Contacts of the helix formed by residues 326 - 356 (chain C) in PDB entry 1EGE
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 THR 326 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASP* 2.9 30.3 + - - +
256C ARG* 5.5 4.7 - - - +
324C ARG* 3.3 34.6 + - - +
325C ASN* 1.3 76.4 + - - +
327C TYR* 1.3 61.8 + - - +
329C ALA* 4.1 4.3 - - - -
330C SER* 3.1 31.6 + - - +
385C ILE* 3.9 18.8 - - + +
388C ARG* 4.4 4.5 - - - +
389C GLU* 3.8 13.7 - - - +
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Residues in contact with TYR 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 6.0 0.5 - - - +
302B ALA* 4.0 13.2 + - + +
306B GLU* 2.9 44.6 + - + +
324C ARG* 4.5 5.4 + - - +
325C ASN 2.7 4.6 + - - -
326C THR* 1.3 78.3 - - - +
328C TYR* 1.3 91.2 + + + +
330C SER* 3.4 3.2 + - - -
331C ILE* 3.1 28.8 + - + +
386C VAL* 4.3 18.2 - - + +
389C GLU* 3.7 35.2 - - + +
390C HIS* 4.3 14.6 - - + -
393C LYS* 3.5 26.3 + - + -
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Residues in contact with TYR 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLU* 3.4 35.8 + - - -
310B MET* 4.0 4.9 - - + -
311C SER 4.4 1.2 - - - +
314C ARG* 3.2 49.0 + - + -
315C ALA* 3.6 22.4 - - + +
318C GLU* 3.9 24.2 - - + -
324C ARG 5.8 1.3 - - - -
325C ASN* 2.9 7.1 + - - +
327C TYR* 1.3 97.9 - + + +
329C ALA* 1.3 59.1 + - - +
331C ILE* 3.2 24.3 - - + +
332C ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASP* 4.5 2.7 - - - +
256C ARG* 3.7 30.0 - - + +
257C PRO* 4.0 1.1 - - + -
315C ALA* 3.4 15.7 - - + +
325C ASN* 2.8 43.1 + - - +
326C THR* 4.4 3.6 - - - +
328C TYR* 1.3 72.7 - - - +
330C SER* 1.3 58.1 + - - +
332C ALA* 3.3 3.4 + - - +
333C LYS* 3.1 28.2 + - - +
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Residues in contact with SER 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ARG* 3.9 11.9 + - - +
326C THR* 3.1 23.2 + - - +
327C TYR* 3.8 3.8 - - - -
328C TYR 3.2 0.8 - - - -
329C ALA* 1.3 76.4 - - - +
331C ILE* 1.3 59.8 + - - +
334C ALA* 3.1 25.6 + - - +
382C GLN* 3.2 29.3 + - - +
385C ILE* 3.4 21.7 - - - +
386C VAL* 3.9 16.8 - - - +
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Residues in contact with ILE 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA 5.9 0.2 - - - -
303B MET* 3.5 20.0 - - + +
306B GLU* 3.9 29.6 - - + -
307B LEU* 4.7 15.7 - - + -
310B MET* 5.0 2.9 - - + -
311C SER* 3.8 7.6 - - - +
327C TYR* 3.1 25.4 - - + +
328C TYR* 3.2 30.8 + - + +
330C SER* 1.3 75.5 - - - +
332C ALA* 1.3 65.7 + - - +
334C ALA* 4.1 4.7 - - - -
335C PHE* 2.8 34.9 + - + +
386C VAL* 3.6 26.5 - - + -
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Residues in contact with ALA 332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C PRO* 5.1 1.3 - - + -
260C ALA* 3.8 8.3 - - + -
311C SER* 2.7 38.4 - - - +
312C TYR* 3.8 10.1 - - - +
315C ALA* 4.1 4.7 - - + -
328C TYR 2.9 16.4 + - - +
329C ALA* 3.5 7.2 - - - +
331C ILE* 1.3 74.3 - - - +
333C LYS* 1.3 60.1 + - - +
336C ALA* 2.9 35.7 + - - +
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Residues in contact with LYS 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ARG* 4.1 10.5 - - - +
259C VAL* 3.3 38.8 - - + -
260C ALA* 4.0 8.9 - - - +
329C ALA 3.1 13.5 + - - +
332C ALA* 1.3 75.8 - - - +
334C ALA* 1.3 67.0 + - - +
337C GLY* 3.0 20.0 + - - -
372C TYR* 2.7 31.8 + - + +
373C GLN* 4.2 2.6 - - - +
374C ILE 4.1 4.4 - - - +
375C TYR* 2.9 22.0 + - - -
376C GLU* 4.3 4.7 - - - -
377C GLY 2.8 22.4 + - - +
378C THR* 4.5 1.6 - - - +
379C SER* 4.8 1.0 + - - +
382C GLN* 3.4 25.4 - - + +
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Residues in contact with ALA 334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 3.8 17.7 - - + -
330C SER 3.1 20.7 + - - +
331C ILE* 3.7 4.0 - - - +
332C ALA 3.3 0.4 - - - -
333C LYS* 1.3 83.1 - - - +
335C PHE* 1.3 60.9 + - - +
337C GLY* 4.0 0.2 - - - -
338C ASP* 3.2 29.5 + - - +
379C SER* 4.9 3.6 + - - +
382C GLN* 3.6 22.6 - - + +
383C ARG* 4.1 14.5 + - - +
386C VAL* 5.3 0.4 - - + -
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Residues in contact with PHE 335 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 3.5 17.5 - - + +
304B LYS* 6.3 3.1 - - + -
307B LEU* 3.6 28.9 - - + -
335B PHE* 5.2 9.0 - + - -
304C LYS* 3.9 17.3 - - + -
307C LEU* 3.9 18.6 - - + -
308C ALA* 3.8 33.2 - - + -
311C SER* 4.3 5.4 - - - +
331C ILE 2.8 20.5 + - - +
334C ALA* 1.3 70.0 - - - +
336C ALA* 1.3 66.9 + - - +
337C GLY 3.1 1.3 - - - -
338C ASP* 3.1 8.2 + - + +
339C ILE* 3.0 47.0 + - + +
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Residues in contact with ALA 336 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ALA* 3.7 17.0 - - + +
263C ALA* 3.3 4.8 - - + +
264C VAL* 3.6 29.6 - - + -
308C ALA* 4.1 17.3 - - + +
311C SER* 4.8 0.4 + - - +
332C ALA 2.9 23.5 + - - +
333C LYS 4.6 0.2 - - - +
335C PHE* 1.3 74.5 - - - +
337C GLY* 1.3 61.2 + - - +
339C ILE* 4.0 3.2 - - - +
340C ALA* 3.1 26.3 + - - +
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Residues in contact with GLY 337 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ALA* 5.8 0.2 - - - +
263C ALA* 4.2 9.3 - - - +
333C LYS* 3.0 19.9 + - - -
334C ALA 4.0 0.7 - - - -
336C ALA* 1.3 81.0 - - - +
338C ASP* 1.3 62.5 + - - +
340C ALA* 3.3 3.6 + - - +
341C ASN* 3.3 24.8 + - - +
372C TYR* 4.1 20.5 - - - +
373C GLN* 4.0 6.3 - - - -
379C SER* 5.9 0.4 - - - -
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Residues in contact with ASP 338 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B MET* 6.0 0.3 - - - +
334C ALA 3.2 15.5 + - - +
335C PHE* 3.1 11.6 + - + +
337C GLY* 1.3 76.5 - - - +
339C ILE* 1.3 63.1 + - + +
341C ASN* 3.2 6.6 + - - +
342C GLN* 3.2 36.2 + - - +
373C GLN* 3.0 21.7 - - - +
379C SER* 3.4 15.4 + - - -
383C ARG* 2.8 32.7 + - - -
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Residues in contact with ILE 339 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C VAL* 5.5 0.7 - - - -
267C ALA* 3.9 22.4 - - + -
304C LYS* 3.7 43.3 - - + -
305C VAL 4.2 0.7 - - - +
308C ALA* 4.1 20.6 - - + -
335C PHE* 3.0 47.0 + - + +
336C ALA 4.0 4.7 - - - +
338C ASP* 1.3 74.5 - - + +
340C ALA* 1.3 68.3 + - - +
342C GLN* 4.1 14.6 - - - +
343C LEU* 2.9 37.0 + - + +
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ALA* 3.7 30.1 - - + +
266C LEU* 5.0 11.7 - - + +
267C ALA* 4.3 8.2 - - + +
336C ALA 3.1 21.7 + - - +
337C GLY* 3.5 5.6 - - - +
339C ILE* 1.3 82.0 - - - +
341C ASN* 1.3 60.9 + - - +
343C LEU* 3.8 1.9 - - - +
344C ALA* 3.0 29.9 + - - +
369C ALA* 4.4 3.8 - - - +
372C TYR* 5.2 3.6 - - + -
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Residues in contact with ASN 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C GLY 3.3 13.2 + - - +
338C ASP 3.2 9.9 + - - +
339C ILE 3.1 0.4 - - - -
340C ALA* 1.3 79.0 - - - +
342C GLN* 1.3 63.8 + - + +
344C ALA* 4.2 2.2 - - - +
345C THR* 3.6 19.9 + - - +
366C MET* 4.6 4.7 + - - +
369C ALA* 2.8 29.3 - - - +
370C LYS* 3.3 38.8 - - - +
373C GLN* 3.6 28.5 + - - +
345D THR* 5.4 2.4 - - + +
366D MET* 4.9 4.2 - - - +
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Residues in contact with GLN 342 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LYS* 2.9 36.9 + - - +
338C ASP* 3.2 30.2 + - - +
339C ILE* 3.2 15.5 + - - +
341C ASN* 1.3 78.5 - - + +
343C LEU* 1.3 62.9 + - + +
345C THR* 3.0 25.8 - - - +
346C ASP* 3.1 15.7 + - - +
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ALA* 3.4 29.4 - - + +
270C ALA* 4.1 4.3 - - + -
271C LEU* 4.8 2.0 - - + -
301C MET* 3.6 42.7 - - + +
304C LYS* 4.0 26.7 - - + +
305C VAL* 3.3 34.3 - - + -
339C ILE* 2.9 22.8 + - + +
340C ALA 3.8 3.1 - - - +
342C GLN* 1.3 77.5 - - + +
344C ALA* 1.3 66.6 + - - +
346C ASP* 2.9 2.8 + - - +
347C ALA* 2.9 25.8 + - - +
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Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LEU* 4.6 3.4 - - + -
270C ALA* 4.1 12.0 - - - +
340C ALA 3.0 17.5 + - - +
341C ASN* 4.5 3.1 - - - +
342C GLN 3.5 0.2 - - - -
343C LEU* 1.3 76.7 - - - +
345C THR* 1.3 60.6 + - - +
347C ALA* 3.6 2.8 + - - +
348C VAL* 3.4 26.0 + - - +
362C VAL 4.4 1.6 - - - +
365C LEU* 3.9 6.7 - - + +
366C MET* 3.5 34.2 - - + +
369C ALA* 3.8 13.7 - - + -
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Residues in contact with THR 345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ASN 3.6 14.6 + - - +
342C GLN* 3.0 21.7 + - - +
343C LEU 3.1 0.4 - - - -
344C ALA* 1.3 76.7 - - - +
346C ASP* 1.3 69.8 + - - +
348C VAL 4.1 1.6 - - - -
349C GLN* 3.4 5.4 + - - +
366C MET* 3.7 20.2 - - - +
341D ASN* 4.8 1.9 + - - +
370D LYS* 3.1 42.9 + - - +
373D GLN* 4.4 2.9 + - - -
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Residues in contact with ASP 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C MET* 4.2 18.6 - - + +
301C MET* 3.8 29.7 - - + +
304C LYS* 4.6 9.5 + - - -
342C GLN* 3.1 21.4 + - - +
343C LEU* 2.9 5.1 + - - +
345C THR* 1.3 85.9 - - - +
347C ALA* 1.3 56.7 + - - +
348C VAL 3.2 0.2 - - - -
349C GLN* 3.0 8.7 + - - +
350C ILE* 2.8 39.5 + - - +
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Residues in contact with ALA 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ALA* 3.4 32.8 - - + +
274C ALA* 3.8 14.8 - - + -
301C MET* 4.1 0.4 - - - +
343C LEU 2.9 15.7 + - - +
344C ALA 3.7 5.2 - - - +
346C ASP* 1.3 77.9 - - - +
348C VAL* 1.3 64.9 + - - +
350C ILE* 3.1 1.2 + - - -
351C LEU* 3.1 25.8 + - - +
362C VAL* 3.6 20.9 - - + -
365C LEU* 6.2 0.2 - - + -
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Residues in contact with VAL 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C ALA 3.4 15.7 + - - +
345C THR 4.0 0.2 - - - +
346C ASP 3.2 0.4 - - - -
347C ALA* 1.3 78.1 - - - +
349C GLN* 1.3 57.6 + - - +
351C LEU* 2.9 21.8 + - - +
352C GLY 3.1 11.1 + - - +
355C GLY* 3.6 19.9 - - - +
356C PHE* 4.1 5.4 - - + +
362C VAL* 3.5 36.5 - - + +
363C GLU* 3.8 7.4 - - - +
366C MET* 4.0 14.1 - - - -
215D MET* 5.4 1.3 - - + -
370D LYS* 3.6 32.3 - - + +
374D ILE* 4.5 5.8 - - + -
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Residues in contact with GLN 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C MET* 4.1 7.2 - - + -
345C THR 3.4 11.0 + - - +
346C ASP* 3.0 14.5 + - - +
348C VAL* 1.3 79.8 - - - +
350C ILE* 1.3 53.2 + - - +
352C GLY* 3.0 16.6 + - - +
370D LYS* 2.7 31.4 - - - +
373D GLN* 3.2 40.8 + - - +
374D ILE* 4.4 7.4 - - - +
378D THR* 4.2 2.8 - - - +
379D SER* 3.7 6.0 + - - -
380D GLN* 3.2 31.0 - - - +
399D FAD 2.7 32.8 + - - +
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Residues in contact with ILE 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ALA* 3.6 39.5 - - + +
277C TYR* 3.5 12.4 - - + -
278C ALA* 4.6 1.8 - - + -
288C LEU* 3.7 13.1 - - + +
294C ILE* 3.9 22.4 - - + -
297C MET* 3.9 22.2 - - + -
298C LEU* 4.0 22.4 - - + -
301C MET* 4.0 15.3 - - - -
346C ASP 2.8 21.6 + - - +
347C ALA 3.1 4.2 + - - +
349C GLN* 1.3 72.8 - - - +
351C LEU* 1.3 57.9 + - + +
352C GLY 3.1 0.4 - - - -
399D FAD 3.2 24.0 - - - +
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Residues in contact with LEU 351 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C GLU* 4.2 3.8 - - + +
274C ALA* 4.0 15.3 - - - -
277C TYR* 3.6 51.8 + - + -
347C ALA 3.1 16.4 + - - +
348C VAL 2.9 8.8 + - - +
350C ILE* 1.3 77.2 - - + +
352C GLY* 1.3 57.7 + - - +
354C ASN* 3.0 12.9 + - - +
355C GLY* 2.8 26.9 + - - +
360C TYR* 4.1 24.9 - - + -
361C PRO* 5.1 4.3 - - + -
362C VAL* 3.5 31.4 - - + -
399D FAD 4.2 4.0 + - - -
----------------------------------------------------------
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Residues in contact with GLY 352 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C VAL 3.1 2.6 + - - +
349C GLN 3.0 17.8 + - - -
350C ILE 3.1 2.6 + - - -
351C LEU* 1.3 75.1 - - - +
353C GLY* 1.3 55.9 + - - -
355C GLY* 2.7 25.5 + - - -
356C PHE 3.3 4.3 + - - -
374D ILE* 3.5 26.0 - - - +
399D FAD 3.5 18.1 - - - -
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Residues in contact with GLY 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C GLY* 1.3 70.7 - - - -
354C ASN* 1.3 62.8 + - - +
356C PHE* 3.0 16.7 + - - +
357C ASN* 3.3 10.2 + - - +
166D TRP* 4.2 13.5 - - - -
374D ILE* 3.4 12.9 - - - +
399D FAD 3.0 42.2 + - - +
----------------------------------------------------------
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Residues in contact with ASN 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C TYR* 3.7 19.2 + - + +
281C ARG* 4.2 9.7 - - - +
351C LEU* 3.0 11.7 + - + +
353C GLY* 1.3 75.2 - - - +
355C GLY* 1.3 57.2 + - - +
357C ASN* 2.9 15.8 + - - +
360C TYR* 3.0 64.5 + - + +
138D PRO 5.2 4.8 + - - -
166D TRP* 3.4 26.6 - - - +
399D FAD 4.5 2.2 + - - -
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Residues in contact with GLY 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C VAL* 3.6 13.7 - - - +
351C LEU* 2.8 16.4 + - - +
352C GLY 2.7 11.4 + - - -
354C ASN* 1.3 78.6 - - - +
356C PHE* 1.3 55.7 + - - +
357C ASN 3.5 0.5 + - - +
362C VAL* 3.4 29.1 - - - +
363C GLU* 3.2 24.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C VAL* 4.1 2.4 - - + +
352C GLY 3.3 2.8 + - - -
353C GLY 3.0 10.4 + - - +
355C GLY* 1.3 76.9 - - - +
357C ASN* 1.3 59.7 + - - +
363C GLU* 4.4 3.4 - - - -
214D ASN* 3.5 19.1 - - + +
215D MET* 3.3 44.7 + - + +
216D GLY* 3.2 44.4 - - - -
217D GLN* 5.2 1.6 - - + -
367D ARG 3.4 20.9 - - - -
368D ASP 4.4 1.8 - - - -
370D LYS* 3.9 18.4 - - + -
371D ILE* 3.9 39.5 - - + -
374D ILE* 4.2 13.5 - - + -
399D FAD 4.1 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