Contacts of the helix formed by residues 448 - 481 (chain A) in PDB entry 2DFS
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 448 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A ILE* 4.2 6.2 + - - -
447A ASN* 1.3 74.3 - - - +
449A PHE* 1.3 67.5 + - - +
450A GLU* 3.4 3.1 - - - -
451A GLN* 2.8 17.2 + - - +
452A PHE* 3.1 21.1 + - - +
559A TYR* 3.7 3.5 - - - -
560A GLN* 4.4 2.0 - - - -
562A GLU 4.0 14.7 + - - -
563A GLY 4.9 0.2 - - - -
564A PHE* 3.7 17.4 - - - -
567A LYS* 2.8 33.1 + - - +
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Residues in contact with PHE 449 (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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247A SER* 4.8 3.8 - - - -
448A SER* 1.3 75.8 + - - +
450A GLU* 1.3 71.1 + - - +
452A PHE* 3.2 4.0 + + - +
453A CYS* 3.0 54.0 + - - -
506A LEU* 4.7 5.8 - - + -
509A LEU* 4.0 20.4 - - + -
564A PHE* 3.6 39.2 - + + -
567A LYS* 3.8 28.7 - - + -
568A ASN* 3.6 28.9 - - + -
636A VAL* 3.8 22.9 - - + -
637A GLY* 3.8 17.0 - - - -
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Residues in contact with GLU 450 (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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219A ARG* 4.7 0.2 - - - +
245A GLU* 3.5 32.6 - - + +
247A SER* 2.7 36.7 + - - +
248A ARG* 5.3 4.5 - - - +
251A PHE* 5.1 2.7 - - - -
448A SER* 3.4 2.6 - - - -
449A PHE* 1.3 79.1 + - + +
451A GLN* 1.3 74.8 + - - +
453A CYS* 3.4 5.7 + - - +
454A ILE* 3.1 29.8 + - - +
567A LYS* 2.6 43.6 + - - +
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Residues in contact with GLN 451 (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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219A ARG* 4.2 2.4 - - - +
442A GLU* 2.9 47.7 + - + +
444A PHE* 3.4 23.9 - - + -
446A ILE 4.3 1.4 - - - +
447A ASN* 3.6 23.5 - - - +
448A SER* 2.8 36.9 + - - +
449A PHE 3.4 0.2 - - - -
450A GLU* 1.3 82.9 - - - +
452A PHE* 1.4 58.9 + - - +
454A ILE* 3.3 7.8 + - - +
455A ASN* 2.9 35.0 + - - -
559A TYR* 4.0 9.9 - - + -
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Residues in contact with PHE 452 (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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448A SER 3.1 13.6 + - - +
449A PHE* 3.2 12.5 + + - +
451A GLN* 1.4 74.6 - - - +
453A CYS* 1.3 62.2 + - - +
455A ASN* 3.6 1.2 + - - +
456A TYR* 3.0 31.7 + + + +
499A ILE* 3.8 41.9 - - + +
505A VAL* 3.6 24.5 - - + -
506A LEU* 3.8 25.1 - - + -
548A PHE* 3.9 22.9 - + - -
550A ILE* 4.3 9.0 - - + -
552A HIS* 5.2 2.8 - - - -
559A TYR* 3.5 36.3 - + + -
564A PHE* 4.1 15.9 - + + -
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Residues in contact with CYS 453 (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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449A PHE* 3.0 52.5 + - - +
450A GLU* 3.6 7.0 - - - +
452A PHE* 1.3 76.7 - - - +
454A ILE* 1.3 63.9 + - + +
456A TYR* 3.5 8.0 + - - +
457A ALA 3.1 18.5 + - - -
506A LEU* 5.6 2.7 - - - -
636A VAL* 5.8 1.1 - - - -
637A GLY* 5.5 1.8 - - - -
640A PHE* 3.1 51.4 - - + -
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Residues in contact with ILE 454 (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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219A ARG* 3.5 19.3 - - - +
245A GLU* 4.4 5.2 - - + +
439A TYR* 3.7 41.7 - - + +
440A GLY 3.2 26.5 - - - +
442A GLU* 3.4 39.5 - - + +
450A GLU 3.1 17.2 + - - +
451A GLN* 3.3 6.0 + - - +
453A CYS* 1.3 75.6 - - + +
455A ASN* 1.3 64.1 + - - +
457A ALA* 3.3 4.7 + - - +
458A ASN* 2.8 30.8 + - - -
640A PHE* 5.6 1.1 - - + -
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Residues in contact with ASN 455 (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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441A PHE* 3.3 27.5 - - + -
442A GLU 2.9 44.6 + - - +
443A THR* 4.5 1.0 + - - -
451A GLN 2.9 13.7 + - - +
452A PHE 4.1 0.4 - - - +
454A ILE* 1.3 73.5 - - - +
456A TYR* 1.4 55.9 + - - +
458A ASN* 3.3 4.1 + - - +
459A GLU* 3.0 33.7 + - - +
552A HIS* 3.9 11.0 - - + +
557A VAL* 4.3 14.1 - - - +
559A TYR* 3.0 29.5 + - - +
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Residues in contact with TYR 456 (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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452A PHE* 3.0 20.9 + + + +
453A CYS* 3.5 6.7 - - - +
455A ASN* 1.4 73.6 - - - +
457A ALA* 1.3 59.4 + - - +
459A GLU* 3.5 5.7 + - + +
460A LYS* 3.3 26.3 + - + +
496A ILE* 5.1 4.9 - - + -
499A ILE* 3.6 35.9 - - + -
500A GLU* 2.6 39.5 + - + +
506A LEU* 3.6 26.2 - - + -
552A HIS* 4.7 1.2 - - - -
637A GLY 5.2 0.2 - - - -
640A PHE* 3.9 25.8 - + - -
641A ARG* 3.2 30.4 - - + +
644A LEU* 3.6 21.2 - - + +
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Residues in contact with ALA 457 (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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243A LEU* 3.8 20.2 - - + -
439A TYR* 4.3 9.9 - - + -
453A CYS 3.1 13.3 + - - +
454A ILE 3.5 8.5 - - - +
456A TYR* 1.3 76.1 - - - +
458A ASN* 1.3 62.7 + - - +
460A LYS* 3.3 6.2 + - - +
461A LEU* 3.1 30.3 + - + +
640A PHE* 4.2 3.4 - - + -
644A LEU* 3.7 28.0 - - + +
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Residues in contact with ASN 458 (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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162A SER* 5.7 0.9 - - - -
439A TYR* 3.8 13.9 - - - +
440A GLY* 2.9 47.0 + - - -
441A PHE* 3.6 28.4 + - + +
454A ILE* 2.8 31.1 + - - +
455A ASN 3.5 7.9 - - - +
457A ALA* 1.3 75.9 - - - +
459A GLU* 1.3 54.9 + - - +
461A LEU* 3.3 13.5 + - - +
462A GLN* 2.8 32.6 + - - +
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Residues in contact with GLU 459 (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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441A PHE* 4.5 2.9 - - + -
455A ASN 3.0 18.2 + - - +
456A TYR* 3.7 10.5 - - + +
457A ALA 3.4 0.2 - - - -
458A ASN* 1.3 74.1 - - - +
460A LYS* 1.4 60.0 + - - +
462A GLN* 4.6 1.9 - - - +
463A GLN* 3.1 12.5 + - - +
492A ASN* 2.9 44.8 + - - +
495A CYS* 3.5 16.4 - - - -
496A ILE* 3.8 17.2 - - + +
499A ILE* 4.8 4.0 - - + -
552A HIS* 3.0 28.9 + - + +
553A PHE* 2.8 43.0 + - - +
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Residues in contact with LYS 460 (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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456A TYR* 3.3 12.0 + - + +
457A ALA 3.3 9.4 + - - +
459A GLU* 1.4 77.2 - - - +
461A LEU* 1.3 59.8 + - - +
463A GLN* 3.2 35.0 + - - +
464A GLN 3.4 5.0 + - - -
493A GLN* 5.5 1.2 + - - -
496A ILE* 4.0 20.9 - - + +
500A GLU* 2.6 44.7 + - - -
644A LEU* 3.7 27.8 - - + -
645A HIS* 2.9 28.9 + - + +
648A MET* 3.4 32.6 - - + +
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Residues in contact with LEU 461 (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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160A ILE* 4.5 19.5 - - + -
162A SER* 6.3 0.7 - - - -
436A LEU* 4.5 4.5 - - + -
438A ILE* 4.1 38.6 - - + -
439A TYR* 5.5 0.9 - - + +
457A ALA* 3.1 21.6 + - + +
458A ASN* 3.3 16.1 + - - +
460A LYS* 1.3 72.4 - - - +
462A GLN* 1.3 64.6 + - - +
464A GLN* 3.2 6.8 + - - +
465A PHE* 3.1 21.7 + - - +
644A LEU* 6.1 0.4 - - + -
647A LEU* 5.2 4.9 - - + -
648A MET* 4.0 13.7 - - + -
651A LEU* 3.8 29.2 - - + -
658A TYR* 4.7 4.9 + - + -
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Residues in contact with GLN 462 (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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441A PHE* 5.3 7.5 - - + -
458A ASN 2.8 21.6 + - - +
459A GLU* 4.1 4.9 - - - +
461A LEU* 1.3 72.0 - - - +
463A GLN* 1.3 55.5 + - - +
465A PHE* 3.3 24.4 + - - +
466A ASN* 2.8 58.6 + - - +
492A ASN* 4.6 2.2 - - - +
553A PHE* 3.4 50.4 - - + -
660A ARG* 2.9 28.9 + - - -
686A GLY* 4.5 3.1 - - - -
690A THR* 3.7 8.9 + - - -
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Residues in contact with GLN 463 (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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459A GLU 3.1 16.1 + - - +
460A LYS* 3.2 27.2 + - - +
461A LEU 3.3 0.2 - - - -
462A GLN* 1.3 74.8 - - - +
464A GLN* 1.4 63.6 + - - +
466A ASN* 3.4 4.7 + - - +
467A MET* 3.1 43.1 + - + +
489A PHE* 5.1 1.1 - - + -
491A ASP* 5.7 1.6 - - - +
492A ASN* 3.3 26.8 + - - +
493A GLN* 2.8 30.3 + - - +
496A ILE* 3.5 11.8 - - + +
648A MET* 4.5 8.5 - - - +
652A ASN* 6.0 1.0 - - - +
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Residues in contact with GLN 464 (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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160A ILE* 4.0 15.9 - - - +
460A LYS 3.4 2.0 + - - -
461A LEU* 3.2 10.9 + - - +
463A GLN* 1.4 80.5 - - - +
465A PHE* 1.4 56.4 + - - +
467A MET* 3.4 10.6 + - + +
468A HIS* 2.9 28.7 + - + +
648A MET* 3.9 20.2 - - + +
651A LEU* 2.9 37.3 + - - +
652A ASN* 2.9 32.5 + - - +
656A PRO* 4.1 12.7 - - + +
658A TYR* 3.5 15.8 + - - +
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Residues in contact with PHE 465 (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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105A ILE* 4.1 4.7 - - + -
106A VAL* 3.4 34.8 - - + -
461A LEU 3.1 13.2 + - - +
462A GLN* 3.3 33.6 + - - +
464A GLN* 1.4 75.7 - - - +
466A ASN* 1.4 59.2 + - - +
468A HIS* 3.2 4.0 + - - +
469A VAL* 2.9 60.0 + - + +
658A TYR* 3.6 49.7 + + + +
660A ARG* 4.4 8.7 - - - +
690A THR* 3.7 32.8 - - + -
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Residues in contact with ASN 466 (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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462A GLN* 2.8 50.4 + - - +
463A GLN* 3.4 6.5 + - - +
465A PHE* 1.4 75.4 - - - +
467A MET* 1.3 61.1 + - - +
469A VAL* 3.6 5.2 + - - +
470A PHE* 3.1 23.6 + - - +
489A PHE* 3.7 19.1 - - + -
490A TYR* 3.6 19.2 + - - +
492A ASN* 3.7 18.2 + - - -
553A PHE* 3.8 22.8 - - - -
693A ILE* 6.6 0.4 - - - -
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Residues in contact with MET 467 (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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463A GLN* 3.1 32.0 + - + +
464A GLN* 3.7 10.8 - - + +
466A ASN* 1.3 76.4 - - - +
468A HIS* 1.3 60.6 + - - +
470A PHE* 3.4 5.0 + - - +
471A LYS* 3.1 23.4 + - - +
489A PHE* 3.9 23.3 - - + -
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Residues in contact with HIS 468 (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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105A ILE* 4.1 9.8 - - + +
464A GLN* 2.9 18.3 + - + +
465A PHE* 3.2 8.3 + - - +
467A MET* 1.3 75.2 - - - +
469A VAL* 1.4 61.4 + - - +
471A LYS* 3.4 10.5 + - + +
472A LEU* 3.2 52.0 + - + +
655A THR* 3.3 28.1 - - + +
656A PRO* 3.3 46.4 + - + +
658A TYR* 4.1 3.5 - - + +
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Residues in contact with VAL 469 (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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105A ILE* 3.5 24.2 - - + -
465A PHE* 2.9 52.7 + - + +
466A ASN* 3.9 5.6 - - - +
468A HIS* 1.4 73.7 - - - +
470A PHE* 1.4 57.7 + - - +
472A LEU* 3.2 6.1 + - + +
473A GLU* 2.9 40.4 + - + +
690A THR* 5.7 3.6 - - + -
694A SER* 6.2 0.2 - - - +
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Residues in contact with PHE 470 (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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466A ASN 3.1 18.3 + - - +
467A MET* 3.5 6.5 - - - +
468A HIS 3.4 0.2 - - - -
469A VAL* 1.4 77.3 - - - +
471A LYS* 1.3 62.3 + - - +
473A GLU* 3.6 5.7 + - - +
474A GLN* 3.1 59.5 + - - +
484A TRP 5.7 0.9 - - - -
487A ILE* 3.5 48.4 - - + +
488A ASP 4.8 0.2 - - - -
489A PHE* 3.7 41.5 - + + -
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Residues in contact with LYS 471 (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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467A MET 3.1 12.9 + - - +
468A HIS* 3.7 14.1 - - + +
470A PHE* 1.3 77.5 - - - +
472A LEU* 1.3 63.9 + - + +
474A GLN* 3.3 20.2 + - + +
475A GLU* 2.6 65.9 + - - +
478A MET* 5.5 2.8 - - - +
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Residues in contact with LEU 472 (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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105A ILE* 3.9 39.7 - - + -
468A HIS* 3.2 39.5 + - + +
469A VAL* 3.2 5.3 + - + +
471A LYS* 1.3 72.8 - - + +
473A GLU* 1.4 63.4 + - - +
475A GLU* 3.2 22.1 + - + +
476A GLU* 3.0 24.5 + - - +
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Residues in contact with GLU 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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469A VAL* 2.9 28.8 + - + +
470A PHE* 3.9 7.0 - - - +
472A LEU* 1.4 73.7 - - - +
474A GLN* 1.3 56.4 + - - +
476A GLU* 3.5 8.5 + - - +
477A TYR* 2.9 45.5 + - - +
487A ILE* 3.9 22.5 - - + +
698A PHE 5.7 0.3 + - - -
701A ARG* 2.6 47.8 + - - -
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Residues in contact with GLN 474 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A PHE* 3.1 48.6 + - + +
471A LYS* 3.3 22.0 + - + +
473A GLU* 1.3 75.7 - - - +
475A GLU* 1.3 55.7 + - + +
477A TYR* 3.4 5.9 + - - +
478A MET* 2.9 45.1 + - + +
484A TRP* 4.4 27.7 + - + +
487A ILE* 4.2 13.5 - - + -
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Residues in contact with GLU 475 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A LYS* 2.6 51.3 + - - +
472A LEU* 3.2 23.8 + - + +
474A GLN* 1.3 75.7 - - + +
476A GLU* 1.3 56.1 + - - +
478A MET* 3.4 19.6 + - + +
479A LYS* 3.1 27.9 + - - +
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Residues in contact with GLU 476 (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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472A LEU 3.0 15.7 + - - +
473A GLU* 3.5 7.6 - - - +
475A GLU* 1.3 71.9 - - - +
477A TYR* 1.4 65.8 + - - +
479A LYS* 3.3 21.4 + - - +
480A GLU* 3.3 13.0 + - - +
701A ARG* 2.7 40.3 + - - +
748A LYS* 2.7 37.7 + - - -
750A PHE* 3.2 10.4 - - + -
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Residues in contact with TYR 477 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473A GLU* 2.9 49.1 + - - +
474A GLN* 3.6 7.9 - - - +
476A GLU* 1.4 71.3 - - - +
478A MET* 1.4 57.0 + - - +
480A GLU* 3.4 4.5 + - - -
481A GLN 3.1 22.0 + - - -
482A ILE* 3.1 39.4 + - + +
483A PRO 3.5 25.1 - - - -
484A TRP* 4.2 8.1 - - + -
486A LEU* 3.5 21.5 + - + -
487A ILE* 3.6 29.6 - - + +
697A GLY* 5.1 1.4 - - - -
698A PHE* 3.6 25.9 + + - +
701A ARG* 4.2 2.9 + - - -
750A PHE* 4.0 27.1 - + - -
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Residues in contact with MET 478 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A LYS* 5.5 2.2 - - - +
474A GLN* 2.9 31.1 + - + +
475A GLU* 3.7 25.1 - - + +
476A GLU 3.4 0.2 - - - -
477A TYR* 1.4 73.2 - - - +
479A LYS* 1.4 63.6 + - - +
481A GLN* 3.1 20.0 + - - +
482A ILE 5.1 1.6 - - - +
484A TRP* 5.0 23.8 - - + -
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Residues in contact with LYS 479 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A GLU 3.1 14.3 + - - +
476A GLU* 3.3 18.8 + - - +
478A MET* 1.4 74.4 - - - +
480A GLU* 1.3 91.5 + - + +
481A GLN* 4.7 2.0 - - - +
746A LYS* 4.1 23.2 - - + +
747A THR* 3.3 15.3 + - - +
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Residues in contact with GLU 480 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU* 3.3 10.8 + - - +
477A TYR 3.9 6.1 - - - +
478A MET 3.2 0.4 - - - -
479A LYS* 1.3 104.2 + - + +
481A GLN* 1.4 69.3 + - - +
482A ILE* 3.6 11.2 - - + -
744A PHE 4.9 0.2 - - - +
745A GLY* 3.3 13.8 - - - -
746A LYS* 2.9 28.6 + - - +
747A THR* 2.8 33.9 + - - -
748A LYS* 2.9 33.0 + - - -
750A PHE* 3.7 20.0 - - + -
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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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477A TYR 3.1 3.8 + - - -
478A MET* 3.1 15.6 + - - +
479A LYS 4.7 2.9 - - - +
480A GLU* 1.4 79.9 - - - +
482A ILE* 1.3 62.1 + - - +
483A PRO* 4.5 1.7 - - - +
744A PHE 5.2 2.9 - - - +
746A LYS* 3.3 35.1 - - + +
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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) + - + + + + + -
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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