Contacts of the helix formed by residues 325 - 350 (chain C) in PDB entry 4OGB
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 PRO 325 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TRP* 4.5 8.1 - - + +
103C GLY* 3.6 30.7 - - - +
323C THR 4.3 2.9 - - - +
324C LYS* 1.3 90.7 - - + +
326C LEU* 1.3 55.1 + - - +
327C GLN* 3.3 20.9 - - - +
328C LEU* 2.8 34.6 + - + +
329C TYR 3.3 1.9 + - - -
398C THR* 4.7 9.4 - - + -
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Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C LYS 3.4 2.7 + - - -
325C PRO* 1.3 70.5 - - - +
327C GLN* 1.3 57.1 + - - +
329C TYR* 4.3 13.9 - - + -
330C ARG* 2.9 39.5 + - + +
402C ASN* 3.2 28.3 + - + +
405C TRP* 3.4 65.1 - - + +
406C TYR* 4.6 0.9 - - + -
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Residues in contact with GLN 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLY 4.8 0.6 + - - -
105C HIS* 4.0 15.0 + - - -
325C PRO* 3.4 19.1 - - - +
326C LEU* 1.3 74.5 + - - +
328C LEU* 1.3 83.0 + - - +
330C ARG* 4.1 5.2 - - - +
331C GLN* 2.8 28.8 + - - +
506C EPE 3.2 35.5 + - + +
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLY* 3.7 25.6 - - - +
104C LEU 3.4 26.9 - - - +
106C VAL* 4.1 9.6 - - + -
107C PHE* 3.7 19.0 - - + -
324C LYS* 4.2 15.9 - - + -
325C PRO* 2.8 15.4 + - + +
327C GLN* 1.3 90.8 - - - +
329C TYR* 1.3 66.0 + - - +
331C GLN* 2.9 16.3 + - - +
332C TRP* 3.0 23.9 + - - +
506C EPE 3.3 23.8 - - - +
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Residues in contact with TYR 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ASN* 3.5 30.4 + - + +
322C PRO* 3.5 32.4 - - + +
324C LYS* 4.1 10.9 - - - +
325C PRO 3.3 2.6 + - - +
326C LEU* 3.9 9.0 - - + +
328C LEU* 1.3 76.9 - - - +
330C ARG* 1.3 57.4 + - - +
332C TRP* 3.0 8.2 + - + +
333C THR* 2.9 41.7 + - - -
369C GLN* 2.9 28.8 + - - +
373C ILE* 3.4 21.4 - - + +
402C ASN* 3.8 27.4 - - + -
406C TYR* 3.4 27.1 - + - -
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Residues in contact with ARG 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C LEU* 2.9 30.3 + - + +
327C GLN* 4.1 6.5 - - - +
329C TYR* 1.3 76.3 - - - +
331C GLN* 1.3 63.9 + - + +
333C THR* 3.9 0.9 - - - -
334C ASP* 3.1 45.1 + - - +
405C TRP* 3.6 38.3 - - + -
406C TYR* 3.9 17.0 - - - +
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Residues in contact with GLN 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 3.6 30.2 - - + -
327C GLN* 2.8 25.7 + - - +
328C LEU 2.9 7.2 + - - +
330C ARG* 1.3 78.5 - - + +
332C TRP* 1.3 64.3 + - - +
334C ASP* 3.5 8.2 + - - +
335C ARG* 3.1 33.3 + - - +
506C EPE 2.8 55.8 + - - -
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Residues in contact with TRP 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 3.9 7.6 - - + -
107C PHE* 3.5 31.1 - + - -
159C TYR* 3.7 25.2 - + - -
161C ASN* 5.0 0.4 - - - -
163C ILE* 3.6 24.9 - - + -
164C HIS* 3.6 33.2 - - + -
167C ASP* 3.4 33.4 + - + -
321C ASN* 3.1 41.9 - - + +
324C LYS* 5.2 4.5 - - + +
328C LEU* 3.0 33.8 + - + +
329C TYR* 3.0 8.2 + - + +
331C GLN* 1.3 76.1 - - - +
333C THR* 1.3 57.2 + - - +
335C ARG* 3.3 9.6 + - - +
336C ILE* 2.9 33.3 + - - +
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Residues in contact with THR 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C TYR* 2.9 35.2 + - - -
330C ARG 3.9 2.2 - - - -
332C TRP* 1.3 73.6 - - - +
334C ASP* 1.3 69.2 + - - +
336C ILE* 3.3 7.1 - - - +
337C MET* 3.1 30.1 + - + +
365C VAL* 3.8 23.8 - - + -
369C GLN* 3.7 25.7 - - + +
406C TYR* 3.2 27.6 + - + +
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Residues in contact with ASP 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330C ARG* 3.1 35.8 + - - +
331C GLN* 3.8 8.3 - - - +
333C THR* 1.3 78.3 - - - +
335C ARG* 1.3 58.9 + - + +
337C MET* 3.6 4.5 + - - +
338C GLU* 3.1 30.5 + - - +
365C VAL* 6.1 0.7 - - - +
406C TYR* 5.6 0.5 + - - -
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Residues in contact with ARG 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C PHE* 3.2 35.8 - - - -
158C ALA* 2.9 51.8 + - + +
159C TYR* 3.9 8.5 - - + -
161C ASN* 3.6 4.6 - - - +
163C ILE* 4.1 12.8 - - - +
331C GLN* 3.1 21.4 + - - +
332C TRP* 3.6 13.0 - - - +
334C ASP* 1.3 79.5 - - + +
336C ILE* 1.3 63.5 + - - +
338C GLU* 3.3 5.5 + - - +
339C GLU* 3.0 19.9 + - - +
503C EDO 3.3 24.7 + - - -
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Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C TYR* 3.6 40.8 - - + -
160C HIS* 4.0 6.3 - - + -
332C TRP 2.9 19.8 + - - +
333C THR* 3.3 16.4 - - - +
335C ARG* 1.3 72.6 - - - +
337C MET* 1.3 69.8 + - + +
339C GLU* 3.2 3.5 + - - +
340C PHE* 2.8 49.3 + - + -
369C GLN* 4.6 2.5 - - - +
502C 2SR 3.7 53.6 - - + +
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Residues in contact with MET 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C THR* 3.1 23.6 + - + +
334C ASP* 3.9 4.5 - - - +
336C ILE* 1.3 80.3 - - - +
338C GLU* 1.3 61.5 + - - +
340C PHE* 3.7 5.8 - - - -
341C PHE* 2.8 77.5 + - + -
357C MET* 3.7 39.0 - - + +
363C ALA* 4.8 3.6 - - + -
365C VAL* 3.7 41.3 - - + +
368C SER* 5.6 0.7 - - - +
369C GLN* 4.7 5.2 - - - -
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Residues in contact with GLU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158C ALA* 3.8 12.0 - - + +
334C ASP 3.1 18.3 + - - +
335C ARG* 3.3 9.7 + - - +
337C MET* 1.3 76.6 - - - +
339C GLU* 1.3 58.4 + - - +
341C PHE* 3.9 7.1 - - - +
342C ARG* 2.3 77.7 + - + +
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Residues in contact with GLU 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C VAL* 3.1 14.6 - - + +
158C ALA* 4.2 6.0 - - + +
159C TYR* 2.8 34.2 + - - +
160C HIS* 2.4 41.9 + - - -
204C HIS* 4.0 0.7 - - - -
206C GLY* 3.4 31.6 - - - +
335C ARG 3.0 12.9 + - - +
336C ILE* 3.5 10.3 - - - +
338C GLU* 1.3 74.9 - - - +
340C PHE* 1.3 71.0 + - + +
342C ARG* 3.3 8.6 + - - +
343C GLN* 3.0 21.9 + - - +
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Residues in contact with PHE 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C HIS* 5.5 3.1 - + - -
336C ILE* 2.8 50.2 + - + +
337C MET* 3.7 9.6 - - - +
339C GLU* 1.3 79.1 - - + +
341C PHE* 1.3 58.0 + - - +
343C GLN* 3.1 8.3 + - + +
344C GLY 2.9 23.2 + - - -
356C PRO 4.8 1.8 - - - -
357C MET* 3.6 54.7 - - + +
358C CYS* 3.2 27.5 - - - +
502C 2SR 3.8 36.6 - + + -
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Residues in contact with PHE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C MET* 2.8 53.9 + - + +
338C GLU* 4.0 6.3 - - - +
340C PHE* 1.3 73.7 - - - +
342C ARG* 1.3 57.7 + - + +
344C GLY* 3.2 1.7 + - - -
345C ASP* 2.8 34.4 + - - +
357C MET 3.5 22.4 - - - -
358C CYS 3.6 6.5 - - - +
359C ASP 3.6 15.5 - - - -
360C LYS* 3.7 39.7 - - + -
363C ALA* 3.8 14.8 - - + -
365C VAL* 4.3 8.7 - - + -
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Residues in contact with ARG 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C ASP* 2.8 29.3 + - - +
157C VAL* 4.8 0.4 - - - +
158C ALA* 4.5 10.4 - - - +
206C GLY 6.0 0.2 - - - +
338C GLU* 2.3 63.9 + - + +
339C GLU* 3.7 7.6 - - - +
340C PHE 3.2 0.2 - - - -
341C PHE* 1.3 73.5 - - + +
343C GLN* 1.3 64.6 + - - +
345C ASP* 3.3 11.9 + - - +
346C ARG* 3.0 29.4 + - + +
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Residues in contact with GLN 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C GLY 4.3 2.5 + - - +
207C VAL* 3.3 21.5 - - + -
208C SER* 3.0 46.8 + - - -
211C PHE* 3.7 12.5 - - + +
339C GLU 3.0 13.2 + - - +
340C PHE* 3.1 13.3 + - + +
342C ARG* 1.3 76.7 - - - +
344C GLY* 1.3 58.3 + - - +
346C ARG* 3.2 7.8 + - - +
347C GLU* 2.8 57.6 + - + +
355C SER* 3.4 11.1 + - - -
358C CYS* 4.3 11.0 - - - -
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Residues in contact with GLY 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C PHE 2.9 10.5 + - - -
341C PHE 3.2 0.9 + - - -
343C GLN* 1.3 78.4 - - - +
345C ASP* 1.3 52.5 + - - +
347C GLU* 3.6 14.6 - - - +
348C ARG* 2.8 40.1 + - - +
354C ILE* 4.1 5.6 - - - +
358C CYS* 3.1 26.2 - - - +
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Residues in contact with ASP 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C PHE* 2.8 22.6 + - - +
342C ARG* 3.7 12.6 - - - +
343C GLN 3.3 0.2 - - - -
344C GLY* 1.3 72.4 - - - +
346C ARG* 1.3 61.4 + - + +
348C ARG* 2.3 39.1 + - - +
349C GLU* 2.8 35.1 + - - +
358C CYS 5.2 0.3 - - - +
360C LYS* 3.1 29.8 + - - +
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Residues in contact with ARG 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 4.7 0.4 - - - +
151A ASP* 3.0 41.1 + - - +
504A PEG 3.7 28.8 + - - +
514A EDO 4.2 6.9 + - - -
205C PRO* 4.1 16.2 + - - +
207C VAL* 3.8 29.7 - - - +
211C PHE* 4.0 23.9 - - + -
342C ARG* 3.0 20.3 + - + +
343C GLN* 3.2 9.6 + - - +
345C ASP* 1.3 73.0 - - + +
347C GLU* 1.3 64.5 - - - +
349C GLU* 3.1 19.3 - - - +
350C ARG* 3.1 41.3 + - - +
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Residues in contact with GLU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C PHE* 3.7 21.3 - - + +
214C ASN* 6.0 0.3 + - - -
343C GLN* 2.8 35.2 + - - +
344C GLY* 3.6 13.8 - - - +
346C ARG* 1.3 76.9 - - - +
348C ARG* 1.3 60.6 + - - +
350C ARG 3.1 2.1 + - - -
351C GLY 3.0 4.2 + - - -
352C MET* 2.9 47.8 + - + +
353C GLU 3.6 17.2 - - - +
354C ILE* 3.4 5.6 - - - -
355C SER* 2.5 51.1 + - - -
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Residues in contact with ARG 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C GLY 2.8 24.7 + - - +
345C ASP* 2.3 42.4 + - - +
347C GLU* 1.3 75.7 - - - +
349C GLU* 1.3 62.4 + - - +
351C GLY* 3.3 11.4 + - - +
352C MET 4.5 5.6 - - - -
354C ILE* 3.6 27.0 - - + +
359C ASP* 3.5 23.6 + - - +
360C LYS* 3.4 20.4 - - - +
361C HIS* 3.9 18.0 + - - -
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Residues in contact with GLU 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 2.6 46.5 + - - +
143A ILE* 5.4 2.9 - - - +
147A MET* 3.6 35.2 - - + +
151A ASP* 4.7 1.0 - - - +
345C ASP* 2.8 21.8 + - - +
346C ARG* 3.1 34.4 - - - +
348C ARG* 1.3 73.1 - - - +
350C ARG* 1.3 61.8 + - + +
351C GLY 3.3 0.7 + - - -
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Residues in contact with ARG 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A THR* 4.4 28.0 + - + +
147A MET* 4.5 11.9 - - + +
148A THR* 3.3 30.5 + - - +
151A ASP* 2.8 28.7 + - - -
243A GLU* 5.1 0.8 + - - -
514A EDO 3.1 25.0 + - - -
211C PHE* 4.0 11.9 - - - -
215C THR* 3.9 16.6 - - - +
346C ARG* 3.1 27.8 + - - +
347C GLU 3.1 3.7 + - - +
349C GLU* 1.3 85.5 + - + +
351C GLY* 1.3 61.1 - - - +
352C MET* 3.4 24.6 + - + +
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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