
551B TYR* 3.6 11.4 - - - +
552B ASP* 2.4 53.7 + - - -
553B ASP 3.0 0.2 - - - -
554B GLU* 1.3 69.7 - - - +
556B CYS* 1.3 56.4 + - - +
558B VAL* 3.3 2.6 + - - +
559B VAL* 2.9 34.1 + - - +
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Residues in contact with CYS 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG* 3.3 36.1 - - - -
298B LEU* 3.4 11.0 - - + +
548B PRO* 3.5 25.4 - - - -
549B TRP* 3.8 11.7 - - - -
552B ASP 4.5 2.0 - - - -
553B ASP* 2.8 15.4 + - - +
555B SER* 1.3 76.6 - - - +
557B ASP* 1.3 62.4 + - - +
559B VAL* 3.9 1.1 - - - -
560B ARG* 2.9 42.3 + - - +
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Residues in contact with ASP 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ASP* 3.9 6.2 - - - +
554B GLU* 2.9 24.6 + - + +
556B CYS* 1.3 77.4 - - - +
558B VAL* 1.3 58.3 + - - +
560B ARG* 2.6 34.9 + - - +
561B PHE* 2.8 32.1 + - - +
657B LEU* 3.9 18.0 - - + +
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Residues in contact with VAL 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LYS* 3.6 29.6 - - + +
528B CYS* 3.6 28.7 - - + -
554B GLU* 3.0 18.2 + - + +
555B SER 3.5 7.6 - - - +
557B ASP* 1.3 76.7 - - - +
559B VAL* 1.3 62.9 + - - +
560B ARG 3.2 0.2 + - - -
561B PHE* 3.2 1.3 + - - -
562B PHE* 3.1 46.1 + - + +
656B PHE* 3.3 25.8 - - + +
657B LEU* 3.6 13.9 - - + -
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Residues in contact with VAL 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.3 17.5 - - + -
293B MET* 5.0 2.5 - - + -
298B LEU* 4.7 10.1 - - + -
524B TYR* 3.9 8.3 - - + +
528B CYS* 3.7 27.8 - - - -
532B LEU* 4.9 6.2 - - + +
539B LEU* 5.1 4.9 - - + -
548B PRO* 3.6 29.6 - - + -
555B SER 2.9 22.0 + - - +
556B CYS 3.9 3.4 - - - +
558B VAL* 1.3 75.3 - - - +
560B ARG* 1.3 57.2 + - - +
562B PHE* 4.7 1.7 - - - +
563B THR* 2.5 46.0 + - - +
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Residues in contact with ARG 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG* 2.7 31.1 + - - +
297B ASN* 2.9 35.0 - - - +
298B LEU* 3.2 23.8 - - + +
299B PRO* 4.5 3.1 - - + -
556B CYS* 2.9 19.7 + - - +
557B ASP* 2.6 38.8 + - - +
559B VAL* 1.3 74.9 - - - +
561B PHE* 1.3 68.0 + - - +
563B THR* 4.5 3.1 - - - -
564B GLN* 3.0 53.9 + - + +
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Residues in contact with PHE 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ASP 2.8 19.1 + - - +
558B VAL* 3.6 4.9 - - - +
560B ARG* 1.3 77.5 - - - +
562B PHE* 1.3 93.4 + + - +
564B GLN* 3.8 9.0 + - - +
565B LEU* 3.0 34.1 + - + +
639B TRP* 3.7 34.5 - + - -
657B LEU* 3.7 44.6 - - + -
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Residues in contact with PHE 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B CYS* 4.8 0.7 - - + -
529B ALA* 3.5 34.3 - - + -
532B LEU* 3.6 26.3 - - + +
533B LEU* 4.3 7.6 - - + -
558B VAL* 3.1 41.9 + - + +
559B VAL* 4.7 0.9 - - - +
561B PHE* 1.3 95.8 - + - +
563B THR* 1.3 60.5 + - - +
565B LEU* 3.5 16.4 - - + +
566B LYS* 2.9 29.8 + - - +
639B TRP* 4.0 5.4 - + - -
656B PHE 3.9 10.1 - - - -
657B LEU* 3.8 22.7 - - - -
658B SER 4.3 1.1 - - - -
659B LEU* 3.7 24.9 - - + -
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Residues in contact with THR 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.9 15.1 - - + +
299B PRO* 3.6 41.1 - - + +
301B HIS* 4.4 10.5 - - + -
532B LEU* 3.7 20.3 - - + +
559B VAL* 2.5 35.9 + - - +
560B ARG* 4.0 4.3 - - - -
562B PHE* 1.3 77.4 - - - +
564B GLN* 1.3 63.9 + - - +
566B LYS* 3.5 2.1 + - - +
567B CYS* 3.3 24.0 + - - -
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Residues in contact with GLN 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ASN* 4.5 2.4 - - - +
299B PRO* 4.6 5.8 - - + -
560B ARG* 3.0 45.5 + - + +
561B PHE* 3.8 6.5 + - - +
563B THR* 1.3 75.0 - - - +
565B LEU* 1.3 65.9 + - - +
567B CYS* 3.2 4.9 + - - +
568B ARG* 3.1 26.1 + - - +
675B ASP* 3.1 47.6 + - + +
676B GLN* 4.0 11.4 + - - +
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Residues in contact with LEU 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B LEU* 4.6 10.8 - - + -
561B PHE* 3.0 23.3 + - + +
562B PHE* 3.5 25.6 - - + +
564B GLN* 1.3 75.5 - - - +
566B LYS* 1.3 63.1 + - - +
568B ARG* 3.0 20.9 + - + +
569B MET* 3.0 39.0 + - + +
638B LEU* 4.3 10.8 - - + -
639B TRP* 3.4 34.8 - - + -
671B LEU* 6.3 2.7 - - + -
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Residues in contact with LYS 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 3.1 33.4 + - - +
270B GLY* 5.5 1.8 - - - +
532B LEU* 3.1 29.2 - - + +
533B LEU* 6.1 0.9 - - + -
534B SER 2.8 28.1 + - - -
535B SER* 3.3 15.2 + - - +
537B SER* 2.9 24.8 + - - +
562B PHE 2.9 17.8 + - - +
563B THR 3.8 4.9 - - - +
564B GLN 3.3 0.2 - - - -
565B LEU* 1.3 77.5 - - - +
567B CYS* 1.3 64.9 + - - +
569B MET* 2.9 21.9 + - - +
570B MET* 3.2 14.8 + - - +
573B LEU* 3.9 20.0 - - + +
678B PRO* 6.6 0.2 - - + -
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Residues in contact with CYS 567 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLY* 5.6 2.5 - - - -
301B HIS* 4.2 9.6 - - - -
563B THR* 3.3 18.5 + - - -
564B GLN 3.2 9.5 + - - +
566B LYS* 1.3 79.8 - - - +
568B ARG* 1.3 58.8 + - - +
570B MET* 3.5 15.6 - - - +
674B ASN 3.6 14.6 - - - +
675B ASP 3.8 8.3 - - - -
676B GLN 3.8 8.3 - - - -
677B ARG* 3.6 31.9 - - - +
678B PRO* 3.8 9.2 - - - -
680B TYR* 2.8 24.9 + - - -
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Residues in contact with ARG 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B GLN 3.1 17.0 + - - +
565B LEU* 3.0 15.9 + - + +
567B CYS* 1.3 80.0 - - - +
569B MET* 1.3 57.1 + - + +
570B MET 3.2 0.7 - - - -
571B PRO* 3.0 7.6 - - - +
671B LEU* 3.4 25.2 - - + +
672B GLY 2.6 53.7 + - - +
673B ASN* 4.8 4.1 - - - +
674B ASN 4.2 1.6 - - - +
675B ASP* 3.5 24.2 - - + +
680B TYR* 3.8 5.6 - - - -
687B ALA* 4.3 6.5 - - - +
3010B SO4 2.9 43.3 + - - -
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Residues in contact with MET 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B LEU* 4.4 12.8 - - + -
565B LEU* 3.0 47.1 + - + +
566B LYS* 2.9 11.8 + - - +
568B ARG* 1.3 73.2 - - + +
570B MET* 1.3 53.5 + - - +
571B PRO* 3.2 4.7 - - - -
572B TYR* 2.9 19.7 + - + +
573B LEU* 2.7 57.3 + - + -
610B LEU* 4.5 13.5 - - + -
614B VAL* 4.7 11.2 - - + -
638B LEU* 3.6 24.9 - - + -
661B VAL* 5.3 0.7 - - + -
669B LEU* 5.9 4.3 - - + -
670B ALA 4.9 3.6 - - - -
671B LEU* 5.1 10.1 - - + +
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Residues in contact with MET 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA 4.2 6.3 - - - +
269B PHE* 3.7 38.1 - - + -
566B LYS* 3.2 14.2 + - - +
567B CYS* 3.5 17.9 - - - +
569B MET* 1.3 77.7 - - - +
571B PRO* 1.3 60.1 - - + +
573B LEU* 4.0 18.4 - - - -
574B TYR* 2.7 62.6 + - + +
678B PRO* 3.5 29.8 - - + +
682B TRP* 3.4 23.3 - - + +
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Residues in contact with PRO 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ARG 3.0 16.2 - - - +
569B MET 3.2 2.7 - - - -
570B MET* 1.3 93.4 - - + +
572B TYR* 1.3 59.8 + - - +
575B ARG* 3.7 1.9 - - - +
670B ALA* 3.3 24.0 - - + +
671B LEU 3.9 1.3 - - - -
672B GLY* 3.6 22.2 - - - +
680B TYR* 3.9 2.5 - - - +
682B TRP* 3.7 36.5 - - + +
686B THR* 4.8 4.3 - - + -
702B GLU 4.4 1.0 - - - +
703B VAL* 4.8 5.3 - - + -
704B PRO* 3.0 29.0 - - + +
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Residues in contact with TYR 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B MET* 2.9 16.0 + - + +
571B PRO* 1.3 78.2 - - - +
573B LEU* 1.3 83.6 + - + +
575B ARG* 2.7 30.7 + - + +
576B GLU* 3.1 35.6 + - + +
610B LEU 2.7 23.2 + - - -
611B GLY 3.3 3.3 - - - -
613B ASN* 3.0 43.6 + - + -
614B VAL* 3.2 24.9 - - + +
669B LEU* 3.3 30.5 - - + -
670B ALA* 3.6 14.9 + - - +
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Residues in contact with LEU 573 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 5.6 3.6 - - + -
532B LEU 5.7 0.4 - - - +
533B LEU* 6.5 0.4 - - + -
534B SER 6.0 0.2 - - - +
566B LYS* 3.9 36.3 - - + +
569B MET* 2.7 47.1 + - + +
570B MET* 4.0 14.4 - - - -
572B TYR* 1.3 98.6 - - + +
574B TYR* 1.3 56.8 + - - +
576B GLU* 3.2 4.6 + - + +
577B ALA* 2.9 23.6 + - - +
587B MET* 3.4 26.7 - - + +
610B LEU* 4.2 20.6 - - + -
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Residues in contact with TYR 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.5 21.4 + - + +
264B PRO 3.0 29.4 + - - -
265B PRO* 4.0 2.3 - - - +
266B ALA* 3.8 17.4 + - + -
269B PHE* 3.7 22.0 - + - -
570B MET* 2.7 38.8 + - + +
573B LEU* 1.3 73.4 - - - +
575B ARG* 1.3 61.5 + - - +
577B ALA* 3.4 5.1 + - + +
578B ALA* 3.1 19.1 + - - +
682B TRP* 3.4 27.1 - + + -
704B PRO* 4.2 9.8 - - + +
705B ALA 3.8 7.6 - - - -
706B ALA 3.1 28.2 + - - -
707B ASP* 5.2 0.2 - - - -
708B GLY* 4.1 11.4 - - - -
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Residues in contact with ARG 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B PRO 3.7 13.2 + - - +
572B TYR* 2.7 20.9 + - + +
574B TYR* 1.3 70.7 - - - +
576B GLU* 1.3 70.7 + - - +
578B ALA* 2.9 29.8 + - - +
579B ARG* 3.1 40.4 + - - +
702B GLU* 3.0 62.4 + - + +
704B PRO* 3.9 14.6 - - + +
708B GLY 4.9 1.3 - - - -
710B VAL* 3.9 13.3 - - - +
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Residues in contact with GLU 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B TYR* 3.1 35.3 + - + +
573B LEU* 3.6 7.6 - - + +
575B ARG* 1.3 81.1 - - - +
577B ALA* 1.3 62.3 + - - +
579B ARG* 3.2 45.4 + - - +
580B ALA* 3.5 4.7 + - - +
585B THR 4.6 0.7 - - - +
587B MET* 4.0 17.4 - - + +
589B ARG* 3.2 13.3 + - - +
611B GLY* 3.2 21.1 - - - -
612B ASP* 2.7 40.1 + - - +
613B ASN* 5.1 1.2 + - - -
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Residues in contact with ALA 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.6 14.1 - - + +
269B PHE* 3.8 14.4 - - + -
507B PHE* 3.5 18.3 - - + -
573B LEU 2.9 13.4 + - - +
574B TYR* 3.5 13.5 - - + +
575B ARG 3.1 0.2 - - - -
576B GLU* 1.3 77.3 - - - +
578B ALA* 1.3 62.4 + - - +
580B ALA* 3.2 17.9 + - - +
581B ASN 3.5 2.9 + - - -
587B MET* 3.6 24.2 - - - -
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Residues in contact with ALA 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.9 11.6 - - + +
574B TYR 3.1 11.5 + - - +
575B ARG* 2.9 28.2 + - - +
577B ALA* 1.3 78.4 - - - +
579B ARG* 1.3 59.4 + - - +
581B ASN* 3.1 7.4 + - - +
582B ALA* 3.0 23.6 + - - +
708B GLY* 4.1 24.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B ARG* 3.1 46.3 + - - +
576B GLU* 3.2 29.9 + - - +
578B ALA* 1.3 77.2 - - - +
580B ALA* 1.3 57.9 + - - +
582B ALA* 4.3 6.5 - - - +
583B ARG* 2.6 40.2 + - + +
584B GLY 3.1 3.3 + - - -
585B THR* 3.8 17.0 + - - +
589B ARG* 4.0 12.1 - - - +
612B ASP* 2.7 28.7 + - - -
702B GLU* 4.2 8.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PRO* 3.1 26.6 - - + +
506B GLY* 4.1 18.6 - - - +
507B PHE* 3.8 22.2 - - + -
576B GLU 3.5 4.4 + - - +
577B ALA 3.2 13.3 + - - +
579B ARG* 1.3 78.3 - - - +
581B ASN* 1.3 56.7 + - - +
584B GLY* 3.2 11.5 + - - -
585B THR 3.2 24.1 + - - +
587B MET 4.9 1.6 - - - +
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Residues in contact with ASN 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG* 3.7 24.7 + - - +
261B PRO 2.8 27.2 + - - +
262B ALA* 3.5 4.7 - - - +
263B LEU* 3.5 35.1 - - + +
507B PHE* 5.2 0.2 - - - -
577B ALA 3.5 3.9 + - - +
578B ALA* 3.1 9.9 + - - +
580B ALA* 1.3 78.2 - - - +
582B ALA* 1.3 64.9 + - - +
584B GLY 4.6 0.2 - - - -
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Residues in contact with ALA 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ARG* 3.1 26.1 + - - -
578B ALA 3.0 15.6 + - - +
579B ARG* 3.9 5.8 - - - +
581B ASN* 1.3 81.0 + - - +
583B ARG* 1.3 67.5 + - + +
584B GLY 3.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LYS* 3.8 35.1 + - - +
249B ALA* 3.9 6.7 - - - +
252B ASP* 3.1 48.5 + - - +
260B ARG* 3.4 10.3 - - - +
579B ARG* 2.6 23.6 + - + +
582B ALA* 1.3 80.8 - - + +
584B GLY* 1.3 60.2 + - - -
585B THR* 3.8 14.6 + - - +
3008B SO4 3.0 39.6 + - - -
----------------------------------------------------------
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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