Contacts of the helix formed by residues 538 - 560 (chain N) in PDB entry 4G7H
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 538 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016M ILE* 5.6 2.8 - - - +
524N LEU 4.9 1.6 + - - -
525N ARG* 3.7 36.3 - - - +
526N PRO* 3.3 9.0 + - - -
537N THR* 1.3 81.3 + - - +
539N ASP* 1.3 66.0 + - - +
540N LEU* 3.5 18.4 + - - +
541N ASN* 3.2 19.9 + - - +
542N ASP* 4.1 2.3 + - - +
606N ILE* 5.7 1.7 - - - +
317P LEU* 3.8 7.0 - - - +
318P GLU* 3.6 17.5 + - - -
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Residues in contact with ASP 539 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537N THR 4.6 0.2 - - - +
538N SER* 1.3 71.1 + - - +
540N LEU* 1.3 65.6 + - - +
542N ASP* 3.0 20.5 + - - +
543N LEU* 3.0 16.1 + - - +
593N ASN* 4.1 4.5 + - - -
598N ARG* 2.7 38.0 + - - -
600N LEU* 3.6 17.1 - - + +
601N ARG 3.1 30.7 + - - +
316P SER* 2.9 19.8 + - - -
318P GLU* 3.1 23.0 + - - +
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Residues in contact with LEU 540 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520N LEU* 3.6 30.3 - - + -
524N LEU 5.2 1.3 - - - +
525N ARG* 4.2 11.9 - - + -
538N SER* 3.1 11.6 + - - +
539N ASP* 1.3 77.7 - - - +
541N ASN* 1.3 56.7 + - - +
543N LEU* 3.2 14.2 + - + +
544N TYR* 2.8 47.1 + - + -
581N LEU* 4.1 15.9 - - + -
601N ARG 3.7 20.0 - - - +
602N SER* 4.1 0.2 - - - -
603N LEU* 3.7 33.9 - - + +
606N ILE* 3.8 15.5 - - + -
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Residues in contact with ASN 541 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31N THR* 5.0 6.1 - - + -
44N LEU* 3.8 11.3 - - + +
45N PHE* 3.4 17.0 - - + -
525N ARG* 2.8 61.9 + - - -
537N THR* 2.9 25.8 + - + +
538N SER* 3.2 12.7 + - - +
539N ASP 3.1 0.8 - - - -
540N LEU* 1.3 77.5 - - - +
542N ASP* 1.3 57.3 + - - +
544N TYR* 3.6 3.3 + - - +
545N ARG* 2.9 34.7 + - - +
257P THR* 5.3 6.1 - - + -
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Residues in contact with ASP 542 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537N THR* 5.2 7.1 - - - +
538N SER 4.1 1.9 + - - +
539N ASP* 3.0 14.6 + - - +
541N ASN* 1.3 77.4 - - - +
543N LEU* 1.3 58.9 + - - +
545N ARG* 3.1 25.1 + - - +
546N ARG* 2.9 36.0 + - + +
593N ASN* 3.4 29.3 + - - +
600N LEU* 4.1 15.3 - - + -
257P THR* 3.0 28.5 + - - +
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Residues in contact with LEU 543 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539N ASP 3.0 15.4 + - - +
540N LEU* 3.7 15.9 - - + +
542N ASP* 1.3 76.2 - - - +
544N TYR* 1.3 61.8 + - - +
546N ARG* 3.4 11.8 + - - +
547N LEU* 3.0 21.7 + - - +
577N ALA 4.9 4.5 - - - +
580N ALA* 4.0 39.7 - - + +
581N LEU* 4.0 19.0 - - + +
584N ASN* 4.9 1.3 - - + +
591N VAL* 4.3 10.8 - - + -
600N LEU* 3.8 32.3 - - + -
601N ARG 3.8 21.3 - - - +
602N SER* 4.1 5.4 - - - +
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Residues in contact with TYR 544 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1094M ALA* 4.1 8.7 + - - +
44N LEU* 3.8 20.2 - - + -
93N ILE* 4.1 17.0 - - + -
517N VAL* 5.0 0.2 - - + -
518N PRO 3.5 17.6 + - - -
519N VAL* 4.0 9.9 - - + -
520N LEU* 3.1 30.9 + - + +
525N ARG* 3.8 30.7 - - - -
540N LEU* 2.8 37.5 + - + +
541N ASN* 3.7 4.7 - - - +
543N LEU* 1.3 71.7 - - - +
545N ARG* 1.3 57.8 + - - +
547N LEU* 3.1 5.9 + - + +
548N ILE* 2.9 36.0 + - + +
581N LEU* 3.4 37.6 - - + +
603N LEU* 4.6 3.5 - - + +
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Residues in contact with ARG 545 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N PRO* 3.1 35.1 + - + +
31N THR* 4.3 6.1 - - - -
44N LEU* 3.7 10.3 - - + -
541N ASN 2.9 23.8 + - - +
542N ASP* 3.1 29.6 + - - +
544N TYR* 1.3 72.9 - - - +
546N ARG* 1.3 66.8 + - - +
548N ILE* 3.3 6.4 + - - +
549N ASN* 2.9 42.0 + - - +
254P GLN* 3.0 29.7 + - - +
255P ALA 4.6 3.4 + - - -
256P ARG 3.7 16.2 + - - +
257P THR* 3.8 27.0 + - - +
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Residues in contact with ARG 546 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542N ASP* 2.9 20.0 + - - +
543N LEU* 3.5 18.4 + - - +
545N ARG* 1.3 74.5 - - - +
547N LEU* 1.3 65.4 + - - +
549N ASN* 3.4 6.2 + - - +
550N ARG* 3.0 71.4 + - - +
576N GLU* 4.5 2.8 + - - +
577N ALA* 3.8 24.0 + - + +
580N ALA* 4.1 11.3 - - - +
591N VAL* 3.9 35.6 - - - +
600N LEU* 5.2 2.5 - - - -
208P SER* 5.3 5.5 + - - -
211P ASP* 4.7 4.2 + - - +
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Residues in contact with LEU 547 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N ILE* 4.1 17.3 - - + -
95N LEU* 4.4 8.1 - - + -
517N VAL* 4.1 20.2 - - + -
543N LEU 3.0 10.8 + - - +
544N TYR* 3.1 10.1 + - + +
546N ARG* 1.3 80.0 - - - +
548N ILE* 1.3 57.8 + - - +
550N ARG* 3.3 1.3 + - - +
551N ASN* 2.9 31.2 + - - +
574N LEU* 3.7 18.8 - - + -
577N ALA* 4.1 17.4 - - + +
578N VAL* 3.5 33.0 - - + +
581N LEU* 4.0 25.6 - - + -
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Residues in contact with ILE 548 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N VAL* 3.4 42.0 - - + +
27N GLU 4.0 4.7 - - - +
28N LYS 3.9 5.6 - - - +
29N PRO* 3.7 24.9 - - + -
44N LEU* 4.9 4.9 - - + -
93N ILE* 3.6 29.6 - - + -
544N TYR* 2.9 26.7 + - + +
545N ARG* 3.8 4.3 - - - +
547N LEU* 1.3 72.1 - - - +
549N ASN* 1.3 63.5 + - - +
551N ASN* 3.3 6.2 + - - +
552N ASN* 2.9 44.3 + - - +
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Residues in contact with ASN 549 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N PRO* 3.4 29.2 - - - +
545N ARG* 2.9 32.5 + - - +
546N ARG* 3.7 6.5 - - - +
548N ILE* 1.3 76.0 - - - +
550N ARG* 1.3 60.7 + - + +
552N ASN* 3.8 6.1 + - - +
553N ARG* 2.9 36.0 + - - +
207P LEU* 6.0 0.4 - - - +
254P GLN* 3.6 48.5 + - - +
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Residues in contact with ARG 550 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546N ARG* 3.0 52.1 + - - +
547N LEU* 3.9 2.9 - - - +
549N ASN* 1.3 76.5 - - + +
551N ASN* 1.3 57.2 + - - +
553N ARG* 4.0 4.0 - - - +
554N LEU* 2.9 22.5 + - - +
570N GLU* 2.9 28.0 - - - +
573N MET* 3.0 53.7 + - - +
574N LEU* 4.1 14.8 - - + -
576N GLU* 4.5 4.8 - - - +
577N ALA* 4.0 9.2 - - - +
208P SER* 3.6 13.7 + - - -
210P LEU* 5.1 3.2 - - - +
211P ASP* 3.1 41.5 + - - +
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Residues in contact with ASN 551 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N GLU* 5.3 0.2 + - - -
93N ILE* 3.9 11.7 - - + +
94N GLU 2.8 28.5 + - - -
95N LEU* 3.3 15.0 - - + +
96N ALA* 3.0 24.7 + - - +
547N LEU 2.9 19.2 + - - +
548N ILE* 3.6 6.3 - - - +
550N ARG* 1.3 76.3 - - - +
552N ASN* 1.3 64.7 + - - +
554N LEU* 3.1 6.4 + - - +
555N LYS* 3.0 36.9 + - - +
574N LEU* 3.6 21.0 - - + +
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Residues in contact with ASN 552 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N GLU* 3.1 27.3 + - - +
29N PRO* 4.2 8.5 - - - +
548N ILE* 2.9 30.7 + - - +
549N ASN* 3.8 5.5 + - - +
551N ASN* 1.3 77.9 + - - +
553N ARG* 1.3 63.6 + - - +
555N LYS* 3.1 29.5 + - - +
556N LYS* 3.0 22.9 + - - +
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Residues in contact with ARG 553 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549N ASN* 2.9 21.6 + - - +
550N ARG* 3.7 13.1 - - - +
552N ASN* 1.3 74.8 - - - +
554N LEU* 1.3 57.2 + - - +
556N LYS* 3.2 7.0 + - - +
557N LEU* 2.9 39.4 + - + +
570N GLU* 3.0 36.0 + - - +
573N MET* 3.4 9.7 - - - +
211P ASP* 3.0 41.7 + - - +
214P GLN* 3.6 25.0 - - - +
215P GLU* 3.1 28.7 + - - +
218P GLN* 4.2 19.5 - - - +
254P GLN* 4.1 11.3 + - - +
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Residues in contact with LEU 554 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N ALA* 3.7 19.7 - - + -
97N THR* 3.5 24.9 - - + +
550N ARG 2.9 14.8 + - - +
551N ASN* 3.1 10.3 + - - +
553N ARG* 1.3 76.8 - - - +
555N LYS* 1.3 62.8 + - - +
557N LEU* 3.4 1.8 + - - +
558N LEU* 2.9 30.0 + - + +
567N ILE* 4.2 22.0 - - + -
570N GLU* 3.6 28.7 - - + +
571N LYS* 4.0 23.1 - - + -
574N LEU* 4.0 16.2 - - + -
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Residues in contact with LYS 555 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N GLU* 4.4 11.3 + - - -
27N GLU* 6.2 3.2 - - - +
94N GLU* 4.1 8.2 + - - +
96N ALA* 3.8 20.6 - - + -
551N ASN* 3.0 33.7 + - - +
552N ASN* 3.1 32.4 + - - +
554N LEU* 1.3 76.6 - - - +
556N LYS* 1.3 56.4 + - - +
558N LEU* 3.3 7.6 + - + +
559N ALA* 3.0 29.7 + - - +
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Residues in contact with LYS 556 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552N ASN 3.0 12.5 + - - +
553N ARG* 3.6 7.9 - - - +
555N LYS* 1.3 78.0 - - - +
557N LEU* 1.3 57.1 + - - +
559N ALA* 3.2 6.3 + - + +
560N GLN* 3.0 63.4 + - + +
218P GLN* 3.1 34.3 - - - +
222P ARG* 5.2 6.5 - - - +
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Residues in contact with LEU 557 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553N ARG* 2.9 32.0 + - + +
554N LEU 3.8 2.7 - - - +
556N LYS* 1.3 72.9 - - - +
558N LEU* 1.3 61.0 + - - +
560N GLN* 3.5 5.8 + - - +
561N GLY 3.2 3.6 + - - -
562N ALA* 3.0 36.9 + - + +
566N ILE* 3.7 22.4 - - + +
567N ILE* 3.6 16.1 - - + +
570N GLU* 4.0 18.6 - - + +
214P GLN* 3.4 31.0 - - - +
218P GLN* 4.1 24.0 - - + +
221P ILE* 4.1 13.7 - - + -
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Residues in contact with LEU 558 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96N ALA* 4.4 26.0 - - + +
97N THR* 5.5 2.2 - - + -
554N LEU* 2.9 27.9 + - + +
555N LYS* 3.6 5.8 - - - +
557N LEU* 1.3 77.2 - - - +
559N ALA* 1.3 62.8 + - - +
561N GLY* 3.0 13.9 + - - -
567N ILE* 3.7 32.5 - - + -
571N LYS* 5.1 7.2 - - - +
140P ARG* 4.1 23.3 - - - +
142P ARG* 3.4 46.7 + - - +
144P ILE* 5.1 0.9 - - - +
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Residues in contact with ALA 559 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555N LYS 3.0 16.9 + - - +
556N LYS* 3.2 6.5 + - - +
558N LEU* 1.3 76.7 - - - +
560N GLN* 1.3 62.1 + - + +
561N GLY 3.3 0.9 + - - -
129P GLU* 4.3 2.4 - - - +
132P ARG* 4.2 8.1 + - - -
142P ARG* 4.7 1.5 - - - +
143P HIS 5.5 0.9 - - - +
144P ILE* 3.5 30.1 - - + +
145P PRO* 4.0 30.7 - - + -
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Residues in contact with GLN 560 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556N LYS* 3.0 55.9 + - + +
557N LEU* 4.3 4.9 - - - +
558N LEU 3.2 0.2 - - - -
559N ALA* 1.3 80.5 - - + +
561N GLY* 1.3 60.1 + - - +
562N ALA* 3.5 2.1 + - - -
132P ARG* 3.7 9.6 + - - +
184P ARG* 2.8 31.8 + - - +
218P GLN* 4.6 8.5 - - - +
221P ILE* 4.7 13.5 - - + +
222P ARG* 3.5 34.8 + - - +
225P GLU* 5.5 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