Contacts of the helix formed by residues 379 - 407 (chain B) in PDB entry 3BRW
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 379 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B HIS* 3.7 25.4 - - + +
341B ASP* 3.4 27.3 + - + +
342B VAL* 4.2 5.6 - - + -
375B ALA 3.8 2.2 + - - -
376B CYS 2.7 25.4 + - - +
377B TYR 3.7 0.2 - - - +
378B LYS* 1.3 74.3 - - - +
380B GLU* 1.3 67.8 + - - +
381B LYS 4.5 0.4 - - - +
382B PHE* 3.3 5.6 + - + -
383B ALA* 2.9 21.1 + - - +
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Residues in contact with GLU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASP* 2.7 28.0 + - - +
378B LYS 3.7 1.7 + - - -
379B ALA* 1.3 70.3 - - - +
381B LYS* 1.3 70.1 + - + +
383B ALA* 4.8 3.1 - - - -
384B LYS* 3.2 50.1 + - - +
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASN* 3.0 39.5 + - - +
315B HIS* 3.8 32.1 - - + +
341B ASP* 3.7 4.7 + - - +
379B ALA 3.3 0.6 - - - -
380B GLU* 1.3 85.5 - - + +
382B PHE* 1.3 61.4 + - + +
384B LYS* 4.7 2.0 - - - +
385B LEU* 3.7 20.6 + - - +
36D ILE* 4.0 23.1 - - + +
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Residues in contact with PHE 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ILE* 4.1 24.7 - - + -
313B PHE* 3.8 25.4 - + - -
315B HIS* 3.7 28.5 - + + -
376B CYS 3.4 19.7 - - - +
377B TYR* 3.6 21.8 - + + +
379B ALA* 3.3 8.5 + - + +
380B GLU 3.3 0.4 - - - -
381B LYS* 1.3 74.2 - - - +
383B ALA* 1.3 62.1 + - - +
384B LYS 3.3 1.8 - - - -
385B LEU* 3.2 13.6 + - + +
386B GLU* 2.9 27.5 + - + +
36D ILE* 4.0 30.1 - - + -
64D PHE* 3.9 34.3 - + + -
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Residues in contact with ALA 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR 3.4 13.6 + - - +
378B LYS* 4.1 11.0 - - - +
379B ALA 2.9 18.2 + - - +
380B GLU* 4.2 3.4 - - - +
382B PHE* 1.3 77.4 - - - +
384B LYS* 1.3 57.2 + - - +
386B GLU* 3.4 8.2 - - - +
387B GLU* 2.9 38.7 + - + +
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Residues in contact with LYS 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLU* 3.2 34.5 + - - +
381B LYS* 4.7 3.4 - - - +
383B ALA* 1.3 79.0 - - - +
385B LEU* 1.3 59.0 + - + +
386B GLU 3.3 0.2 - - - -
387B GLU* 3.8 6.4 + - - +
388B ARG* 3.3 22.0 + - - +
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LYS 3.7 15.9 - - - +
382B PHE* 3.2 22.2 + - + +
384B LYS* 1.3 77.4 - - + +
386B GLU* 1.3 60.8 + - - +
388B ARG* 3.5 25.4 - - - +
389B THR* 2.8 23.2 + - - -
36D ILE* 4.5 15.5 - - + -
37D GLU* 3.7 43.3 - - + +
64D PHE* 5.3 6.3 - - + -
67D MET* 3.6 21.6 - - + +
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Residues in contact with GLU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 5.5 4.0 + - - -
135B CYS 4.9 1.4 - - - +
187B HIS* 5.1 2.1 + - - -
188B VAL* 3.4 35.1 - - + +
377B TYR* 5.5 9.9 - - + +
382B PHE* 2.9 12.8 + - + +
383B ALA* 3.1 15.4 + - - +
385B LEU* 1.3 79.9 - - + +
387B GLU* 1.3 63.9 + - - +
388B ARG 3.4 0.4 - - - -
389B THR* 3.3 6.8 + - - -
390B ARG* 2.9 41.1 + - - +
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Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LYS 3.7 2.5 - - - +
135B CYS* 3.4 44.5 - - + +
136B ARG* 5.7 1.0 - - - +
383B ALA* 2.9 21.2 + - + +
384B LYS* 4.0 6.5 - - - +
386B GLU* 1.3 79.1 - - - +
388B ARG* 1.3 64.8 + - - +
390B ARG* 3.7 7.3 - - - +
391B ALA* 3.1 25.1 + - - +
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Residues in contact with ARG 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LYS 3.3 15.4 + - - +
385B LEU* 3.5 23.6 - - - +
386B GLU 3.4 0.4 - - - -
387B GLU* 1.3 78.1 - - - +
389B THR* 1.3 65.6 + - - +
391B ALA* 4.1 3.0 - - - +
392B ALA* 3.1 26.8 + - + +
37D GLU* 2.8 41.3 + - - -
67D MET* 4.3 12.8 - - - +
70D LEU* 5.8 4.8 - - - +
71D TYR* 4.4 13.5 + - - -
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Residues in contact with THR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B HIS* 4.3 9.6 - - + -
385B LEU 2.8 18.0 + - - -
386B GLU* 3.3 10.2 + - - -
387B GLU 3.2 0.2 - - - -
388B ARG* 1.3 81.4 + - - +
390B ARG* 1.3 67.3 + - - +
392B ALA* 3.6 4.5 + - - +
393B LEU* 3.2 22.2 + - + +
66D ALA* 4.3 12.3 - - + -
67D MET* 3.4 43.6 - - + +
70D LEU* 4.4 11.8 - - + +
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Residues in contact with ARG 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 5.5 6.7 - - - +
86B THR* 5.2 0.2 + - - -
87B ALA* 5.7 4.0 - - - +
133B THR 4.4 1.8 + - - +
134B LYS 4.0 11.7 - - - +
135B CYS 3.4 25.5 + - - -
136B ARG* 3.3 13.7 + - - +
137B THR* 3.4 27.4 - - - +
184B PHE* 3.8 26.3 - - + -
185B ASP* 4.5 15.8 + - - -
187B HIS* 3.2 39.3 + - + +
188B VAL* 3.6 17.6 - - - +
386B GLU* 2.9 28.0 + - - +
387B GLU* 3.7 8.1 - - - +
388B ARG 3.4 0.4 - - - -
389B THR* 1.3 77.8 - - - +
391B ALA* 1.3 58.2 + - - +
393B LEU* 3.2 1.7 + - - +
394B LEU* 2.9 29.6 + - + +
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Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B HIS* 5.7 0.7 - - - -
134B LYS* 3.2 44.8 + - + +
387B GLU 3.1 11.2 + - - +
388B ARG* 4.1 3.4 - - - +
390B ARG* 1.3 78.5 - - - +
392B ALA* 1.3 64.1 + - - +
394B LEU* 3.6 4.5 - - - +
395B GLU* 2.9 26.3 + - - +
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Residues in contact with ALA 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ARG* 3.1 20.7 + - + +
389B THR* 4.0 5.6 - - - +
391B ALA* 1.3 79.3 - - - +
393B LEU* 1.3 59.5 + - - +
395B GLU* 3.7 8.1 + - - +
396B THR* 3.1 22.9 + - - -
70D LEU* 5.2 15.3 - - + -
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B THR 6.0 0.2 - - - +
184B PHE* 4.1 23.3 - - + -
187B HIS* 4.0 29.2 - - + -
389B THR* 3.2 12.9 + - + +
390B ARG* 3.2 3.3 + - - +
391B ALA 3.2 0.4 - - - -
392B ALA* 1.3 77.6 - - + +
394B LEU* 1.3 61.1 + - - +
395B GLU 3.2 0.2 - - - -
396B THR* 3.3 10.6 + - + +
397B LEU* 2.9 26.5 + - + +
66D ALA* 4.4 10.8 - - + -
70D LEU* 4.0 26.9 - - + -
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B HIS* 3.8 22.9 - - + +
113B VAL* 3.8 26.9 - - + +
132B ARG* 4.2 11.9 - - + +
133B THR* 3.5 10.8 - - - +
134B LYS* 3.4 39.5 - - + +
184B PHE* 3.6 27.9 - - + -
390B ARG 2.9 17.1 + - - +
391B ALA 3.2 3.6 + - - +
393B LEU* 1.3 74.4 - - - +
395B GLU* 1.3 56.0 - - - +
397B LEU* 3.4 7.0 + - + +
398B TYR* 2.7 32.6 + - - +
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Residues in contact with GLU 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B HIS* 3.0 39.5 + - + +
391B ALA 2.9 17.1 + - - +
392B ALA* 3.7 9.0 - - - +
394B LEU* 1.3 75.7 - - - +
396B THR* 1.3 61.6 + - - +
398B TYR* 3.7 5.5 - - - +
399B GLU* 3.0 36.7 + - + +
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B ALA 3.1 14.1 + - - -
393B LEU* 3.3 16.0 + - + -
394B LEU 3.3 0.4 - - - -
395B GLU* 1.3 77.7 + - - +
397B LEU* 1.3 65.9 + - - +
399B GLU* 3.3 6.1 + - - +
400B GLU* 3.0 31.2 + - + +
73D LYS* 5.3 11.7 + - - +
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 4.1 26.2 - - + -
132B ARG* 4.9 0.9 - - - -
180B LEU* 3.4 44.0 - - + +
181B ILE* 4.2 7.4 - - + +
184B PHE* 3.7 35.4 - - + -
393B LEU* 2.9 15.5 + - + +
394B LEU* 3.5 11.7 - - + +
396B THR* 1.3 75.3 - - - +
398B TYR* 1.3 62.0 + - - +
400B GLU* 3.1 9.8 + - - +
401B LEU* 3.0 40.4 + - + +
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Residues in contact with TYR 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.5 48.5 - + + -
104B SER* 3.8 16.3 - - - -
105B LEU* 3.8 22.0 + - + +
111B HIS* 3.1 44.4 - + + +
112B LEU 4.1 7.9 - - - -
113B VAL* 4.5 10.1 - - + -
170B TYR* 6.0 0.2 - - - -
394B LEU 2.7 21.0 + - - +
395B GLU 3.7 4.0 - - - +
397B LEU* 1.3 75.3 - - - +
399B GLU* 1.3 80.8 + - + +
401B LEU* 3.3 5.5 + - - +
402B HIS* 3.0 30.6 + + + +
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Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B HIS* 5.5 1.9 - - + -
395B GLU* 3.0 27.5 + - + +
396B THR* 3.3 5.8 + - + +
398B TYR* 1.3 90.3 - - + +
400B GLU* 1.3 61.7 + - - +
402B HIS* 4.0 18.6 + - - +
403B ILE* 3.2 43.8 + - - +
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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
----------------------------------------------------------
174B TYR* 5.3 2.2 - - + -
180B LEU* 3.9 30.3 - - + +
396B THR* 3.0 28.0 + - + +
397B LEU* 3.3 10.5 - - - +
399B GLU* 1.3 77.8 - - + +
401B LEU* 1.3 63.2 + - + +
403B ILE* 5.0 1.0 - - - +
404B HIS* 3.0 51.6 + - + -
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Residues in contact with LEU 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 4.0 10.7 - - + -
113B VAL* 3.8 33.7 - - + -
172B VAL* 3.6 20.2 - - + -
174B TYR* 4.9 7.4 - - + +
177B ALA* 3.5 40.8 - - + +
180B LEU* 5.2 2.9 - - + -
181B ILE* 4.4 5.4 - - + -
397B LEU* 3.0 34.3 + - + +
398B TYR* 3.8 4.0 - - - +
400B GLU* 1.3 80.5 - - + +
402B HIS* 1.3 56.2 + - - +
404B HIS* 4.4 2.8 - - - +
405B SER* 2.7 36.9 + - - -
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Residues in contact with HIS 402 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.1 51.3 + + + -
398B TYR* 3.0 26.7 + + + +
399B GLU* 4.0 17.7 + - - +
401B LEU* 1.3 74.8 - - - +
403B ILE* 1.3 78.3 + - + +
405B SER 3.4 0.3 + - - -
406B GLN* 3.0 53.1 + - + +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLU* 3.2 34.5 + - + +
400B GLU* 4.0 2.9 - - - +
402B HIS* 1.3 87.8 - - + +
404B HIS* 1.3 73.1 + - + +
406B GLN* 3.3 9.7 - - + +
407B SER* 3.0 29.4 + - - -
411B LEU 5.0 1.4 - - - +
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Residues in contact with HIS 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B TYR* 3.4 64.9 + + + -
400B GLU* 3.0 46.1 + - - +
401B LEU 4.4 0.2 - - - +
403B ILE* 1.3 84.4 - - + +
405B SER* 1.3 65.7 + - - +
407B SER* 3.6 11.9 + - - -
408B MET* 3.3 31.4 + - - +
148C THR* 5.9 7.0 - - + -
150C PHE* 5.9 1.8 - - - +
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Residues in contact with SER 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 4.0 11.4 - - - -
171B PRO 3.7 12.6 - - - -
172B VAL* 3.3 8.7 - - - +
173B LEU* 2.8 36.5 + - - +
174B TYR* 3.9 3.6 + - - +
401B LEU 2.7 23.7 + - - -
402B HIS 4.0 3.4 - - - -
404B HIS* 1.3 72.5 - - - +
406B GLN* 1.3 68.6 + - - +
408B MET* 3.3 17.2 - - - +
409B MET* 3.7 11.4 - - - +
----------------------------------------------------------
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Residues in contact with GLN 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.9 13.9 + - - -
170B TYR* 6.1 2.4 - - - -
402B HIS* 3.0 45.9 + - + +
403B ILE* 3.3 11.9 - - + +
405B SER* 1.3 72.3 - - - +
407B SER* 1.3 52.5 + - - +
408B MET 2.6 16.5 + - - -
409B MET* 2.7 22.6 + - - +
410B GLY 3.2 5.4 + - - -
411B LEU* 3.4 42.7 + - - +
----------------------------------------------------------
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Residues in contact with SER 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ILE* 3.0 14.0 + - - +
404B HIS* 3.6 18.5 + - - -
405B SER 3.5 0.2 - - - -
406B GLN* 1.3 75.5 - - - +
408B MET* 1.3 60.0 + - - +
409B MET 3.4 0.4 - - - -
410B GLY* 3.7 5.1 + - - -
411B LEU 4.0 18.6 + - - +
412B GLY* 6.0 0.7 - - - -
149C GLU 5.7 0.9 + - - -
150C PHE 4.7 6.2 + - - +
152C ASN* 3.5 18.2 + - - +
----------------------------------------------------------
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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