Contacts of the helix formed by residues 360 - 389 (chain R) in PDB entry 5GJQ
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 360 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358R ARG 4.7 3.6 - - - +
359R PRO* 1.3 81.9 - - - +
361R SER* 1.3 68.8 + - - +
362R LYS* 4.3 8.7 - - + +
363R ASN* 3.0 32.9 + - + +
364R TRP* 3.3 5.2 + - - +
466S ILE* 3.9 23.2 - - + +
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Residues in contact with SER 361 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392Q PRO* 5.2 5.2 - - - -
393Q VAL* 3.9 36.2 - - - +
394Q ASP 4.5 1.7 + - - -
398Q GLU* 5.4 1.6 + - - +
359R PRO 4.1 1.4 + - - -
360R ASP* 1.3 69.9 - - - +
362R LYS* 1.3 81.4 + - - +
364R TRP* 2.8 26.3 + - - +
365R GLN* 3.2 6.9 + - - +
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Residues in contact with LYS 362 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394Q ASP* 4.6 13.9 + - + -
397Q TYR* 3.0 71.5 - - + +
398Q GLU* 5.9 1.2 - - - +
360R ASP* 3.1 7.3 - - + +
361R SER* 1.3 94.1 + - - +
363R ASN* 1.3 58.3 + - - +
364R TRP 2.8 1.0 + - - -
365R GLN* 3.0 13.8 + - - +
366R TYR* 2.7 36.1 + - - +
467S TYR* 3.6 26.7 - - + -
251U LEU* 4.8 15.5 - - + -
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Residues in contact with ASN 363 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359R PRO* 5.0 8.2 - - + +
360R ASP* 3.0 28.5 + - - +
362R LYS* 1.3 76.7 - - - +
364R TRP* 1.3 62.2 + - - +
366R TYR* 4.2 11.3 - - - +
367R GLN* 3.5 21.8 + - - +
463S MET* 5.3 8.3 - - - +
466S ILE* 4.1 31.7 - - - +
467S TYR* 5.1 1.7 - - - -
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Residues in contact with TRP 364 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341R GLY 5.7 5.4 - - - -
344R HIS* 6.4 1.1 - - + -
359R PRO* 6.0 3.6 - - + -
360R ASP 3.3 4.7 + - - +
361R SER* 2.8 15.4 + - - +
363R ASN* 1.3 79.1 - - - +
365R GLN* 1.3 67.8 + - + +
367R GLN* 3.3 9.3 + - + +
368R GLU* 2.9 61.7 + - + +
371R LYS* 6.1 1.3 - - - -
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Residues in contact with GLN 365 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397Q TYR* 3.0 59.7 + - + +
398Q GLU* 5.8 0.4 - - - -
400Q ALA* 4.8 1.2 - - - +
401Q LEU* 3.7 23.5 - - + +
361R SER* 3.2 3.2 + - - +
362R LYS* 3.0 17.1 + - - +
364R TRP* 1.3 77.7 - - + +
366R TYR* 1.3 82.7 + - - +
368R GLU* 2.7 12.3 + - - +
369R THR* 2.4 55.1 + - - +
467S TYR* 5.0 0.7 + - - -
258U VAL* 3.9 10.8 - - - +
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Residues in contact with TYR 366 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362R LYS 2.7 23.5 + - - +
363R ASN* 4.2 10.3 - - - +
365R GLN* 1.3 82.2 + - - +
367R GLN* 1.3 72.2 + - + +
369R THR* 2.9 19.4 - - + +
370R ILE* 2.9 39.4 + - + +
466S ILE 5.4 3.1 - - - -
467S TYR* 3.6 41.3 - + + +
471S GLU* 4.3 14.0 + - + +
472S PRO* 3.5 34.2 - - + +
475S ALA* 5.6 2.1 - - - +
476S PHE* 5.1 0.7 - + - -
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Residues in contact with GLN 367 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363R ASN* 3.5 16.8 + - - +
364R TRP* 3.3 12.6 + - + +
365R GLN 3.1 0.6 - - - -
366R TYR* 1.3 90.9 + - + +
368R GLU* 1.3 61.6 + - - +
370R ILE* 5.2 8.5 - - - +
371R LYS* 2.9 42.1 + - - +
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Residues in contact with GLU 368 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401Q LEU* 3.7 21.4 - - + +
364R TRP* 2.9 61.3 + - + +
365R GLN* 2.7 14.9 + - - +
367R GLN* 1.3 70.2 - - - +
369R THR* 1.3 65.4 + - - +
371R LYS* 3.2 9.7 + - - +
372R LYS* 2.9 40.8 + - + +
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Residues in contact with THR 369 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400Q ALA* 6.0 0.7 - - - +
401Q LEU* 3.2 32.0 - - - +
404Q ILE* 5.1 3.1 - - - +
365R GLN* 2.4 43.8 + - - +
366R TYR* 2.9 26.2 - - + +
368R GLU* 1.3 66.9 - - - +
370R ILE* 1.3 80.7 + - + +
372R LYS* 3.6 1.8 - - - +
373R GLY* 2.8 28.2 + - - -
467S TYR* 5.8 0.7 - - - +
476S PHE* 5.6 4.5 - - + -
258U VAL* 5.9 1.1 - - + +
261U TYR* 4.5 17.0 + - + -
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Residues in contact with ILE 370 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366R TYR* 2.9 46.1 + - + +
367R GLN* 4.3 9.9 - - - +
369R THR* 1.3 84.9 - - + +
371R LYS* 1.3 64.8 + - - +
373R GLY* 3.3 0.9 + - - -
374R ASP* 3.0 39.8 + - - +
472S PRO* 5.3 1.6 - - + -
475S ALA* 5.5 10.3 - - + -
476S PHE* 3.5 35.2 - - + -
479S ARG* 5.3 3.8 - - - +
261U TYR* 4.6 9.7 + - + +
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Residues in contact with LYS 371 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364R TRP* 6.1 1.8 - - - -
367R GLN* 2.9 50.1 + - - +
368R GLU* 3.2 9.4 + - - +
370R ILE* 1.3 82.3 - - - +
372R LYS* 1.3 62.2 + - - +
374R ASP* 3.4 5.7 + - - +
375R LEU* 3.1 39.9 + - + +
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Residues in contact with LYS 372 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401Q LEU* 5.1 9.6 - - + +
404Q ILE* 4.3 22.9 - - + +
405Q GLN* 5.3 18.2 - - + +
368R GLU* 2.9 32.4 + - + +
369R THR* 3.6 6.5 - - - +
371R LYS* 1.3 75.3 - - + +
373R GLY* 1.3 63.6 + - - +
375R LEU* 3.1 17.7 + - - +
376R LEU* 3.1 13.5 + - - +
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Residues in contact with GLY 373 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404Q ILE* 4.9 6.7 - - - +
369R THR 2.8 16.8 + - - -
370R ILE 3.8 0.2 - - - -
372R LYS* 1.3 72.8 - - - +
374R ASP* 1.3 55.0 + - - +
376R LEU* 3.4 9.5 + - - +
377R LEU* 3.0 32.8 + - - +
261U TYR* 3.4 29.6 - - - -
265U LEU* 5.5 4.1 - - - +
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Residues in contact with ASP 374 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370R ILE* 3.0 31.0 + - - +
371R LYS* 3.6 8.2 - - - +
373R GLY* 1.3 75.8 - - - +
375R LEU* 1.3 64.4 + - + +
377R LEU* 3.2 12.8 + - - +
378R ASN* 2.9 32.3 + - - +
479S ARG* 3.0 36.1 + - - -
261U TYR* 4.7 2.9 + - - -
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Residues in contact with LEU 375 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371R LYS* 3.1 30.7 - - + +
372R LYS* 3.1 12.1 + - - +
374R ASP* 1.3 85.4 - - + +
376R LEU* 1.3 58.9 + - - +
378R ASN* 3.6 9.7 + - + +
379R ARG* 3.0 57.7 + - + +
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Residues in contact with LEU 376 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404Q ILE* 4.7 17.9 - - + +
407Q MET* 4.9 8.3 - - + -
408Q SER* 3.9 33.0 - - - +
411Q VAL* 3.6 33.7 - - + -
372R LYS 3.1 10.8 + - - +
373R GLY* 3.6 9.9 - - - +
374R ASP 3.2 0.2 - - - -
375R LEU* 1.3 74.3 - - - +
377R LEU* 1.3 57.6 + - + +
379R ARG* 3.4 8.0 + - + +
380R VAL* 2.7 47.0 + - + +
265U LEU* 4.6 28.5 - - + -
269U VAL* 5.3 4.3 - - + -
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Residues in contact with LEU 377 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373R GLY 3.0 20.8 + - - +
374R ASP* 3.5 13.9 - - - +
376R LEU* 1.3 76.8 - - + +
378R ASN* 1.3 58.5 + - - +
380R VAL* 3.6 9.8 - - + +
381R GLN* 3.0 44.3 + - + +
479S ARG* 3.0 42.2 - - + +
482S PHE* 6.3 1.3 - - + -
483S CYS* 3.5 30.1 - - - -
261U TYR* 4.8 6.5 - - + +
265U LEU* 4.5 17.0 - - + -
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Residues in contact with ASN 378 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374R ASP 2.9 16.1 + - - +
375R LEU* 4.0 11.6 - - + +
377R LEU* 1.3 76.4 - - - +
379R ARG* 1.3 61.3 + - + +
381R GLN* 4.1 13.3 + - - +
382R LYS* 3.0 46.0 + - - +
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Residues in contact with ARG 379 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408Q SER* 4.9 10.9 + - - -
411Q VAL* 5.4 4.9 - - + -
412Q ASP* 5.5 6.3 + - - +
415Q TYR* 4.1 3.4 + - - -
375R LEU* 3.0 43.6 + - + +
376R LEU* 3.9 8.1 - - + +
377R LEU 3.2 0.2 - - - -
378R ASN* 1.3 81.3 - - + +
380R VAL* 1.3 66.5 + - + +
382R LYS* 3.6 13.6 - - - +
383R LEU* 3.3 33.3 + - + +
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Residues in contact with VAL 380 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411Q VAL* 4.5 9.9 - - + -
415Q TYR* 3.0 17.6 + - - +
376R LEU* 2.7 50.1 + - + +
377R LEU* 3.6 14.4 - - + +
379R ARG* 1.3 76.8 - - - +
381R GLN* 1.3 59.1 + - + +
384R SER* 2.9 30.8 + - - -
483S CYS* 5.9 4.3 - - - -
486S ILE* 5.6 6.3 - - + -
265U LEU* 6.1 2.5 - - + -
269U VAL* 5.5 6.7 - - + -
272U LEU* 3.6 24.7 - - + -
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Residues in contact with GLN 381 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377R LEU* 3.0 30.7 + - + +
378R ASN* 4.1 11.0 + - - +
380R VAL* 1.3 72.6 - - + +
382R LYS* 1.3 70.2 + - - +
384R SER* 2.0 32.6 + - - +
385R ARG* 3.0 5.7 + - - +
314S ARG* 5.0 10.7 - - - +
482S PHE* 2.8 41.6 - - + -
486S ILE* 3.2 25.4 - - + -
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Residues in contact with LYS 382 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378R ASN* 3.0 51.6 + - - +
379R ARG* 3.6 14.2 - - - +
381R GLN* 1.3 83.6 - - - +
383R LEU* 1.3 75.3 + - + +
385R ARG* 3.4 12.8 + - - +
386R VAL* 3.5 14.3 + - + +
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Residues in contact with LEU 383 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415Q TYR* 3.5 50.7 - - + -
379R ARG* 3.3 18.7 + - + +
382R LYS* 1.3 89.0 - - + +
384R SER* 1.3 65.8 + - - +
386R VAL* 3.3 21.6 + - + +
387R ILE* 3.1 27.2 + - + +
----------------------------------------------------------
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Residues in contact with SER 384 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415Q TYR* 4.2 4.0 - - - -
380R VAL* 2.9 17.7 + - - -
381R GLN* 2.0 33.2 + - - +
383R LEU* 1.3 75.8 - - - +
385R ARG* 1.3 54.7 + - - +
386R VAL 3.2 0.3 + - - -
387R ILE* 3.2 5.3 + - - +
388R ASN* 2.7 37.2 + - - +
486S ILE* 3.7 30.5 - - - +
272U LEU* 5.0 14.6 - - - -
----------------------------------------------------------
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Residues in contact with ARG 385 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381R GLN 3.0 5.2 + - - +
382R LYS* 3.7 8.7 - - - +
384R SER* 1.3 81.9 + - - +
386R VAL* 1.3 75.6 + - - +
388R ASN* 3.1 14.5 + - - +
389R MET* 2.9 52.8 + - + +
282S ASN* 6.2 2.0 - - - -
314S ARG* 4.6 33.2 + - + +
315S LYS* 5.5 3.2 + - - +
316S ALA 4.8 6.3 + - - -
317S PRO* 5.7 3.2 - - - +
318S GLN* 5.9 4.4 - - - +
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Residues in contact with VAL 386 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419Q LYS* 6.1 7.0 - - + -
422Q THR* 5.3 6.5 - - - -
382R LYS* 3.5 15.7 + - + +
383R LEU* 3.3 25.7 + - + +
384R SER 3.2 0.2 - - - -
385R ARG* 1.3 92.5 + - - +
387R ILE* 1.3 68.3 + - + +
389R MET* 3.3 16.8 + - - +
----------------------------------------------------------
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Residues in contact with ILE 387 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415Q TYR* 3.5 28.3 - - + -
418Q ALA* 3.0 40.8 - - + -
419Q LYS* 5.0 0.9 - - - +
422Q THR* 4.7 14.7 - - - -
383R LEU* 3.1 11.9 + - + +
384R SER* 3.9 4.0 - - - +
386R VAL* 1.3 83.0 - - + +
388R ASN* 1.3 61.9 + - - +
389R MET 3.6 3.5 + - - -
272U LEU* 5.2 2.9 - - + -
275U LEU* 4.0 12.1 - - + -
276U ILE* 3.7 20.2 - - + -
279U LYS* 3.3 41.3 - - + +
----------------------------------------------------------
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Residues in contact with ASN 388 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384R SER 2.7 17.2 + - - +
385R ARG* 3.1 15.9 + - - +
387R ILE* 1.3 80.5 - - - +
389R MET* 1.3 65.0 + - - +
489S MET* 4.9 12.9 + - - +
490S SER* 4.1 15.4 - - - +
493S ALA* 3.5 25.4 - - - +
494S MET* 5.1 0.7 + - - -
275U LEU* 5.3 0.2 - - - +
279U LYS* 2.9 27.7 + - - +
----------------------------------------------------------
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Residues in contact with MET 389 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385R ARG* 2.9 50.6 + - + +
386R VAL 3.3 11.8 + - - +
387R ILE 4.4 3.4 - - - -
388R ASN* 1.3 86.0 - - - +
283U ARG* 5.2 7.2 + - - -
----------------------------------------------------------
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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
------------------------------------------------------------
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