Contacts of the helix formed by residues 357 - 391 (chain A) in PDB entry 5CXV
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 LEU 357 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A THR* 5.4 2.5 - - + -
218A ARG* 3.8 9.6 - - - +
355A PHE* 4.0 21.3 + - + +
356A SER* 1.3 80.3 + - - +
358A VAL* 1.3 59.6 + - - +
359A LYS 3.5 1.8 - - - -
360A GLU* 3.4 16.4 + - + +
361A LYS* 2.9 51.3 + - + +
1001A ASN* 3.9 28.7 - - - +
1157A TRP* 4.5 11.2 - - + -
3C LYS* 3.7 33.9 - - + +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A SER* 3.6 10.2 + - - +
357A LEU* 1.3 76.5 - - - +
359A LYS* 1.3 67.3 + - - +
361A LYS* 3.1 10.4 + - + +
362A LYS* 3.0 33.2 + - - +
365A ARG* 5.1 3.2 + - - +
7C ASP* 3.4 34.3 - - + +
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Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A SER 5.5 0.2 + - - -
357A LEU 3.5 0.2 - - - -
358A VAL* 1.3 81.7 - - - +
360A GLU* 1.3 57.4 + - - +
362A LYS* 3.5 10.7 + - - +
363A ALA* 2.9 28.4 + - - +
2C TYR* 4.4 7.7 - - + +
3C LYS 5.6 1.1 - - - +
5C ASP* 3.8 39.6 + - + +
6C ASP 4.7 7.9 - - - +
7C ASP* 5.0 3.2 + - - -
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Residues in contact with GLU 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A VAL* 5.1 0.5 - - - +
215A THR* 4.8 3.6 - - - +
218A ARG* 2.2 45.0 + - - -
357A LEU* 3.4 17.6 + - - +
358A VAL 3.1 0.8 - - - -
359A LYS* 1.3 77.8 - - - +
361A LYS* 1.3 62.2 + - - +
363A ALA* 3.2 3.6 + - - +
364A ALA* 2.9 27.4 + - - +
504A PGE 3.5 32.1 + - - +
1C ASP* 6.0 0.2 - - - -
2C TYR* 4.0 13.9 + - + +
3C LYS* 3.3 37.6 - - - +
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Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 2.9 40.1 + - + +
358A VAL* 3.6 7.4 - - + +
360A GLU* 1.3 78.7 - - + +
362A LYS* 1.3 58.4 + - - +
364A ALA* 3.2 10.0 + - - +
365A ARG* 3.0 49.1 + - - +
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Residues in contact with LYS 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL* 3.0 25.2 + - + +
359A LYS* 3.9 10.1 - - - +
361A LYS* 1.3 74.2 - - - +
363A ALA* 1.3 61.5 + - - +
365A ARG* 3.1 24.9 + - + +
366A THR* 2.9 33.3 + - - +
421A CYS* 3.8 35.0 + - + +
422A ASN* 4.9 9.9 - - + +
423A LYS 5.5 1.8 - - - +
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Residues in contact with ALA 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A LYS 2.9 17.8 + - - +
360A GLU 3.2 5.6 + - - +
362A LYS* 1.3 76.7 - - - +
364A ALA* 1.3 57.1 + - - +
366A THR* 3.3 8.9 + - - +
367A LEU* 3.0 29.8 + - - +
504A PGE 3.9 7.0 - - - +
2C TYR* 3.6 44.4 - - + -
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG* 3.5 31.5 + - - +
208A TYR* 5.1 2.5 + - + -
360A GLU 2.9 12.4 + - - +
361A LYS* 3.2 13.2 + - - +
363A ALA* 1.3 77.3 - - - +
365A ARG* 1.3 62.1 + - + +
367A LEU* 3.3 1.8 + - - +
368A SER* 2.9 27.1 + - - -
504A PGE 4.6 5.4 - - - +
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Residues in contact with ARG 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL* 5.1 3.2 + - - +
361A LYS* 3.0 30.3 + - - +
362A LYS* 3.1 31.2 + - + +
364A ALA* 1.3 76.8 - - + +
366A THR* 1.3 61.2 + - - +
368A SER* 2.8 21.6 + - - +
369A ALA* 3.0 13.7 + - - +
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Residues in contact with THR 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 6.0 1.8 - - + -
362A LYS* 2.9 17.0 + - - +
363A ALA* 3.5 11.8 - - - +
364A ALA 3.3 0.2 - - - -
365A ARG* 1.3 75.0 - - - +
367A LEU* 1.3 64.2 + - - +
369A ALA* 3.2 8.0 + - - +
370A ILE* 3.0 34.8 + - + +
417A CYS* 4.2 7.4 + - + +
418A TYR* 3.6 43.4 - - + +
421A CYS* 4.2 10.7 - - - -
422A ASN* 6.0 0.7 - - - +
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Residues in contact with LEU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 5.4 2.0 - - + -
119A ILE* 3.7 35.7 - - + -
120A SER* 5.3 6.5 - - - +
123A ARG* 3.5 40.4 - - + +
208A TYR* 5.1 3.6 - - + -
363A ALA 3.0 16.0 + - - +
364A ALA* 3.9 4.9 - - - +
366A THR* 1.3 78.9 - - + +
368A SER* 1.3 57.7 + - - +
370A ILE* 3.2 14.6 + - + +
371A LEU* 2.9 62.1 + - + +
504A PGE 4.8 6.1 - - - +
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Residues in contact with SER 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TYR* 3.3 36.9 - - - -
364A ALA 2.9 14.3 + - - -
365A ARG* 2.8 24.6 + - - -
367A LEU* 1.3 75.6 - - - +
369A ALA* 1.3 61.6 + - - +
371A LEU* 3.9 2.9 - - - +
372A LEU* 3.0 28.7 + - - +
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A ARG 3.0 13.4 + - - +
366A THR* 3.4 10.8 - - - +
368A SER* 1.3 78.6 + - - +
370A ILE* 1.3 63.1 + - - +
372A LEU* 3.9 7.4 - - - +
373A ALA* 3.0 25.6 + - - +
417A CYS* 3.9 20.1 - - + -
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.8 7.2 - - + -
67A LEU* 4.7 6.7 - - + -
116A LEU* 4.0 26.2 - - + -
119A ILE* 6.4 0.7 - - + -
366A THR* 3.0 24.1 + - + +
367A LEU* 3.2 15.7 + - + +
369A ALA* 1.3 77.3 - - - +
371A LEU* 1.3 59.0 + - + +
373A ALA* 3.3 5.5 + - - +
374A PHE* 2.9 26.8 + - + +
414A ASN* 3.3 30.9 - - - +
417A CYS* 3.9 16.8 - - + -
418A TYR* 3.7 34.8 - - + -
----------------------------------------------------------
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.8 30.5 - - + +
120A SER* 4.6 10.5 - - - +
204A MET* 3.9 28.7 - - + +
208A TYR* 4.4 20.2 - - + -
367A LEU* 2.9 49.7 + - + +
368A SER* 4.2 2.9 - - - +
370A ILE* 1.3 76.6 - - + +
372A LEU* 1.3 57.3 + - - +
374A PHE* 3.3 7.8 + - + +
375A ILE* 2.9 40.8 + - + +
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A SER 3.0 19.5 + - - +
369A ALA* 3.9 6.5 - - - +
371A LEU* 1.3 73.4 - - - +
373A ALA* 1.3 65.7 + - - +
375A ILE* 3.2 14.5 + - + +
376A LEU* 3.0 45.8 + - + +
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ALA 3.0 18.1 + - - +
370A ILE* 3.5 5.4 - - - +
372A LEU* 1.3 78.3 - - - +
374A PHE* 1.3 55.2 + - - +
376A LEU* 3.3 11.9 - - + +
377A THR* 2.4 38.5 + - - -
410A ASN* 4.3 5.2 - - + -
413A ILE* 3.8 38.1 - - + -
414A ASN* 5.2 0.9 - - - +
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Residues in contact with PHE 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A SER* 5.0 2.5 - - - -
113A VAL* 3.7 27.1 - - + -
116A LEU* 3.6 26.5 - - + -
197A PHE* 3.6 20.2 - + - -
201A VAL* 3.7 24.2 - - + -
204A MET* 3.8 17.3 - - + -
370A ILE* 2.9 14.7 + - + +
371A LEU* 3.4 12.8 - - + +
372A LEU 3.3 0.2 - - - -
373A ALA* 1.3 76.4 - - - +
375A ILE* 1.3 71.7 + - + +
377A THR* 3.3 4.5 + - - -
378A TRP* 2.9 58.0 + + - +
410A ASN* 3.8 23.2 - - - +
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 5.2 2.7 - - + -
201A VAL* 4.5 17.0 - - + -
205A CYS* 4.2 25.1 - - - -
371A LEU* 2.9 29.6 + - + +
372A LEU* 3.2 13.9 + - + +
374A PHE* 1.3 88.7 - - + +
376A LEU* 1.3 60.8 + - + +
378A TRP* 5.1 0.9 - - - -
379A THR* 2.2 50.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LEU* 3.0 43.4 + - + +
373A ALA* 3.3 17.3 - - + +
375A ILE* 1.3 77.5 - - + +
377A THR* 1.3 89.6 + - + +
379A THR* 4.5 3.1 - - - -
380A PRO* 3.1 25.3 - - - +
406A LEU* 4.0 3.1 - - - +
413A ILE* 5.7 2.0 - - + -
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Residues in contact with THR 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ALA 2.4 24.6 + - - +
374A PHE 3.3 5.4 + - - -
376A LEU* 1.3 91.4 - - + +
378A TRP* 1.3 63.5 + - - +
380A PRO* 4.2 1.0 - - - +
381A TYR 5.5 0.3 + - - -
403A GLY 4.7 0.3 - - - +
406A LEU* 3.5 49.7 - - + +
407A CYS* 3.6 14.0 + - - -
409A VAL* 4.2 19.1 - - + -
410A ASN* 3.4 20.8 - - + +
413A ILE* 4.7 5.8 - - + -
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Residues in contact with TRP 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 5.7 3.8 - - + -
109A SER* 3.5 42.2 - - - -
112A SER* 4.9 7.4 - - - -
113A VAL* 3.8 12.6 - - + -
197A PHE* 3.5 22.9 - + + -
374A PHE* 2.9 38.8 + + - +
377A THR* 1.3 93.9 - - - +
379A THR* 1.3 61.8 + - - +
380A PRO 3.5 2.1 - - - -
381A TYR* 3.7 5.2 + - - +
382A ASN* 2.9 27.5 + - - -
407A CYS* 2.8 39.1 + - + -
410A ASN* 3.1 13.0 + - - -
501A 0HK 3.7 52.3 - - + -
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Residues in contact with THR 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 4.1 16.7 - - + -
375A ILE* 2.2 42.9 + - + +
376A LEU* 4.5 2.2 - - - -
378A TRP* 1.3 76.0 - - - +
380A PRO* 1.3 73.5 - - + +
382A ASN* 3.2 2.6 + - - +
383A ILE* 2.9 42.1 + - + +
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Residues in contact with PRO 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU 3.1 21.5 - - - +
377A THR 4.2 4.3 - - - +
378A TRP 3.7 2.7 - - - -
379A THR* 1.3 92.7 - - + +
381A TYR* 1.3 56.7 + - - +
383A ILE* 3.5 6.7 + - + +
384A MET* 2.9 42.4 + - - +
403A GLY* 5.1 5.6 - - - +
406A LEU* 3.9 18.2 - - + -
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Residues in contact with TYR 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 4.4 3.1 + - - -
189A THR* 5.6 0.2 + - - -
377A THR 5.5 0.2 + - - -
378A TRP 3.7 3.5 + - - +
379A THR 3.3 0.8 - - - -
380A PRO* 1.3 78.3 - - - +
382A ASN* 1.3 59.3 + - - +
384A MET* 3.0 14.9 + - + +
385A VAL* 2.9 39.0 + - + +
400A TRP* 3.8 31.3 - + - -
403A GLY* 3.7 15.5 + - - +
404A TYR* 3.5 54.6 - + + -
407A CYS* 3.9 14.6 - - - -
501A 0HK 3.5 53.2 - - + +
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Residues in contact with ASN 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA* 3.7 13.6 - - + +
197A PHE* 3.3 33.8 - - + +
198A TYR* 3.0 29.6 + - + +
378A TRP 2.9 21.8 + - - -
379A THR 3.2 3.6 + - - +
381A TYR* 1.3 75.9 - - - +
383A ILE* 1.3 61.4 + - - +
385A VAL* 3.3 8.6 + - - +
386A LEU* 2.9 23.2 + - - +
501A 0HK 2.7 46.3 + - - +
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Residues in contact with ILE 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 3.5 20.4 - - + +
379A THR* 2.9 39.0 + - + +
380A PRO* 3.7 7.6 - - + +
382A ASN* 1.3 75.7 - - - +
384A MET* 1.3 59.6 + - + +
386A LEU* 3.2 18.0 + - + +
387A VAL* 2.9 39.9 + - + +
----------------------------------------------------------
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Residues in contact with MET 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A PRO* 2.9 28.4 + - - +
381A TYR* 3.0 16.5 + - + +
383A ILE* 1.3 76.1 - - + +
385A VAL* 1.3 57.8 + - - +
387A VAL* 3.9 5.5 - - - +
388A SER* 2.9 30.5 + - - -
395A VAL* 3.8 21.1 - - + +
399A LEU* 3.3 45.5 - - + +
400A TRP* 3.5 45.6 - - + +
403A GLY* 4.4 6.1 - - - -
----------------------------------------------------------
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO 4.6 0.7 - - - +
189A THR* 4.0 23.1 - - + +
190A PHE* 3.6 37.7 - - + +
193A ALA* 4.3 7.0 - - + -
381A TYR* 2.9 41.8 + - + +
382A ASN* 3.5 13.2 - - - +
384A MET* 1.3 75.9 - - - +
386A LEU* 1.3 63.3 + - - +
388A SER* 2.9 25.3 + - - +
389A THR* 3.0 10.9 + - - +
400A TRP* 3.9 12.8 - - + -
501A 0HK 5.1 0.7 - - + -
----------------------------------------------------------
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 3.5 36.3 - - + -
198A TYR* 4.0 17.9 - - + +
382A ASN 2.9 13.6 + - - +
383A ILE* 3.2 22.6 + - + +
385A VAL* 1.3 76.7 - - - +
387A VAL* 1.3 63.8 + - + +
389A THR* 2.7 23.7 + - - -
390A PHE* 3.6 33.3 + - + -
----------------------------------------------------------
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 2.9 30.4 + - + +
384A MET* 3.9 6.7 - - - +
386A LEU* 1.3 79.8 - - + +
388A SER* 1.3 59.1 + - - +
390A PHE* 3.1 12.6 + - + +
391A CYS* 3.0 26.3 + - + +
394A CYS* 4.4 24.2 - - + -
395A VAL* 5.3 7.9 - - + -
----------------------------------------------------------
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 3.8 25.3 - - - +
189A THR* 5.4 1.6 - - - +
384A MET 2.9 17.1 + - - -
385A VAL* 2.9 17.2 + - - +
387A VAL* 1.3 77.6 - - - +
389A THR* 1.3 60.6 + - - +
391A CYS 2.8 21.7 - - - +
392A LYS* 4.6 2.8 - - - -
393A ASP 5.8 2.7 - - - -
394A CYS* 6.0 0.2 - - - -
395A VAL* 4.4 7.0 - - - -
400A TRP* 3.7 21.2 - - - -
----------------------------------------------------------
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Residues in contact with THR 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A PRO* 3.6 18.1 - - - +
187A ILE* 4.7 19.8 - - - +
190A PHE* 3.3 41.9 - - + -
385A VAL 3.0 16.4 - - - +
386A LEU* 2.7 16.5 + - - +
388A SER* 1.3 76.5 - - - +
390A PHE* 1.3 81.2 + - - +
391A CYS 4.8 0.5 - - - -
----------------------------------------------------------
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Residues in contact with PHE 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 5.6 4.7 - + - -
386A LEU* 3.6 39.7 - - + -
387A VAL* 3.1 10.8 + - + +
389A THR* 1.3 95.8 + - - +
391A CYS* 1.3 61.1 + - + +
392A LYS 4.4 0.2 + - - -
----------------------------------------------------------
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Residues in contact with CYS 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A VAL* 3.0 9.9 + - + +
388A SER* 2.8 27.4 - - - +
389A THR 4.8 0.4 - - - -
390A PHE* 1.3 79.9 - - + +
392A LYS* 1.3 74.4 + - - +
393A ASP 3.6 1.7 + - - -
394A CYS* 2.0 52.7 + - + +
----------------------------------------------------------
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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