Contacts of the helix formed by residues 398 - 424 (chain B) in PDB entry 5YGP
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 GLU 398 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ASN* 4.0 15.8 - - - +
396B LEU* 3.3 5.1 + - - +
397B ARG* 1.3 120.9 + - - +
399B ALA* 1.3 61.1 + - - +
400B GLU* 3.2 29.2 - - + +
401B ILE* 3.2 23.4 + - + +
402B GLU* 2.9 32.6 + - - +
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Residues in contact with ALA 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B THR* 5.2 3.8 - - - +
397B ARG 4.4 0.6 + - - -
398B GLU* 1.3 73.9 - - - +
400B GLU* 1.3 63.0 + - - +
402B GLU* 3.7 14.6 + - - +
403B ALA* 2.8 31.9 + - - +
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Residues in contact with GLU 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ALA 5.4 1.0 - - - +
342B TYR* 3.7 38.5 - - - +
343B ALA* 3.8 13.4 + - + +
346B THR* 3.0 34.8 + - - +
364B ALA* 5.3 0.3 - - - +
365B ALA* 6.2 0.2 - - - -
368B ASN* 2.4 47.7 + - + +
372B ALA* 4.8 1.8 - - - +
398B GLU* 3.2 17.6 - - + +
399B ALA* 1.3 81.8 + - - +
401B ILE* 1.3 63.4 + - - +
403B ALA* 3.8 1.5 + - - -
404B VAL* 3.8 15.6 + - - +
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Residues in contact with ILE 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ASN* 3.7 46.2 - - + +
371B ALA* 4.4 4.9 - - + -
372B ALA* 4.2 17.3 - - + -
375B LEU* 4.3 7.0 - - + -
396B LEU* 3.6 44.6 - - + +
398B GLU* 3.2 29.5 + - + +
399B ALA 3.2 0.2 - - - -
400B GLU* 1.3 75.3 - - + +
402B GLU* 1.3 65.2 + - - +
403B ALA 3.2 0.4 - - - -
404B VAL* 3.2 5.5 + - - +
405B GLU* 3.0 29.3 + - - +
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Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU 4.2 14.7 - - - +
397B ARG 4.8 3.8 - - - +
398B GLU 2.9 25.3 + - - +
399B ALA* 3.2 15.5 + - - +
401B ILE* 1.3 75.1 - - - +
403B ALA* 1.3 59.9 + - - +
405B GLU* 3.2 22.0 + - - +
406B VAL* 2.9 37.7 + - + +
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TYR* 3.6 38.4 - - + -
399B ALA 2.8 16.9 + - - +
400B GLU* 3.9 3.1 - - - +
401B ILE 3.2 0.2 - - - -
402B GLU* 1.3 76.2 - - - +
404B VAL* 1.3 61.0 + - - +
406B VAL* 3.3 7.4 + - - +
407B GLU* 3.0 30.7 + - - +
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B SER* 4.2 1.1 - - - -
339B ALA* 3.6 40.8 - - + +
342B TYR* 4.2 9.9 - - + -
372B ALA* 3.7 27.8 - - + +
375B LEU* 3.8 14.4 - - + -
376B TYR* 4.1 13.9 - - + +
400B GLU 3.8 4.4 + - - +
401B ILE 3.2 8.5 + - - +
403B ALA* 1.3 74.9 - - - +
405B GLU* 1.3 66.1 + - - +
407B GLU* 3.2 6.8 + - - +
408B ILE* 3.0 37.3 + - + +
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Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LEU* 3.7 16.6 - - + +
387B TRP* 2.8 32.4 + - - +
388B LYS* 4.1 2.8 + - - +
391B VAL* 3.4 49.9 - - + +
394B LEU* 4.3 6.4 - - - +
396B LEU* 4.3 12.2 - - - +
401B ILE* 3.0 27.7 + - - +
402B GLU* 3.5 25.0 - - - +
404B VAL* 1.3 77.7 - - - +
406B VAL* 1.3 57.0 + - + +
408B ILE 3.6 0.2 + - - -
409B GLY* 3.0 11.4 + - - -
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LYS* 4.3 17.4 + - - +
402B GLU* 2.9 23.5 + - + +
403B ALA* 3.7 7.0 - - - +
405B GLU* 1.3 76.2 - - + +
407B GLU* 1.3 65.7 + - - +
409B GLY* 3.1 2.4 + - - -
410B ARG* 3.0 56.1 + - + +
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU 5.4 1.2 - - - +
46B GLU* 5.1 4.9 - - - +
49B PRO* 4.5 10.2 - - - +
67B ARG* 4.0 13.6 + - - -
338B SER* 5.3 5.6 - - - +
342B TYR* 2.4 36.5 + - + -
376B TYR* 5.2 5.8 - - - +
403B ALA 3.0 22.7 + - - +
404B VAL* 3.2 6.7 + - - +
406B VAL* 1.3 77.7 - - - +
408B ILE* 1.3 59.0 + - + +
410B ARG* 3.0 36.0 + - - +
411B PHE* 2.9 46.1 + - + -
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LEU* 3.7 42.8 - - + +
376B TYR* 3.9 29.6 - - + +
379B MET* 3.7 27.6 - - + -
387B TRP* 3.5 28.3 - - + -
404B VAL* 3.0 27.3 + - + +
407B GLU* 1.3 75.7 - - + +
409B GLY* 1.3 58.2 + - - +
411B PHE* 3.3 8.3 + - + +
412B ARG* 2.9 32.7 + - - +
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Residues in contact with GLY 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B TRP* 3.6 23.3 - - - +
388B LYS* 4.5 6.3 - - - -
405B GLU 3.0 12.8 + - - -
406B VAL 3.1 5.1 + - - -
408B ILE* 1.3 78.3 - - - +
410B ARG* 1.3 56.9 + - - +
412B ARG* 3.5 6.6 + - - +
413B ASP* 3.1 33.1 + - - +
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Residues in contact with ARG 410 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.7 26.5 + - - +
49B PRO* 3.3 32.6 - - + +
50B GLN* 3.4 47.9 + - + +
406B VAL* 3.0 39.2 + - + +
407B GLU* 3.0 28.8 + - - +
409B GLY* 1.3 74.8 - - - +
411B PHE* 1.3 64.9 + - - +
413B ASP* 3.4 12.2 + - - +
414B GLN* 3.2 18.7 + - - +
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Residues in contact with PHE 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO* 3.7 26.2 - - + -
70B GLY* 4.0 19.3 - - - -
71B TYR* 3.9 31.9 - + - -
74B SER* 3.4 26.9 - - - +
76B LEU* 4.1 14.5 - - + +
376B TYR* 4.8 15.9 - + - -
379B MET* 3.9 13.9 - - + -
407B GLU* 2.9 30.6 + - + -
408B ILE* 3.3 10.7 + - - +
410B ARG* 1.3 74.0 - - - +
412B ARG* 1.3 64.5 + - - +
414B GLN* 3.4 5.2 + - - +
415B GLN* 3.2 29.0 + - - +
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Residues in contact with ARG 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B MET* 2.7 38.8 + - + +
382B VAL* 3.1 24.9 + - - +
383B PRO 3.0 28.3 + - - -
384B ALA* 4.1 1.2 - - - +
385B ARG 4.6 2.2 - - - +
387B TRP* 3.3 41.9 - - - +
408B ILE* 2.9 28.7 + - + +
409B GLY* 3.6 6.5 - - - +
410B ARG 3.3 0.2 - - - -
411B PHE* 1.3 77.1 - - - +
413B ASP* 1.3 62.2 + - - +
415B GLN* 3.3 5.3 + - - +
416B TYR* 3.0 35.6 + - + -
439B ARG* 3.0 44.4 - - - +
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Residues in contact with ASP 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLY 3.1 17.3 + - - +
410B ARG* 3.7 15.0 - - - +
411B PHE 3.3 0.6 - - - -
412B ARG* 1.3 79.7 - - - +
414B GLN* 1.3 67.8 + - - +
416B TYR* 3.1 15.5 + - - +
417B GLU* 2.9 31.8 + - + +
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Residues in contact with GLN 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO 3.3 20.9 + - - +
50B GLN* 3.0 27.7 + - - +
52B ALA* 3.5 18.9 + - + -
53B ALA* 2.8 35.6 + - + +
54B THR* 3.5 16.8 + - - +
76B LEU* 3.8 26.0 - - + -
410B ARG* 3.2 10.2 + - - +
411B PHE 4.0 2.5 - - - +
412B ARG 3.4 0.2 - - - -
413B ASP* 1.3 86.9 - - - +
415B GLN* 1.3 53.0 + - - +
417B GLU* 4.0 3.8 - - - +
418B MET* 2.7 31.4 + - - +
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN 4.6 1.4 + - - -
74B SER* 3.0 42.9 + - - +
76B LEU* 5.0 1.3 - - + -
379B MET* 3.7 17.6 - - - +
380B ASP* 4.3 3.0 + - - +
411B PHE 3.2 15.7 + - - +
412B ARG 3.7 5.6 - - - +
413B ASP 3.2 0.2 - - - -
414B GLN* 1.3 76.8 - - - +
416B TYR* 1.3 56.4 + - - +
418B MET* 3.5 0.9 + - - +
419B LEU* 2.9 26.7 + - - +
432B ALA* 3.4 27.3 - - + +
435B ALA* 3.4 28.5 - - - +
436B ALA* 3.7 3.8 - - + +
439B ARG* 2.5 34.5 + - - +
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Residues in contact with TYR 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ALA* 3.2 30.2 - - + +
385B ARG* 4.0 33.7 - - - +
412B ARG* 3.0 26.6 + - + -
413B ASP* 3.1 14.6 + - - +
415B GLN* 1.3 76.1 - - - +
417B GLU* 1.3 60.5 + - + +
419B LEU* 3.2 6.9 + - + +
420B LYS* 3.0 35.8 + - - +
436B ALA* 3.6 15.5 - - + -
439B ARG* 2.4 36.6 + - - -
440B MET* 3.4 34.3 - - + -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 3.6 20.3 - - + +
54B THR* 4.0 22.0 - - + +
413B ASP* 2.9 21.4 + - + +
414B GLN* 3.3 19.0 + - - +
416B TYR* 1.3 76.5 - - - +
418B MET* 1.3 58.7 + - - +
420B LYS* 3.3 24.8 + - - +
421B ARG* 3.0 31.2 + - - +
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Residues in contact with MET 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA 5.4 0.2 - - - -
53B ALA* 3.6 20.8 - - + +
75B GLY 4.4 2.0 - - - +
76B LEU* 4.2 17.0 - - + -
268B ASN* 4.3 4.9 - - - +
269B ALA* 4.3 7.0 - - + -
270B ALA* 3.6 33.7 - - + +
414B GLN 2.7 21.2 + - - +
415B GLN 3.7 5.6 - - - +
417B GLU* 1.3 70.4 - - - +
419B LEU* 1.3 64.9 + - - +
421B ARG* 3.4 4.3 + - - -
422B TRP 3.1 17.3 + - - -
428B ALA* 3.3 17.4 - - + +
429B GLY 3.3 42.8 - - - +
432B ALA* 3.9 10.3 - - + -
433B VAL* 3.3 9.9 - - + +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLN 2.9 17.4 + - - +
416B TYR* 3.2 8.3 + - + +
418B MET* 1.3 75.0 - - - +
420B LYS* 1.3 60.3 - - - +
422B TRP* 3.2 3.7 + - + -
423B ARG* 2.9 67.0 + - + +
433B VAL* 3.6 30.9 - - + +
436B ALA* 4.4 6.3 - - + -
437B LEU* 3.7 21.8 - - + -
440B MET* 3.3 33.4 - - + -
447B GLU* 4.1 0.9 - - - +
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Residues in contact with LYS 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TYR* 3.0 18.1 + - - +
417B GLU* 3.3 32.9 + - - +
419B LEU* 1.3 77.4 - - - +
421B ARG* 1.3 62.5 + - + +
423B ARG* 3.3 8.4 + - - +
424B GLN* 3.1 55.5 + - - +
426B GLN* 5.0 0.2 - - - -
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Residues in contact with ARG 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B GLU 5.6 5.9 - - - +
53B ALA 3.4 22.7 + - - +
54B THR 4.7 3.0 + - - -
55B GLY* 4.1 20.2 - - - +
270B ALA* 3.0 38.5 + - - +
272B PRO* 5.1 4.9 - - - +
417B GLU 3.0 19.8 + - - +
418B MET* 3.6 10.1 - - - +
419B LEU 3.3 0.2 - - - -
420B LYS* 1.3 75.6 - - + +
422B TRP* 1.3 62.9 + - - +
424B GLN 3.1 6.4 + - - -
426B GLN* 2.8 66.8 + - + +
427B PRO* 3.2 42.0 + - - +
428B ALA* 4.2 0.7 - - + -
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Residues in contact with TRP 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B MET 3.1 10.6 + - - +
419B LEU* 3.8 4.7 - - + +
420B LYS 3.2 0.2 - - - -
421B ARG* 1.3 77.3 - - - +
423B ARG* 1.3 74.0 + - + +
424B GLN 3.3 0.7 + - - -
425B GLN* 3.6 12.0 + - - -
426B GLN 3.9 9.6 - - - -
428B ALA* 3.6 21.8 - - + -
430B LEU* 3.5 30.6 - - + +
433B VAL* 3.8 22.0 - - + -
437B LEU* 5.2 0.4 - - + -
447B GLU* 4.5 13.7 - - + -
451B SER* 3.1 44.4 - - - -
454B GLN* 4.3 25.8 - - - +
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Residues in contact with ARG 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU* 2.9 45.1 + - + +
420B LYS* 3.7 9.6 - - - +
422B TRP* 1.3 86.3 - - + +
424B GLN* 1.3 63.6 - - + +
425B GLN* 3.5 10.1 + - - -
437B LEU* 3.8 9.9 - - - +
440B MET* 4.6 8.1 - - - -
444B GLY* 6.1 0.2 - - - -
447B GLU* 2.6 44.9 + - - +
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Residues in contact with GLN 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LYS* 3.1 44.5 + - - +
421B ARG 3.4 1.8 - - - +
422B TRP 3.1 1.0 - - - -
423B ARG* 1.3 85.4 - - + +
425B GLN* 1.3 72.1 + - - +
426B GLN* 3.2 26.6 + - + +
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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