Contacts of the helix formed by residues 390 - 413 (chain E) in PDB entry 3IFS
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 ASN 390 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E HIS* 5.9 1.4 - - - -
95E MSE 5.5 0.3 - - - +
96E LEU* 3.5 13.4 - - - +
388E GLU* 3.5 32.5 + - - +
389E LEU* 1.3 75.6 - - - +
391E GLU* 1.3 72.2 + - - +
392E TYR* 3.5 9.6 + - - +
393E THR* 2.7 33.7 + - - -
394E PHE* 3.0 22.0 + - - +
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Residues in contact with GLU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E LEU* 3.8 14.5 - - + +
224E GLY 4.7 0.5 - - - +
225E LEU* 3.4 29.5 - - + +
226E ASN* 2.8 56.4 + - - +
229E GLU* 4.2 5.7 - - + +
230E MSE 3.4 22.7 - - + +
390E ASN* 1.3 81.8 - - - +
392E TYR* 1.3 63.3 + - - +
394E PHE* 3.2 2.9 + - - +
395E GLY 3.0 19.2 + - - -
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Residues in contact with TYR 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E HIS* 3.6 40.5 - + - +
229E GLU* 3.5 33.3 + - + +
232E LYS* 3.9 14.4 - - + -
233E GLY* 3.3 37.1 - - - -
236E ALA* 3.2 21.6 - - + +
390E ASN* 3.3 12.0 + - - +
391E GLU* 1.3 78.9 - - - +
393E THR* 1.3 65.5 + - - +
395E GLY 3.3 0.2 + - - -
396E TYR* 3.0 24.7 + + - +
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Residues in contact with THR 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E HIS* 2.8 32.8 + - - +
5E VAL* 4.1 13.2 - - + -
386E ILE* 3.5 22.9 - - + -
387E PRO* 4.4 2.7 - - + -
388E GLU* 3.3 26.0 + - - +
389E LEU* 5.1 0.4 - - + -
390E ASN* 2.7 26.5 + - - -
392E TYR* 1.3 73.4 - - - +
394E PHE* 1.3 61.1 + - - +
396E TYR* 3.6 0.5 - - - +
397E LEU* 2.8 31.1 + - + +
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Residues in contact with PHE 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E GLY* 4.0 11.2 - - - -
91E ALA* 4.2 2.9 - - + -
92E ALA* 3.5 39.7 - - + -
95E MSE 3.8 28.0 - - + -
96E LEU* 4.1 11.2 - - + -
211E VAL* 4.4 14.4 - - + -
212E LEU* 4.9 1.6 - - + -
230E MSE 3.7 27.6 - - + -
281E PHE* 4.1 20.9 - + - -
284E TRP* 6.2 1.3 - + - -
390E ASN 3.0 14.4 + - - +
391E GLU 3.6 6.7 - - - +
393E THR* 1.3 77.4 - - - +
395E GLY* 1.3 60.5 + - - +
397E LEU* 3.7 5.4 - - - +
398E VAL* 2.8 52.6 + - + +
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Residues in contact with GLY 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E LEU* 4.9 2.2 - - - -
230E MSE 3.6 29.6 - - - -
234E ALA* 3.4 22.9 - - - +
391E GLU 3.0 10.7 + - - -
392E TYR 3.8 0.4 - - - -
394E PHE* 1.3 81.6 - - - +
396E TYR* 1.3 60.6 + - - +
398E VAL* 3.5 5.3 + - - +
399E TYR 3.2 16.8 + - - -
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Residues in contact with TYR 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E THR* 3.1 20.1 - - - +
4E HIS* 3.3 24.7 + + + -
5E VAL* 3.3 37.5 - - + -
233E GLY* 3.4 25.7 - - - +
234E ALA* 4.3 1.3 - - - +
236E ALA* 3.7 11.9 - - + -
237E GLY* 3.5 14.3 - - - -
240E ASP* 2.5 34.9 + - - +
241E PHE* 3.4 26.9 - + - -
392E TYR* 3.0 20.0 + + + +
393E THR* 3.6 7.4 - - - +
395E GLY* 1.3 75.8 - - - +
397E LEU* 1.3 57.8 + - - +
399E TYR* 3.2 5.0 + - - +
400E PHE* 3.0 24.4 + - - +
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Residues in contact with LEU 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E VAL* 4.0 19.7 - - + -
95E MSE 4.7 12.6 - - + -
281E PHE* 3.7 34.5 - - + -
330E LEU* 5.1 1.3 - - + -
384E VAL* 3.9 22.2 - - + -
386E ILE* 3.6 29.4 - - + -
393E THR* 2.8 18.4 + - + +
394E PHE* 3.7 4.7 - - - +
396E TYR* 1.3 73.1 - - - +
398E VAL* 1.3 66.3 + - - +
400E PHE* 3.3 8.2 + - + +
401E PHE* 3.2 46.3 + - + -
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Residues in contact with VAL 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E VAL* 3.8 16.6 - - + -
212E LEU* 4.2 12.3 - - + -
281E PHE* 4.2 7.0 - - + -
284E TRP* 3.7 24.5 - - + -
394E PHE* 2.8 55.4 + - + +
395E GLY* 3.8 5.8 - - - +
397E LEU* 1.3 78.8 - - - +
399E TYR* 1.3 57.6 + - - +
401E PHE 3.4 0.5 + - - -
402E GLU* 2.9 52.8 + - - +
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Residues in contact with TYR 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E HIS* 5.6 0.5 - - - -
48E TRP* 3.7 19.7 - + - -
49E VAL* 2.5 46.4 + - - +
52E PRO* 3.9 22.0 - - + -
212E LEU* 5.3 2.0 - - + -
234E ALA* 3.9 14.6 - - + +
237E GLY* 3.6 20.2 - - - -
238E ARG* 3.4 24.3 + - + +
241E PHE* 4.3 5.2 - + + -
395E GLY 3.2 17.2 + - - +
396E TYR 3.2 4.4 + - - +
398E VAL* 1.3 74.6 - - + +
400E PHE* 1.3 67.4 + - - +
402E GLU* 4.1 12.8 - - - -
403E LYS* 2.9 49.0 + - + +
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Residues in contact with PHE 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E VAL* 4.9 9.9 - - + -
7E PHE* 4.2 15.7 - + + -
241E PHE* 3.6 36.3 - + + -
250E PRO* 3.7 14.6 - - + -
251E ALA* 3.6 27.0 - - - +
254E TYR* 4.1 26.7 - + + -
384E VAL* 4.1 16.4 - - + -
396E TYR* 3.0 14.5 + - + +
397E LEU* 3.4 16.8 - - + +
399E TYR* 1.3 77.0 - - - +
401E PHE* 1.3 96.5 + + - +
404E ALA* 2.9 30.3 + - - +
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Residues in contact with PHE 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E TYR* 3.6 33.7 - + - -
271E LEU* 4.4 5.2 - - + -
281E PHE* 3.8 31.9 - + - -
284E TRP* 3.9 7.6 - + + -
285E TRP* 3.6 28.5 - + - -
288E LEU* 3.6 17.7 - - + +
289E PHE* 3.9 4.9 - + - -
330E LEU* 4.0 20.6 - - + -
384E VAL* 4.2 6.7 - - + -
397E LEU* 3.2 39.1 + - + +
400E PHE* 1.3 93.6 - + - +
402E GLU* 1.3 60.8 + - - +
404E ALA* 3.8 1.6 - - - +
405E CYS* 2.8 32.4 + - - +
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Residues in contact with GLU 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E TRP* 3.6 35.1 - - + +
209E PHE* 3.6 51.0 - - + +
211E VAL* 4.2 4.2 - - - +
212E LEU* 4.9 5.5 - - - +
284E TRP* 4.1 15.1 - - + -
288E LEU* 4.1 5.4 - - + -
398E VAL* 2.9 41.6 + - + +
399E TYR* 3.8 15.6 - - - +
401E PHE* 1.3 75.4 - - - +
403E LYS* 1.3 62.4 + - - +
405E CYS* 3.6 2.4 - - - +
406E ALA 3.1 18.4 + - - -
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Residues in contact with LYS 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ILE* 4.0 20.4 - - + -
36E HIS* 2.9 35.4 + - - -
48E TRP* 4.0 19.7 - - + -
49E VAL* 4.7 1.6 - - - -
241E PHE* 2.7 38.6 + - + +
242E GLY* 3.7 2.8 - - - -
251E ALA* 4.3 7.4 - - + -
252E TYR* 3.0 26.9 + - + -
399E TYR* 2.9 39.4 + - + +
400E PHE 4.0 2.0 - - - +
402E GLU* 1.3 73.8 - - - +
404E ALA* 1.3 65.8 + - - +
406E ALA* 3.3 3.6 + - - +
407E MSE 3.1 22.7 + - - +
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Residues in contact with ALA 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ALA* 3.3 31.7 - - + +
254E TYR* 3.7 28.0 - - + -
255E ALA* 3.4 5.9 - - - +
289E PHE* 4.5 2.0 - - + -
400E PHE* 2.9 20.5 + - + +
401E PHE* 3.8 5.4 - - - +
403E LYS* 1.3 75.7 - - - +
405E CYS* 1.3 57.6 + - - +
407E MSE 3.4 1.5 + - - -
408E SER* 2.8 31.9 + - - -
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Residues in contact with CYS 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E PHE* 4.6 3.6 - - + -
288E LEU* 3.4 29.2 - - + -
289E PHE* 3.7 26.2 - - + -
292E SER* 3.3 38.1 - - - -
293E GLU* 4.5 1.7 - - - +
401E PHE 2.8 18.3 + - - +
402E GLU 3.6 4.9 - - - +
404E ALA* 1.3 74.7 - - - +
406E ALA* 1.3 64.9 + - - +
408E SER* 3.3 0.9 + - - -
409E GLY* 3.0 22.3 + - - -
416E PRO* 4.6 1.8 - - - +
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Residues in contact with ALA 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ILE* 4.0 16.8 - - + -
48E TRP* 3.8 20.9 - - + -
209E PHE* 5.2 0.8 - - - -
402E GLU 3.1 6.3 + - - -
403E LYS* 3.3 8.9 + - + +
405E CYS* 1.3 76.2 - - - +
407E MSE 1.3 62.7 + - - +
410E TYR* 3.2 30.8 + - + -
416E PRO* 3.9 5.4 - - - +
417E PHE* 3.7 30.7 - - + -
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Residues in contact with MSE 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E VAL* 3.6 31.0 - - + +
31E THR* 3.5 25.1 - - + -
32E HIS* 3.8 12.8 - - - +
35E ILE* 4.3 6.2 - - + +
252E TYR* 3.6 50.5 - - + +
255E ALA* 3.5 18.8 - - + -
403E LYS 3.1 10.6 + - - +
404E ALA 3.7 6.3 - - - +
406E ALA* 1.3 79.9 - - - +
408E SER* 1.3 63.6 + - - +
410E TYR* 3.4 1.4 + - - -
411E LEU* 2.9 48.0 + - + +
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Residues in contact with SER 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E ALA* 3.5 13.8 - - - +
258E ARG* 2.8 21.5 + - - -
259E ASN* 3.2 28.6 + - - +
289E PHE* 4.5 2.0 - - - -
293E GLU* 2.4 24.5 + - - -
404E ALA 2.8 21.3 + - - -
405E CYS* 3.3 6.7 + - - -
407E MSE 1.3 73.2 - - - +
409E GLY* 1.3 55.7 + - - +
411E LEU* 3.2 1.8 + - - -
412E LEU* 2.8 27.4 + - - +
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Residues in contact with GLY 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293E GLU* 3.2 13.8 + - - -
405E CYS 3.0 15.0 + - - -
406E ALA 4.0 1.1 - - - -
408E SER* 1.3 76.2 - - - +
410E TYR* 1.3 62.7 + - - +
412E LEU* 3.2 3.3 + - - +
413E GLY 3.0 17.5 + - - -
414E VAL* 3.1 32.4 + - - +
416E PRO* 4.2 9.6 - - - -
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Residues in contact with TYR 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E THR* 3.4 34.8 + - + +
34E ALA* 5.0 6.1 + - + -
35E ILE* 3.6 27.6 - - + -
40E GLY* 3.6 15.8 + - - -
41E ALA* 2.5 44.3 + - + -
43E ASN 4.7 1.6 + - - -
46E LEU* 4.7 7.2 - - + +
406E ALA 3.2 21.7 + - - +
407E MSE 3.9 0.4 - - - +
409E GLY* 1.3 74.8 - - - +
411E LEU* 1.3 63.8 + - - +
413E GLY* 3.2 13.0 + - - -
414E VAL 4.0 6.1 - - - -
416E PRO* 3.6 15.4 - - + +
417E PHE* 3.4 23.7 - + - -
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Residues in contact with LEU 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E LEU* 4.6 12.6 - - + -
27E ALA* 4.4 22.7 - - + +
28E VAL* 4.6 3.6 - - + -
31E THR* 4.2 11.2 - - - +
255E ALA 4.2 4.3 - - - -
256E VAL* 3.8 39.9 - - + +
259E ASN* 3.7 14.8 - - + +
407E MSE 2.9 51.6 + - + +
408E SER 3.6 4.3 - - - +
410E TYR* 1.3 75.9 - - - +
412E LEU* 1.3 61.0 + - - +
413E GLY* 3.4 1.0 + - - -
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Residues in contact with LEU 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ASN* 3.7 15.7 + - - +
262E TYR* 3.9 29.6 - - + -
293E GLU* 3.8 41.7 - - + +
298E LYS* 4.2 21.6 + - + +
299E GLY* 4.1 13.7 - - - +
300E ILE 5.4 0.4 - - - +
408E SER 2.8 12.8 + - - +
409E GLY 3.2 9.4 + - - +
411E LEU* 1.3 76.9 - - - +
413E GLY* 1.3 59.2 + - - +
414E VAL* 3.9 16.8 - - + +
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Residues in contact with GLY 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E ASP* 4.9 2.3 - - - +
298E LYS* 4.2 10.8 + - - -
409E GLY 3.0 3.4 + - - -
410E TYR 3.2 10.2 + - - -
411E LEU 3.2 4.5 - - - -
412E LEU* 1.3 80.5 - - - +
414E VAL* 1.3 63.1 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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