Contacts of the helix formed by residues 469 - 503 (chain A) in PDB entry 3LZI
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 GLY 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A ASN* 3.8 8.5 + - - -
426A SER* 3.7 5.2 - - - -
428A GLU* 3.4 7.9 - - - -
429A THR* 3.7 13.9 - - - -
468A ASP* 1.3 78.0 + - - +
470A VAL* 1.3 60.5 + - - -
471A VAL 3.2 3.3 + - - -
472A PRO* 3.3 7.8 - - - +
473A THR* 2.9 33.6 + - - -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 6.0 0.4 - - + -
369A ILE* 3.8 31.8 - - + +
372A SER* 3.6 32.5 - - - +
373A LEU* 3.8 22.9 - - + -
376A GLN* 5.8 0.9 - - - +
426A SER* 3.4 2.4 + - - +
427A PRO* 4.6 7.0 - - + -
428A GLU* 2.7 30.5 + - - +
469A GLY* 1.3 71.2 - - - -
471A VAL* 1.3 66.3 + - + +
473A THR* 4.5 4.0 - - - -
474A GLU* 2.9 32.6 + - + +
577A TYR* 5.8 0.2 - - + -
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ILE* 4.4 19.1 - - + -
420A ILE* 3.7 25.4 - - + -
425A ILE 3.8 6.1 - - - +
426A SER* 3.2 12.7 + - - +
427A PRO* 3.8 17.5 - - + -
470A VAL* 1.3 80.5 - - + +
472A PRO* 1.4 67.4 - - + +
474A GLU* 5.1 1.3 - - - -
475A ILE* 2.9 34.7 + - + +
566A LEU* 3.8 30.1 - - + +
570A LEU* 5.3 12.3 - - + -
577A TYR* 5.9 1.8 - - + -
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Residues in contact with PRO 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ILE* 3.8 19.3 - - + +
421A ARG* 4.4 10.5 - - + +
424A ASN* 3.5 28.3 - - - +
425A ILE 3.4 17.5 - - - +
426A SER* 3.7 4.7 - - - -
468A ASP* 6.2 0.4 - - + -
469A GLY* 3.3 15.5 - - - +
471A VAL* 1.4 95.5 - - + +
473A THR* 1.3 56.8 + - - +
475A ILE* 3.4 8.8 - - + +
476A THR* 2.4 36.2 + - - +
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Residues in contact with THR 473 (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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372A SER* 5.2 1.6 - - - +
468A ASP* 4.0 18.7 + - - +
469A GLY 2.9 26.2 + - - -
470A VAL* 3.9 5.6 - - - -
471A VAL 3.2 0.2 - - - -
472A PRO* 1.3 78.5 - - - +
474A GLU* 1.3 77.5 + - - +
476A THR* 3.4 11.4 + - - -
477A LYS* 3.5 20.8 + - + +
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Residues in contact with GLU 474 (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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350A TYR* 4.4 1.7 + - - -
365A TRP* 3.9 10.6 - - + -
368A ILE* 3.6 30.9 - - + +
369A ILE* 4.9 4.3 - - + -
372A SER* 2.5 39.6 + - - +
470A VAL* 2.9 23.0 + - + +
471A VAL* 4.4 1.8 - - - +
473A THR* 1.3 84.3 - - - +
475A ILE* 1.3 62.0 + - - +
477A LYS* 3.0 46.0 + - - +
478A VAL* 3.6 18.5 + - - +
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Residues in contact with ILE 475 (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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365A TRP* 4.1 6.3 - - + -
417A PRO* 3.9 15.7 - - + +
420A ILE* 3.8 29.4 - - + -
421A ARG* 3.7 21.8 - - + -
471A VAL 2.9 23.3 + - - +
472A PRO* 3.4 9.9 - - + +
474A GLU* 1.3 76.0 - - - +
476A THR* 1.3 63.7 + - - +
478A VAL 3.5 0.7 + - - -
479A PHE* 2.9 29.0 + - - +
563A ILE* 3.5 44.9 - - + +
566A LEU* 3.8 17.9 - - + -
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Residues in contact with THR 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ARG* 3.3 45.0 + - - +
472A PRO 2.4 28.0 + - - -
473A THR* 3.6 6.5 - - - -
474A GLU 3.4 0.2 - - - -
475A ILE* 1.3 74.0 - - - +
477A LYS* 1.3 61.2 + - - +
479A PHE* 3.5 2.8 - - + +
480A ASN* 2.8 47.2 + - - +
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Residues in contact with LYS 477 (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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350A TYR* 3.4 26.2 + - - +
473A THR* 3.5 17.4 + - + +
474A GLU* 3.0 38.8 + - - +
475A ILE 3.3 0.6 - - - -
476A THR* 1.3 79.7 - - + +
478A VAL* 1.3 61.5 + - - +
480A ASN* 3.5 7.4 + - - +
481A GLN* 3.3 29.3 + - - +
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Residues in contact with VAL 478 (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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350A TYR* 3.7 30.5 - - + +
365A TRP* 3.9 15.3 - - + -
474A GLU 3.6 10.5 + - - +
475A ILE 3.5 2.1 + - - +
476A THR 3.3 0.2 - - - -
477A LYS* 1.3 71.9 - - - +
479A PHE* 1.3 66.4 + - - +
481A GLN* 3.3 13.1 + - - +
482A ARG* 3.0 21.5 + - - +
559A ARG* 4.1 29.6 - - + +
562A LEU* 4.3 17.3 - - + -
563A ILE* 3.6 23.1 - - + -
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Residues in contact with PHE 479 (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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413A THR* 4.3 16.8 - - + -
414A SER* 3.6 36.1 - - - -
417A PRO* 5.4 3.1 - - + -
418A SER* 5.2 3.4 - - - -
421A ARG* 3.5 34.5 - - - +
475A ILE 2.9 17.9 + - - +
476A THR* 3.5 6.7 - - - +
478A VAL* 1.3 76.9 - - - +
480A ASN* 1.3 79.7 + - - +
482A ARG* 3.0 23.0 + - - +
483A LYS* 3.1 36.0 + - + +
563A ILE* 3.9 17.3 - - + +
682A PHE* 6.5 1.3 - + - -
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Residues in contact with ASN 480 (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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421A ARG* 5.4 1.6 + - - -
476A THR* 2.8 40.3 + - - +
477A LYS* 3.9 7.2 - - - +
478A VAL 3.3 0.4 - - - -
479A PHE* 1.3 91.0 - - - +
481A GLN* 1.3 62.4 + - + +
483A LYS* 3.4 26.5 - - + +
484A GLU* 3.4 10.2 + - - +
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Residues in contact with GLN 481 (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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350A TYR* 3.4 35.4 + - - -
477A LYS* 3.3 18.0 + - - +
478A VAL* 3.3 14.7 + - - +
479A PHE 3.2 0.2 - - - -
480A ASN* 1.3 76.4 - - + +
482A ARG* 1.3 64.0 + - - +
484A GLU* 3.4 12.6 + - - +
485A HIS* 3.2 30.4 + - + +
559A ARG* 3.5 30.7 + - - +
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Residues in contact with ARG 482 (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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413A THR* 4.7 5.7 - - - +
414A SER* 4.2 14.2 + - - -
478A VAL 3.0 13.2 + - - +
479A PHE* 3.0 21.3 + - - +
481A GLN* 1.3 77.3 - - - +
483A LYS* 1.3 61.8 + - - +
485A HIS* 3.3 1.6 + - - -
486A LYS* 2.8 46.5 + - - +
556A GLN* 2.9 51.4 + - - +
559A ARG* 3.8 16.3 - - + +
560A LYS* 3.7 31.2 - - - +
563A ILE* 5.1 2.5 - - + -
904A DTP 2.7 48.6 + - - -
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Residues in contact with LYS 483 (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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413A THR* 6.4 0.7 - - + -
479A PHE* 3.1 43.1 + - + +
480A ASN* 3.4 20.9 - - - +
482A ARG* 1.3 75.5 - - - +
484A GLU* 1.3 62.9 + - - +
486A LYS* 3.4 9.7 + - + +
487A GLY* 2.9 24.6 + - - -
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Residues in contact with GLU 484 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A ASN 3.4 7.8 + - - +
481A GLN* 3.4 16.8 + - - +
483A LYS* 1.3 82.6 - - + +
485A HIS* 1.3 72.0 + - - +
487A GLY* 3.1 12.4 + - - -
488A TYR* 2.7 56.1 + - + +
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Residues in contact with HIS 485 (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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481A GLN* 3.2 24.4 + - + +
482A ARG 3.8 5.4 - - - +
484A GLU* 1.3 85.9 + - + +
486A LYS* 1.3 57.5 + - - +
488A TYR* 3.2 27.0 + + - +
489A MET* 2.9 27.5 + - - +
552A GLY* 4.0 7.5 - - - +
555A ALA* 3.4 34.0 - - + +
556A GLN* 3.9 11.0 - - + +
559A ARG* 4.0 28.4 + - - -
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Residues in contact with LYS 486 (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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413A THR* 6.0 2.0 - - + +
482A ARG* 2.8 44.9 + - - +
483A LYS* 3.6 9.9 - - + +
484A GLU 3.2 0.2 - - - -
485A HIS* 1.3 76.4 - - - +
487A GLY* 1.3 57.5 + - - +
489A MET* 3.2 15.4 + - + +
490A LEU* 2.9 44.0 + - + +
556A GLN* 3.6 25.3 - - + +
716A GLU* 2.9 36.5 + - - -
904A DTP 4.4 10.0 + - - -
908A CA 3.9 6.9 - - - -
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Residues in contact with GLY 487 (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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483A LYS 2.9 15.3 + - - -
484A GLU* 3.1 5.5 + - - -
486A LYS* 1.3 74.9 - - - +
488A TYR* 1.3 66.5 + - - +
490A LEU* 4.1 6.3 - - - +
491A ALA* 3.0 26.5 + - - +
494A ARG* 4.7 2.5 + - - -
519A ARG 4.2 0.4 - - - +
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Residues in contact with TYR 488 (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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484A GLU* 2.7 51.5 + - + +
485A HIS* 3.5 27.4 - + - +
487A GLY* 1.3 74.1 - - - +
489A MET* 1.3 66.8 + - - +
491A ALA* 4.0 1.4 - - - +
492A ALA* 3.1 24.6 + - - +
519A ARG* 3.7 66.4 + - + +
520A PHE* 3.8 28.5 - + - -
548A THR* 5.5 2.2 - - + +
552A GLY* 5.2 6.3 - - - -
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Residues in contact with MET 489 (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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485A HIS 2.9 13.6 + - - +
486A LYS* 3.2 23.5 + - + +
488A TYR* 1.3 78.3 - - - +
490A LEU* 1.3 80.7 + - + +
492A ALA* 3.2 4.2 + - - +
493A GLN* 3.0 33.6 + - - +
548A THR 5.2 0.2 - - - -
549A GLU* 3.5 31.8 - - + +
552A GLY* 4.0 12.3 - - - +
553A MET* 3.5 46.7 - - + +
556A GLN* 3.9 15.9 - - - +
716A GLU* 5.9 0.7 - - - +
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Residues in contact with LEU 490 (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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486A LYS* 2.9 42.6 + - + +
487A GLY* 4.1 5.2 - - - +
489A MET* 1.3 93.4 - - + +
491A ALA* 1.3 57.7 + - - +
493A GLN* 3.1 26.3 + - - +
494A ARG* 2.8 48.7 + - - +
716A GLU* 4.3 37.0 - - + +
718A THR* 4.5 3.5 + - - +
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Residues in contact with ALA 491 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A GLY 3.0 14.9 + - - +
488A TYR 4.0 0.2 - - - +
490A LEU* 1.3 75.0 - - - +
492A ALA* 1.3 57.7 + - - +
494A ARG* 3.2 22.4 + - - +
495A ASN* 2.8 34.7 + - - -
518A TYR 3.9 2.5 - - - -
519A ARG 3.2 28.9 - - - +
520A PHE* 4.1 0.2 - - - -
521A ASP* 3.8 18.3 - - - +
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Residues in contact with ALA 492 (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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488A TYR 3.1 18.4 + - - +
489A MET 3.2 5.4 + - - +
491A ALA* 1.3 76.4 - - - +
493A GLN* 1.3 56.7 + - - +
495A ASN* 3.8 3.9 - - - +
496A GLY* 3.0 23.2 + - - -
518A TYR* 3.2 19.2 + - + +
545A ALA* 3.7 15.4 - - - +
548A THR* 3.9 7.9 - - + -
549A GLU* 3.6 32.1 - - - +
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Residues in contact with GLN 493 (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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489A MET* 3.0 21.5 + - - +
490A LEU* 3.1 29.3 + - - +
492A ALA* 1.3 75.1 - - - +
494A ARG* 1.3 64.0 + - - +
496A GLY* 3.1 11.3 + - - -
497A GLU* 3.3 18.1 + - + +
549A GLU* 3.2 35.3 + - - +
553A MET* 6.3 0.4 - - - +
715A MET* 4.1 5.7 - - - +
718A THR* 2.5 35.3 + - + +
720A TYR* 5.1 8.6 + - + -
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Residues in contact with ARG 494 (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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487A GLY* 4.7 2.2 + - - -
490A LEU* 2.8 42.5 + - - +
491A ALA* 3.5 22.4 - - - +
493A GLN* 1.3 72.2 - - - +
495A ASN* 1.3 63.5 + - - +
497A GLU* 3.0 14.9 + - - +
498A ILE* 3.2 18.5 + - + +
521A ASP* 2.7 45.1 + - - +
716A GLU 4.7 7.7 + - - -
717A GLY* 3.9 17.2 - - - -
718A THR* 3.7 27.1 + - - +
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Residues in contact with ASN 495 (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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491A ALA 2.8 20.0 + - - +
492A ALA* 3.8 6.1 - - - +
494A ARG* 1.3 71.7 - - - +
496A GLY* 1.3 61.4 + - - +
498A ILE* 3.3 14.8 + - - +
499A ILE* 3.2 27.1 + - - +
518A TYR* 3.3 23.5 + - + +
520A PHE 2.9 25.1 + - - -
521A ASP* 3.5 6.3 - - - +
522A PHE* 2.9 56.2 + - + +
545A ALA* 5.0 0.2 - - - -
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Residues in contact with GLY 496 (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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492A ALA 3.0 16.5 + - - -
493A GLN* 3.1 7.0 + - - -
495A ASN* 1.3 76.6 - - - +
497A GLU* 1.3 58.2 + - - +
499A ILE* 3.4 2.5 + - - +
500A LYS* 3.2 31.6 + - - +
542A LEU* 3.5 21.5 - - - +
545A ALA* 4.4 9.4 - - - +
546A GLN* 6.0 1.3 - - - -
549A GLU* 6.0 0.4 - - - -
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Residues in contact with GLU 497 (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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493A GLN* 3.3 14.6 + - + +
494A ARG* 3.0 9.2 + - - +
496A GLY* 1.3 74.5 - - - +
498A ILE* 1.3 63.8 + - + +
500A LYS* 3.4 31.2 + - - +
501A GLU* 3.2 28.9 + - + +
718A THR* 3.8 14.3 - - + +
719A ARG 3.8 18.4 - - - +
720A TYR* 3.4 17.8 - - - +
721A ALA* 2.8 37.3 + - - +
722A GLU 4.7 0.3 + - - -
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Residues in contact with ILE 498 (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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494A ARG* 3.2 13.5 + - + +
495A ASN* 3.3 28.0 + - - +
497A GLU* 1.3 75.8 - - + +
499A ILE* 1.3 65.6 + - - +
501A GLU* 3.4 7.2 + - - +
502A ALA* 3.1 21.4 + - + +
521A ASP* 5.9 1.3 - - + +
522A PHE* 4.1 21.8 - - + +
527A LYS* 4.1 38.8 - - + +
530A ILE* 4.8 13.0 - - + -
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Residues in contact with ILE 499 (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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495A ASN 3.2 15.5 + - - +
496A GLY* 3.4 6.5 + - - +
497A GLU 3.4 0.2 - - - -
498A ILE* 1.3 76.0 - - - +
500A LYS* 1.3 57.5 + - - +
502A ALA* 3.2 8.1 + - - +
503A LEU* 3.0 29.2 + - + +
518A TYR* 4.3 7.9 - - + -
522A PHE* 4.2 12.8 - - + -
530A ILE* 4.9 8.1 - - + -
538A LEU* 3.2 40.8 - - + +
541A MET* 3.5 38.4 - - + +
542A LEU* 3.6 15.5 - - + +
545A ALA* 4.1 10.8 - - + -
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Residues in contact with LYS 500 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496A GLY* 3.2 13.4 + - - +
497A GLU* 3.4 35.3 + - - +
498A ILE 3.3 0.2 - - - -
499A ILE* 1.3 77.8 - - - +
501A GLU* 1.3 62.7 + - - +
503A LEU* 3.3 22.9 + - + +
504A HIS* 3.7 15.2 + - - -
542A LEU* 3.9 34.8 - - + -
546A GLN* 4.6 9.7 + - - -
721A ALA* 4.4 13.5 - - + -
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Residues in contact with GLU 501 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A GLU* 3.2 20.4 + - + +
498A ILE* 3.8 6.7 - - - +
499A ILE 3.3 0.2 - - - -
500A LYS* 1.3 75.0 - - - +
502A ALA* 1.3 62.5 + - - +
504A HIS* 3.3 37.2 + - - +
505A ASN* 4.6 1.0 + - - +
720A TYR 5.1 0.2 - - - +
721A ALA* 3.8 31.1 - - + +
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Residues in contact with ALA 502 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A ILE 3.1 17.3 + - - +
499A ILE* 3.2 6.7 + - - +
501A GLU* 1.3 73.0 - - - +
503A LEU* 1.3 56.1 + - - +
504A HIS 3.0 9.9 + - - -
505A ASN* 3.1 24.9 + - - +
530A ILE* 3.6 31.4 - - + +
531A LYS* 5.3 8.1 - - + +
538A LEU* 3.6 14.9 - - + +
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Residues in contact with LEU 503 (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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499A ILE* 3.0 26.0 + - + +
500A LYS* 3.4 20.4 - - + +
501A GLU 3.2 0.6 - - - -
502A ALA* 1.3 74.0 - - - +
504A HIS* 1.3 61.4 + - - +
505A ASN 3.3 0.7 - - - -
506A PRO* 3.5 13.2 - - + +
535A ALA* 4.0 14.8 - - + +
538A LEU* 3.7 28.5 - - + -
539A ASN* 3.6 37.2 - - - +
542A LEU* 4.4 11.9 - - + -
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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
------------------------------------------------------------
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