Contacts of the helix formed by residues 552 - 584 (chain A) 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 552 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ALA* 3.5 20.0 - - + +
525A LYS* 3.6 11.6 + - - -
548A PRO 3.3 13.0 + - - +
549A TRP* 4.1 7.1 - - - -
551A TYR* 1.3 84.3 - - - +
553A ASP* 1.3 64.8 + - - +
554A GLU* 3.1 9.1 + - - +
555A SER* 2.6 46.5 + - - -
556A CYS* 3.8 6.4 + - - -
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Residues in contact with ASP 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A ASP* 1.3 75.5 - - - +
554A GLU* 1.3 67.1 + - - +
556A CYS* 3.1 24.0 + - - +
557A ASP* 3.5 10.8 + - - +
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Residues in contact with GLU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525A LYS* 3.3 19.1 + - - +
552A ASP* 3.1 10.3 + - - +
553A ASP* 1.3 78.8 - - - +
555A SER* 1.3 56.7 + - - +
557A ASP* 3.1 17.6 + - + +
558A VAL* 2.9 34.3 + - + +
656A PHE* 3.5 29.2 + - - +
657A LEU* 5.1 6.9 + - + +
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Residues in contact with SER 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A TYR* 3.7 17.7 - - - -
525A LYS* 3.2 23.5 - - - +
548A PRO* 3.3 24.5 - - - -
551A TYR* 3.5 16.3 - - - +
552A ASP* 2.6 28.3 + - - -
553A ASP 3.1 0.2 - - - -
554A GLU* 1.3 72.0 - - - +
556A CYS* 1.3 57.6 + - - +
558A VAL* 3.3 3.2 + - - +
559A VAL* 2.9 33.8 + - - +
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Residues in contact with CYS 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ARG* 3.7 27.4 - - - -
298A LEU* 3.4 17.2 - - + +
548A PRO* 3.7 25.6 - - + -
549A TRP* 3.7 20.0 - - - -
552A ASP 3.8 5.8 + - - -
553A ASP* 3.1 11.9 + - - +
555A SER* 1.3 80.6 - - - +
557A ASP* 1.3 59.0 + - - +
559A VAL* 3.4 1.4 + - - +
560A ARG* 3.0 36.8 + - - +
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Residues in contact with ASP 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ASP* 3.8 9.0 - - - +
554A GLU* 3.1 23.1 + - + +
556A CYS* 1.3 76.0 - - - +
558A VAL* 1.3 65.7 + - - +
560A ARG* 3.4 23.8 + - - +
561A PHE* 2.9 26.5 + - - +
657A LEU* 4.4 16.8 - - + -
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Residues in contact with VAL 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A LYS* 3.4 46.2 - - + +
528A CYS* 4.0 10.3 - - + -
554A GLU* 2.9 20.0 + - + +
555A SER* 3.3 6.9 + - - +
557A ASP* 1.3 77.2 - - - +
559A VAL* 1.3 62.0 + - - +
561A PHE* 3.4 1.0 + - - +
562A PHE* 3.1 45.4 + - + +
656A PHE* 3.3 29.8 - - + +
657A LEU* 3.7 15.0 - - + -
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Residues in contact with VAL 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 4.4 16.8 - - + -
293A MET* 5.0 0.4 - - + -
298A LEU* 4.3 14.6 - - + -
299A PRO* 6.2 0.2 - - + -
524A TYR* 3.9 2.5 - - + +
528A CYS* 3.7 30.1 - - + -
532A LEU* 5.0 5.3 - - + +
539A LEU* 5.2 5.8 - - + -
548A PRO* 3.4 33.2 - - + -
555A SER 2.9 17.3 + - - +
556A CYS* 3.8 4.3 - - - +
558A VAL* 1.3 76.6 - - - +
560A ARG* 1.3 53.6 + - - +
562A PHE* 4.5 0.8 - - - +
563A THR* 2.6 47.3 + - - +
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Residues in contact with ARG 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A ARG* 2.5 38.0 + - - +
297A ASN* 3.1 29.9 + - - +
298A LEU* 3.6 14.6 - - + +
299A PRO* 4.5 4.9 - - + -
556A CYS* 3.0 17.7 + - - +
557A ASP* 3.4 30.4 + - - +
559A VAL* 1.3 75.8 - - - +
561A PHE* 1.3 64.6 + - - +
563A THR* 3.8 3.2 - - - -
564A GLN* 3.0 55.1 + - - +
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Residues in contact with PHE 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A ASP 2.9 19.0 + - - +
558A VAL* 3.7 5.4 - - - +
560A ARG* 1.3 77.3 - - - +
562A PHE* 1.3 81.8 + + - +
564A GLN* 3.4 12.5 + - - +
565A LEU* 3.0 35.4 + - + +
639A TRP* 3.6 44.9 - + - -
657A LEU* 3.6 37.5 - - + -
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Residues in contact with PHE 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A CYS* 4.6 0.9 - - + +
529A ALA* 3.6 22.9 - - + -
532A LEU* 3.7 26.6 - - + +
533A LEU* 4.2 13.7 - - + +
558A VAL* 3.1 42.7 + - + +
559A VAL 4.5 0.2 - - - +
561A PHE* 1.3 89.8 - + - +
563A THR* 1.3 65.4 + - - +
565A LEU* 3.6 13.5 - - + +
566A LYS* 2.9 24.1 + - - +
639A TRP* 3.8 15.9 - + - -
656A PHE 4.0 10.3 - - - -
657A LEU* 3.8 20.4 - - - -
658A SER 4.3 1.1 - - - -
659A LEU* 3.6 33.9 - - + -
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Residues in contact with THR 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU* 4.0 13.4 - - + +
299A PRO* 3.8 39.9 - - + +
301A HIS* 4.2 13.5 - - + -
532A LEU* 3.8 20.7 - - + +
559A VAL* 2.6 36.2 + - - +
560A ARG* 3.8 4.7 - - - -
562A PHE* 1.3 75.5 - - - +
564A GLN* 1.3 62.9 + - - +
566A LYS* 3.3 3.3 + - - +
567A CYS* 3.1 24.7 + - - -
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Residues in contact with GLN 564 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ASN 4.9 0.2 - - - +
299A PRO* 4.8 4.5 - - + -
560A ARG* 3.0 48.5 + - + +
561A PHE* 3.6 11.4 - - - +
563A THR* 1.3 75.1 - - - +
565A LEU* 1.3 64.8 + - - +
567A CYS* 3.2 1.6 + - - +
568A ARG* 3.0 27.9 + - - +
675A ASP* 3.2 49.5 + - + +
676A GLN* 4.1 11.8 + - - +
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Residues in contact with LEU 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 4.6 10.1 - - + -
561A PHE* 3.0 24.6 + - + +
562A PHE* 3.3 19.7 + - + +
564A GLN* 1.3 75.8 - - - +
566A LYS* 1.3 63.1 + - - +
568A ARG* 3.3 10.6 + - + +
569A MET* 3.1 51.9 + - + +
638A LEU* 4.2 13.5 - - + -
639A TRP* 3.4 40.8 - - + -
671A LEU* 6.3 3.6 - - + -
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Residues in contact with LYS 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A PHE* 3.0 32.4 + - - +
270A GLY 5.6 0.9 - - - -
532A LEU* 3.1 31.4 - - + +
533A LEU* 5.7 2.4 - - + +
534A SER 3.0 16.7 + - - -
535A SER* 2.9 27.2 + - - +
536A HIS* 3.8 3.6 - - - +
537A SER* 3.0 23.7 + - - +
562A PHE 2.9 16.9 + - - +
563A THR 3.6 5.6 - - - +
564A GLN 3.2 0.2 - - - -
565A LEU* 1.3 77.0 - - - +
567A CYS* 1.3 63.7 + - - +
569A MET* 3.0 18.3 + - - +
570A MET* 3.2 16.3 + - - +
573A LEU* 3.9 20.5 - - + +
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Residues in contact with CYS 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLY* 5.7 1.3 - - - -
301A HIS* 4.1 17.5 - - - -
563A THR* 3.1 17.6 + - - -
564A GLN 3.2 6.0 + - - +
566A LYS* 1.3 82.4 - - - +
568A ARG* 1.3 59.6 + - - +
569A MET 3.5 0.2 + - - -
570A MET* 3.6 14.5 + - - +
674A ASN 3.3 9.9 - - - +
675A ASP* 3.8 10.1 - - - -
676A GLN 4.2 2.7 - - - -
677A ARG* 3.4 36.8 - - - +
678A PRO* 3.9 5.6 - - - -
680A TYR* 2.8 25.8 + - - -
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Residues in contact with ARG 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A GLN 3.0 20.9 + - - +
565A LEU* 3.7 12.3 - - + +
566A LYS 3.1 0.4 - - - -
567A CYS* 1.3 76.7 - - - +
569A MET* 1.3 59.5 + - + +
570A MET 3.4 0.2 - - - -
571A PRO* 3.4 1.7 - - - +
671A LEU* 3.3 40.9 - - + +
672A GLY 2.7 52.8 + - - +
673A ASN* 4.9 4.6 - - - +
674A ASN 3.7 8.3 - - - +
675A ASP* 3.6 21.5 - - + -
680A TYR* 3.9 2.5 - - - -
687A ALA* 4.3 13.1 - - - +
689A HIS* 5.1 2.4 + - - -
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Residues in contact with MET 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A LEU* 4.3 20.2 - - + -
565A LEU* 3.1 41.2 + - + +
566A LYS* 3.0 2.9 + - - +
568A ARG* 1.3 76.7 - - - +
570A MET* 1.3 64.5 + - - +
571A PRO* 3.1 4.7 - - - -
572A TYR* 2.8 24.5 + - + +
573A LEU* 2.9 45.6 + - + -
610A LEU* 4.8 5.2 - - + -
614A VAL* 4.5 21.3 - - + -
638A LEU* 3.9 26.0 - - + -
661A VAL* 5.5 0.2 - - + -
669A LEU* 5.7 3.1 - - + -
671A LEU* 4.7 16.8 - - + -
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Residues in contact with MET 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ALA 3.9 8.7 - - - +
269A PHE* 3.6 45.3 - - + +
566A LYS* 3.2 17.5 + - - +
567A CYS* 3.7 8.7 - - - +
568A ARG 3.4 0.2 - - - -
569A MET* 1.3 75.6 - - - +
571A PRO* 1.3 65.1 - - + +
573A LEU* 4.0 19.1 - - - -
574A TYR* 2.9 40.7 + - + +
678A PRO* 3.6 32.8 - - + +
682A TRP* 3.4 32.2 - - + +
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Residues in contact with PRO 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568A ARG 3.4 10.8 - - - +
569A MET 3.1 6.5 - - - +
570A MET* 1.3 94.0 - - + +
572A TYR* 1.3 57.9 + - - +
575A ARG* 3.8 2.9 + - - +
670A ALA* 3.0 28.3 - - + +
671A LEU 3.9 1.3 - - - +
672A GLY* 3.4 25.8 - - - +
680A TYR* 3.9 5.2 - - - +
682A TRP* 3.9 35.7 - - + +
686A THR* 5.3 0.9 - - + -
702A GLU 4.4 2.4 - - - +
703A VAL* 4.9 5.3 - - + -
704A PRO* 3.3 27.7 - - + +
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Residues in contact with TYR 572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A MET* 2.8 17.9 + - + +
571A PRO* 1.3 77.8 - - - +
573A LEU* 1.3 95.8 + - + +
575A ARG* 2.8 18.4 + - + +
576A GLU* 3.1 35.1 + - + +
610A LEU 2.7 25.4 + - - -
611A GLY 3.4 2.8 - - - -
613A ASN* 2.9 38.9 + - - -
614A VAL* 3.3 23.0 - - + +
668A LEU 6.1 0.2 - - - -
669A LEU* 3.5 32.5 - - + -
670A ALA* 3.5 15.1 + - - +
671A LEU* 5.5 0.7 - - + -
702A GLU 5.8 0.7 - - - -
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Residues in contact with LEU 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A PHE* 5.6 4.3 - - + -
533A LEU* 6.2 0.9 - - + -
535A SER* 6.4 0.7 - - - -
566A LYS* 3.9 34.3 - - + +
569A MET* 2.9 38.9 + - + +
570A MET* 4.0 14.8 - - - +
572A TYR* 1.3 102.5 - - + +
574A TYR* 1.3 57.5 + - - +
576A GLU* 3.1 4.8 + - + +
577A ALA* 3.0 23.5 + - - +
587A MET* 3.3 26.7 - - + +
610A LEU* 4.1 28.3 - - + -
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Residues in contact with TYR 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.6 20.2 - - + +
264A PRO 2.9 29.4 + - - -
265A PRO* 4.2 1.4 - - - +
266A ALA* 3.8 16.6 + - - -
269A PHE* 3.5 25.8 - + - -
570A MET* 2.9 35.8 + - + +
573A LEU* 1.3 73.4 - - - +
575A ARG* 1.3 60.6 + - - +
577A ALA* 3.7 4.6 - - + +
578A ALA* 3.3 18.0 + - - +
682A TRP* 3.3 33.0 - + + -
704A PRO* 4.2 9.4 - - + +
705A ALA 4.0 6.3 - - - -
706A ALA 3.3 27.1 + - - -
708A GLY* 4.0 10.8 - - - -
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Residues in contact with ARG 575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571A PRO 3.8 13.0 + - - +
572A TYR* 2.8 13.2 + - + +
574A TYR* 1.3 73.8 - - - +
576A GLU* 1.3 66.7 + - - +
577A ALA 3.0 4.9 - - - -
578A ALA* 3.1 19.2 + - - +
579A ARG* 3.0 47.7 + - - +
702A GLU* 3.3 56.8 + - + +
704A PRO* 4.1 15.0 - - + +
708A GLY 4.9 2.0 - - - -
710A VAL* 3.8 15.4 - - - +
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Residues in contact with GLU 576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A TYR* 3.1 35.6 + - + +
573A LEU* 3.1 7.5 + - - +
575A ARG* 1.3 81.8 - - - +
577A ALA* 1.3 60.2 + - - +
579A ARG* 2.8 44.8 + - - +
580A ALA* 3.5 4.7 + - - +
585A THR 4.6 2.3 - - - +
587A MET* 3.9 19.8 - - + +
589A ARG* 3.3 8.0 + - - +
611A GLY* 3.3 22.2 - - - -
612A ASP* 2.5 43.5 + - - +
613A ASN* 5.5 0.5 + - - -
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Residues in contact with ALA 577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.8 13.6 - - + +
269A PHE* 3.9 15.0 - - + -
507A PHE* 3.6 18.2 - - + -
573A LEU 3.0 14.7 + - - +
574A TYR* 3.7 10.1 - - + +
575A ARG 3.0 0.2 - - - -
576A GLU* 1.3 76.6 - - - +
578A ALA* 1.3 62.7 + - - +
579A ARG 3.1 1.6 - - - -
580A ALA* 3.1 14.8 + - - +
581A ASN* 3.4 8.0 + - - +
587A MET* 3.7 21.3 - - - -
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Residues in contact with ALA 578 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 4.1 11.8 - - + +
574A TYR 3.3 9.3 + - - +
575A ARG* 3.1 20.9 + - - +
577A ALA* 1.3 78.6 - - - +
579A ARG* 1.3 57.3 + - - +
581A ASN* 3.4 8.0 + - - +
582A ALA* 3.1 26.9 + - - +
708A GLY* 3.6 31.9 - - - +
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Residues in contact with ARG 579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A ARG* 3.0 46.4 + - - +
576A GLU* 2.8 34.5 + - - +
577A ALA 3.1 0.2 - - - -
578A ALA* 1.3 75.4 - - - +
580A ALA* 1.3 61.4 + - - +
581A ASN 3.1 1.3 - - - -
582A ALA* 4.3 5.4 - - - +
583A ARG* 2.9 34.2 + - + +
584A GLY 3.5 2.8 + - - -
585A THR* 3.6 18.0 + - - +
589A ARG* 3.9 15.7 - - - +
612A ASP* 2.8 29.9 + - - -
702A GLU* 4.1 14.5 + - - -
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Residues in contact with ALA 580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A PRO* 3.3 12.9 - - + +
506A GLY* 4.1 18.6 - - - +
507A PHE* 3.7 22.7 - - + -
576A GLU 3.5 4.3 + - - +
577A ALA 3.1 12.0 + - - +
579A ARG* 1.3 78.1 - - - +
581A ASN* 1.3 56.9 + - - +
584A GLY* 2.9 26.0 + - - -
585A THR 2.8 26.5 + - - +
586A PRO* 4.5 0.7 - - + -
587A MET 4.7 0.9 - - - +
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Residues in contact with ASN 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ARG* 3.8 20.8 - - - +
261A PRO* 3.0 28.0 + - - +
262A ALA* 3.7 5.5 - - - +
263A LEU* 3.7 35.3 - - + +
577A ALA 3.4 6.0 + - - +
578A ALA* 3.8 9.7 - - - +
579A ARG 3.1 0.6 - - - -
580A ALA* 1.3 81.2 - - - +
582A ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ARG* 3.0 25.9 + - - -
578A ALA 3.1 15.3 + - - +
579A ARG* 3.1 7.2 + - - +
581A ASN* 1.3 82.2 - - - +
583A ARG* 1.3 68.6 + - + +
584A GLY 3.6 0.7 - - - -
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Residues in contact with ARG 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LYS* 3.5 32.7 + - - +
249A ALA* 3.7 7.7 - - - +
252A ASP* 3.0 44.7 + - - +
260A ARG* 3.5 12.8 - - - +
579A ARG* 2.9 11.6 + - + +
582A ALA* 1.3 83.1 - - + +
584A GLY* 1.3 63.4 + - - +
585A THR* 3.1 18.4 + - - +
3013A SO4 2.7 44.0 + - - -
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Residues in contact with GLY 584 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A LEU* 4.1 13.5 - - - +
255A THR* 3.5 28.6 + - - +
260A ARG* 3.9 0.6 - - - +
261A PRO* 4.1 7.5 - - - +
504A GLY* 5.0 5.9 - - - +
506A GLY* 5.5 0.5 - - - -
580A ALA* 2.9 21.5 + - - -
581A ASN 4.7 0.2 - - - -
582A ALA 3.6 1.0 - - - -
583A ARG* 1.3 78.0 - - - +
585A THR* 1.3 63.1 + - - +
586A PRO* 3.3 10.2 - - - +
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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