Contacts of the strand formed by residues 441 - 466 (chain A) in PDB entry 2W77
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 ALA 441 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A ILE* 4.2 10.1 - - + -
434A TRP* 3.7 25.6 - - + -
440A SER* 1.3 78.7 + - - +
442A LYS* 1.3 65.7 - - - +
499A THR* 3.3 6.1 - - - -
500A THR* 2.9 46.5 + - + -
503A PHE* 4.1 20.0 - - + -
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Residues in contact with LYS 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE* 3.6 1.9 - - - -
431A MET 3.2 30.2 + - - +
434A TRP* 3.5 42.7 + - + +
441A ALA* 1.3 79.8 - - - +
443A ILE* 1.3 66.6 + - - +
444A VAL* 6.4 0.2 - - + -
498A ASN* 3.5 23.8 - - - +
499A THR* 3.9 26.9 - - + -
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Residues in contact with ILE 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ALA* 5.8 0.4 - - + -
388A TRP* 5.4 0.9 - - + -
428A GLY* 4.2 4.5 - - - -
429A ALA 3.6 17.7 - - - +
430A ILE* 3.3 32.3 - - + +
442A LYS* 1.3 74.1 - - - +
444A VAL* 1.3 81.6 + - - +
445A ALA* 4.2 11.2 + - + +
496A TYR* 4.5 4.8 - - + +
498A ASN* 2.8 44.4 + - + +
500A THR* 4.2 11.4 - - + -
506A TRP* 4.0 11.9 - - + -
510A ILE* 2.9 38.8 - - + -
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Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TRP* 4.9 9.8 - - + +
427A LEU 4.4 0.3 - - - +
428A GLY* 3.5 1.4 - - - -
429A ALA* 3.0 31.0 + - - +
431A MET* 4.1 43.7 - - + +
442A LYS* 4.0 1.7 + - + +
443A ILE* 1.3 78.1 - - - +
445A ALA* 1.3 62.7 + - - +
446A GLN* 3.9 27.5 + - + +
498A ASN* 5.8 0.4 - - - +
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TRP* 4.0 19.5 - - + -
427A LEU 3.3 12.6 - - - +
428A GLY* 4.2 1.3 - - - -
443A ILE* 4.0 8.8 + - + -
444A VAL* 1.3 75.1 - - - +
446A GLN* 1.3 64.6 + - - +
491A TRP 5.3 0.7 - - - +
493A LEU* 3.4 37.8 - - + +
496A TYR* 4.3 7.0 - - + -
513A PRO* 4.2 8.5 - - + -
515A TRP* 3.8 2.7 - - + -
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TRP* 3.5 29.1 + - - +
425A ALA 3.6 1.0 - - - +
427A LEU* 3.0 30.9 + - - +
444A VAL* 3.9 19.5 - - + +
445A ALA* 1.3 78.0 - - - +
447A LYS* 1.3 61.3 + - - +
448A TYR* 2.2 46.7 + - + +
490A TYR 3.7 9.9 - - - +
491A TRP* 4.4 17.5 - - + +
515A TRP* 3.5 6.1 - - - -
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Residues in contact with LYS 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A HIS* 4.4 10.1 - - - -
425A ALA 3.3 9.6 - - - +
426A PRO* 4.0 10.1 - - + -
446A GLN* 1.3 75.9 - - - +
448A TYR* 1.3 66.6 + - - +
449A THR* 3.9 23.3 - - + -
489A SER* 3.6 2.1 - - - -
490A TYR* 2.9 57.0 + - + -
515A TRP* 3.6 41.3 - - + +
1818A PO4 2.8 40.0 + - - -
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Residues in contact with TYR 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A TRP* 4.8 11.7 - + - -
423A TYR* 3.8 20.1 - - + +
424A HIS 3.7 0.2 - - - -
425A ALA* 2.6 50.5 + - + +
427A LEU* 4.9 11.4 - - + -
446A GLN* 2.2 51.9 + - + +
447A LYS* 1.3 75.5 - - - +
449A THR* 1.3 57.2 + - - +
488A LYS 3.6 3.8 - - - +
489A SER* 3.5 32.5 - - - -
490A TYR 5.3 0.4 - - - -
491A TRP* 4.6 13.7 - + - -
520A GLN* 5.5 0.9 - - - -
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Residues in contact with THR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A TYR* 3.5 17.6 + - - -
424A HIS* 4.1 18.8 - - + +
425A ALA 4.7 0.2 - - - +
447A LYS* 3.9 28.5 - - + -
448A TYR* 1.3 76.8 - - - +
450A GLY* 1.3 59.8 + - - +
487A GLY* 3.4 1.4 - - - -
488A LYS* 3.0 50.8 + - - +
490A TYR* 5.0 8.0 - - + -
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Residues in contact with GLY 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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394A TYR* 4.7 2.6 + - - -
422A GLY* 3.6 0.9 - - - -
423A TYR* 2.9 51.9 + - - +
449A THR* 1.3 78.2 - - - +
451A GLU* 1.3 62.1 + - - +
486A GLU 3.3 11.7 - - - -
487A GLY* 3.9 1.6 - - - -
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Residues in contact with GLU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 3.1 23.4 + - - +
396A ARG* 4.8 4.0 + - - -
420A ILE* 3.4 36.0 - - + +
421A ASN 3.7 5.4 - - - +
422A GLY* 4.2 0.2 - - - -
423A TYR* 4.3 1.4 - - - -
450A GLY* 1.3 75.2 - - - +
452A THR* 1.3 69.8 + - - +
453A LYS* 4.1 22.7 - - + -
484A HIS 3.8 1.0 - - - +
485A TRP* 3.6 1.5 - - - -
486A GLU* 2.8 40.1 + - + +
1821A PO4 4.5 2.1 + - - -
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Residues in contact with THR 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 6.2 0.2 - - - -
230A GLY 3.4 18.7 + - - -
231A TYR* 3.6 37.5 - - + +
419A LYS 3.7 0.5 - - - +
420A ILE* 3.3 8.8 - - - +
421A ASN* 2.9 42.5 + - + +
451A GLU* 1.3 79.5 + - - +
453A LYS* 1.3 64.9 + - - +
454A SER* 4.3 10.8 - - - +
484A HIS 3.4 20.6 - - - +
485A TRP* 3.5 11.4 - - - -
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Residues in contact with LYS 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A HIS* 5.0 9.2 - - + -
419A LYS 3.4 4.9 - - - +
420A ILE* 4.3 6.3 - - + -
451A GLU* 4.1 27.4 - - + +
452A THR* 1.3 77.0 - - - +
454A SER* 1.3 61.1 + - - +
482A PHE 4.1 0.3 - - - +
483A SER* 3.2 2.1 - - - -
484A HIS* 2.9 38.3 + - + +
486A GLU* 5.5 9.7 + - - +
1821A PO4 3.4 30.4 + - - +
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Residues in contact with SER 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 4.5 10.0 + - - -
417A ASP 4.2 0.2 - - - -
418A HIS* 3.4 1.4 + - - -
419A LYS* 2.8 42.9 + - - +
421A ASN* 5.3 3.8 + - - -
452A THR* 4.3 6.1 - - - +
453A LYS* 1.3 72.8 - - - +
455A ASN* 1.3 75.4 + - - +
456A SER* 5.7 2.0 - - - -
481A SER* 6.5 1.3 - - - -
482A PHE 3.4 5.2 - - - -
483A SER* 2.9 24.2 - - - -
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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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417A ASP 3.1 12.4 + - - +
418A HIS* 3.0 31.7 + - - +
454A SER* 1.3 83.9 + - - +
456A SER* 1.3 62.1 + - - +
480A ALA 3.9 0.3 - - - +
481A SER* 3.3 5.2 - - - -
482A PHE* 2.7 47.6 + - + +
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Residues in contact with SER 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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222A ILE* 4.3 19.2 - - - +
223A PRO 4.9 4.0 + - - -
415A GLN 4.1 1.3 - - - -
416A LEU* 3.4 11.6 - - - +
417A ASP* 2.9 46.7 + - - +
454A SER* 5.7 2.9 - - - -
455A ASN* 1.3 77.2 + - - +
457A LEU* 1.3 64.0 + - - +
458A ASP* 5.9 1.3 - - - -
480A ALA 3.4 6.1 - - - -
481A SER* 3.8 13.7 - - - -
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Residues in contact with LEU 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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414A VAL* 3.9 20.4 - - + -
415A GLN 3.4 3.4 - - - +
416A LEU* 4.8 13.0 - - + -
456A SER* 1.3 77.0 - - - +
458A ASP* 1.3 62.6 + - - +
459A ILE* 3.9 27.1 - - + -
478A THR* 6.5 0.2 - - + -
479A SER* 3.5 4.4 - - - -
480A ALA* 2.9 45.6 + - + +
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Residues in contact with ASP 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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157A ARG* 3.3 20.0 + - - -
222A ILE* 4.0 25.1 - - + +
223A PRO* 4.8 10.7 - - - +
413A LYS 3.6 1.2 - - - +
414A VAL* 3.5 1.4 - - - -
415A GLN* 2.8 42.4 + - + +
456A SER* 5.9 1.1 - - - -
457A LEU* 1.3 75.0 - - - +
459A ILE* 1.3 68.5 + - - +
460A TYR* 4.5 3.8 - - + -
478A THR 3.8 3.8 - - - +
479A SER* 3.3 22.3 - - - -
532A TYR* 3.2 24.7 + - - -
550A ARG* 5.5 0.2 + - - -
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Residues in contact with ILE 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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413A LYS 3.4 7.9 - - - +
414A VAL* 4.4 19.3 - - + -
457A LEU* 3.9 29.8 - - + -
458A ASP* 1.3 80.3 + - - +
460A TYR* 1.3 62.8 + - - +
461A LEU* 6.3 2.9 - - + -
477A GLY* 3.0 2.4 - - - -
478A THR* 2.8 56.0 + - + +
532A TYR* 4.5 0.5 + - - -
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Residues in contact with TYR 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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136A GLN* 3.3 40.1 + - - +
137A LEU* 6.0 0.5 - - - +
157A ARG* 3.9 35.6 - - + +
411A VAL* 5.3 2.0 - - + -
412A GLY* 3.6 2.9 - - - -
413A LYS* 3.1 66.3 + - + +
415A GLN* 4.0 18.6 - - - -
458A ASP* 4.5 6.1 - - - -
459A ILE* 1.3 80.7 - - - +
461A LEU* 1.3 66.2 + - - +
462A THR* 4.5 5.2 - - + -
475A VAL* 4.2 14.4 - - + -
476A VAL 3.2 13.5 - - - +
477A GLY* 3.8 0.9 - - - -
532A TYR* 3.6 18.8 - - + +
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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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406A PHE* 4.2 30.1 - - + -
410A TRP* 3.3 34.0 - - + -
411A VAL 3.8 4.5 - - - +
412A GLY* 4.8 3.8 - - - -
459A ILE* 6.3 2.5 - - + -
460A TYR* 1.3 76.9 - - - +
462A THR* 1.3 61.7 + - - +
474A LEU 3.8 0.9 - - - +
475A VAL* 3.3 4.7 - - - +
476A VAL* 2.7 51.1 + - + +
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Residues in contact with THR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE* 6.3 2.5 - - + -
136A GLN* 3.5 29.4 - - - +
157A ARG 5.2 3.0 + - - +
158A LEU* 3.8 18.4 - - - +
409A GLY 4.3 0.2 - - - +
410A TRP* 3.1 8.5 - - - -
411A VAL* 2.7 59.3 + - + +
460A TYR* 4.5 4.9 - - + -
461A LEU* 1.3 76.3 - - - +
463A GLY* 1.3 56.6 + - - +
473A GLU* 4.7 2.8 + - - -
474A LEU 3.2 13.4 + - - -
475A VAL* 3.9 11.7 - - - +
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Residues in contact with GLY 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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132A ILE* 4.8 4.7 - - - +
409A GLY 4.7 0.7 - - - -
410A TRP* 3.2 24.8 - - - -
462A THR* 1.3 77.0 + - - +
464A PRO* 1.3 73.6 - - - +
473A GLU* 3.2 6.9 - - - +
474A LEU* 2.9 32.0 + - - +
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Residues in contact with PRO 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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74A PRO* 3.8 28.7 - - + -
130A THR* 4.4 2.2 - - + -
132A ILE* 4.0 22.9 - - + -
408A ASN 5.3 2.7 - - - +
409A GLY* 4.0 12.8 - - - +
410A TRP* 3.0 29.9 + - + +
463A GLY* 1.3 86.4 - - - +
465A PHE* 1.3 64.5 + - - +
471A GLU* 3.8 13.2 - - - +
472A HIS 3.0 12.8 - - - +
473A GLU* 3.9 1.8 - - + -
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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
----------------------------------------------------------
410A TRP* 5.0 6.5 - + + +
463A GLY 4.5 0.7 - - - -
464A PRO* 1.3 77.1 - - - +
466A GLN* 1.3 67.8 + - - +
467A PHE* 4.4 11.0 - + + -
471A GLU* 3.9 6.4 + - - -
472A HIS* 2.7 65.9 + + + -
473A GLU* 3.7 28.5 - - - -
474A LEU* 4.0 24.9 - - + -
535A ALA* 5.3 3.6 - - + -
537A PHE* 3.9 22.4 - + - -
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Residues in contact with GLN 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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78A ARG* 4.9 14.6 - - - +
465A PHE* 1.3 79.2 - - - +
467A PHE* 1.3 64.1 + - - +
469A GLY* 3.5 30.1 + - - +
470A ARG 3.3 9.4 - - - +
471A GLU* 3.2 22.5 + - - +
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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