Contacts of the helix formed by residues 318 - 343 (chain s) in PDB entry 3J7Y
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 ASP 318 (chain s).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101U HIS* 5.2 21.4 - - + +
316s CYS 3.5 0.2 - - - -
317s ALA* 1.3 80.1 - - - +
319s GLN* 1.3 68.0 + - - +
320s ILE 3.2 4.9 + - - -
321s GLU* 4.2 6.9 + - - +
322s VAL* 3.4 16.2 - - - +
325s ARG* 5.3 1.6 + - - -
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Residues in contact with GLN 319 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U ALA* 5.4 1.6 - - - +
99U LEU 5.7 2.2 + - - -
100U ALA* 6.0 1.0 - - - +
101U HIS 5.6 4.8 + - - +
99s ALA 5.4 0.9 - - - +
100s LEU* 3.6 36.2 - - + +
101s ASN* 3.0 35.2 + - - +
311s LEU* 3.9 6.5 - - + +
316s CYS* 3.2 30.5 - - + +
317s ALA 3.3 1.0 - - - -
318s ASP* 1.3 87.0 + - - +
320s ILE* 1.3 62.7 + - - +
321s GLU 3.5 0.7 - - - -
322s VAL* 3.7 18.6 - - + -
323s VAL* 3.2 29.2 + - + +
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Residues in contact with ILE 320 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302s LEU* 5.6 0.3 - - - +
308s ARG* 3.4 53.6 - - + +
311s LEU* 3.6 27.9 - - + +
312s LEU* 3.6 30.7 - - + -
317s ALA* 3.1 24.9 - - + +
318s ASP 3.2 2.0 - - - -
319s GLN* 1.3 78.1 - - - +
321s GLU* 1.3 63.6 - - - +
323s VAL* 3.9 7.3 + - - +
324s PHE* 3.2 20.1 - - + -
398s SER* 4.9 0.9 - - - +
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Residues in contact with GLU 321 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114s PHE* 5.4 0.7 - - - -
318s ASP 4.2 4.8 + - - +
320s ILE* 1.3 77.9 - - - +
322s VAL* 1.3 66.2 + - - +
324s PHE* 3.2 21.4 + - - +
325s ARG* 2.8 60.4 + - - +
368s SER* 4.2 1.9 + - - -
370s PHE* 4.0 6.6 - - - -
396s THR 3.8 14.6 - - - +
397s GLN* 4.2 26.3 - - + +
398s SER* 3.9 24.1 + - - +
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Residues in contact with VAL 322 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99s ALA 5.7 1.6 - - - +
101s ASN* 4.3 20.4 - - - +
102s ALA* 4.4 3.6 - - + +
103s ASP* 3.9 27.8 - - + +
318s ASP* 3.4 25.6 - - - +
319s GLN* 3.7 18.8 - - + -
320s ILE 3.3 1.0 - - - -
321s GLU* 1.3 75.7 - - - +
323s VAL* 1.3 59.8 + - + +
325s ARG* 3.2 29.4 + - - +
326s ALA* 2.9 27.0 + - + +
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Residues in contact with VAL 323 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95s PRO 4.3 1.6 - - - +
96s GLN* 5.3 0.9 - - - -
97s THR 4.0 24.9 + - - +
98s PHE* 5.8 0.9 - - - +
99s ALA 5.5 4.3 - - - +
102s ALA* 6.3 0.7 - - - -
302s LEU* 3.8 28.3 - - + -
306s LEU* 3.9 29.2 - - + -
311s LEU* 4.6 9.6 - - + -
319s GLN* 3.2 22.4 + - + +
320s ILE 4.1 6.1 - - - +
321s GLU 3.2 0.6 - - - -
322s VAL* 1.3 77.2 - - + +
324s PHE* 1.3 58.6 + - - +
326s ALA* 3.2 9.3 + - - +
327s ASN* 2.9 28.1 + - - +
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Residues in contact with PHE 324 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302s LEU* 3.4 33.4 - - + -
308s ARG* 3.8 14.6 - - - -
320s ILE* 3.2 28.5 - - + -
321s GLU* 3.2 21.0 + - - +
323s VAL* 1.3 81.0 - - - +
325s ARG* 1.3 57.6 + - - +
327s ASN* 3.2 8.5 + - - +
328s ALA* 2.9 29.3 + - - +
361s ILE* 3.0 45.2 - - + +
362s THR 4.3 12.1 - - - -
363s ASP* 4.7 7.9 - - + -
366s TYR* 4.4 10.3 - - + -
368s SER* 4.2 1.6 - - - +
370s PHE* 4.7 3.1 - - + -
398s SER* 3.8 26.0 - - - -
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Residues in contact with ARG 325 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103s ASP* 3.1 29.7 + - - +
114s PHE* 3.3 47.1 - - + -
318s ASP* 5.3 1.6 + - - -
321s GLU* 2.8 45.2 + - - +
322s VAL* 3.2 31.6 + - - +
324s PHE* 1.3 81.0 - - - +
326s ALA* 1.3 56.4 + - - +
328s ALA* 3.2 4.5 + - - +
329s ILE* 2.9 32.1 + - - +
370s PHE* 4.2 10.9 - - + -
397s GLN* 5.7 4.0 - - - +
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Residues in contact with ALA 326 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95s PRO 4.0 7.9 - - - +
97s THR* 4.5 2.9 - - + -
102s ALA* 4.2 13.5 - - + -
103s ASP* 3.9 28.7 + - - +
106s TYR* 3.7 10.6 - - + -
322s VAL 2.9 13.2 + - - +
323s VAL* 3.3 12.1 - - - +
325s ARG* 1.3 75.2 - - - +
327s ASN* 1.3 58.4 + - - +
329s ILE* 3.2 7.4 + - - +
330s ALA* 2.9 29.8 + - - +
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Residues in contact with ASN 327 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95s PRO* 3.3 26.8 + - - +
96s GLN* 3.5 30.4 - - + +
235s ASP* 4.9 0.7 - - - +
300s HIS* 3.2 21.3 - - - +
302s LEU* 4.0 9.3 - - + +
323s VAL 2.9 11.6 + - - +
324s PHE* 3.4 11.0 - - - +
326s ALA* 1.3 76.3 - - - +
328s ALA* 1.3 61.0 + - - +
330s ALA 3.2 0.7 + - - -
331s SER* 2.9 35.9 + - - -
361s ILE* 3.4 19.8 - - + +
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Residues in contact with ALA 328 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300s HIS* 5.6 0.9 - - - -
324s PHE 2.9 10.6 + - - +
325s ARG 3.3 8.5 - - - +
327s ASN* 1.3 77.9 - - - +
329s ILE* 1.3 63.7 + - - +
331s SER* 4.6 2.0 - - - -
332s LEU* 3.1 34.6 + - + +
359s ALA* 6.1 0.9 - - - -
361s ILE* 4.7 6.0 - - + +
370s PHE* 3.3 48.5 - - + -
372s TYR* 4.5 1.0 - - - -
393s CYS* 4.6 4.3 - - - -
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Residues in contact with ILE 329 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103s ASP* 3.1 33.2 - - - +
106s TYR* 4.0 22.7 - - + -
107s GLN* 3.6 27.8 - - + +
110s THR* 4.0 15.7 - - - +
112s THR* 4.3 14.8 - - + +
114s PHE* 4.7 9.2 - - + -
325s ARG 2.9 14.5 + - - +
326s ALA* 3.5 8.1 - - - +
328s ALA* 1.3 78.1 - - - +
330s ALA* 1.3 59.5 + - - +
333s PHE* 2.9 28.1 + - - +
372s TYR* 3.9 8.4 - - - -
393s CYS* 4.6 16.2 - - + -
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Residues in contact with ALA 330 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95s PRO* 3.6 32.3 - - + -
106s TYR* 3.9 12.8 - - + -
110s THR* 5.7 0.4 - - - -
233s ILE* 3.2 28.9 - - + +
326s ALA 2.9 15.5 + - - +
327s ASN 3.7 0.2 - - - +
329s ILE* 1.3 79.0 - - - +
331s SER* 1.3 62.6 + - - +
333s PHE* 3.2 2.6 + - - +
334s ALA* 2.9 24.4 + - - +
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Residues in contact with SER 331 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95s PRO* 4.5 0.9 - - - -
206s VAL* 4.5 2.1 - - - +
235s ASP* 3.2 35.2 - - - -
298s GLN* 3.7 9.5 + - - +
300s HIS* 2.6 33.9 + - - -
327s ASN* 2.9 19.3 + - - -
328s ALA* 4.4 1.2 + - - -
330s ALA* 1.3 77.0 - - - +
332s LEU* 1.3 60.4 + - - +
334s ALA* 3.2 5.8 + - - +
335s TRP* 2.9 28.4 + - - +
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Residues in contact with LEU 332 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298s GLN* 3.9 9.9 - - - +
328s ALA* 3.1 23.1 + - - +
331s SER* 1.3 83.0 + - - +
333s PHE* 1.3 57.7 + - - +
335s TRP* 3.2 9.3 + - + +
336s THR* 2.9 33.4 + - - +
357s SER* 3.6 19.2 + - - +
358s GLN 3.6 15.7 - - - +
359s ALA* 3.3 29.8 - - + -
370s PHE* 3.2 35.7 - - + +
371s CYS 4.2 0.9 - - - +
372s TYR* 3.6 22.7 - - + +
393s CYS* 5.1 0.9 - - - -
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Residues in contact with PHE 333 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110s THR* 3.0 47.1 - - + -
208s PHE* 3.9 16.4 - + - -
210s TRP* 3.5 44.9 - + - -
233s ILE* 4.1 15.5 - - + -
329s ILE 2.9 20.6 + - - +
330s ALA 3.2 2.1 + - - +
332s LEU* 1.3 80.1 - - - +
334s ALA* 1.3 55.1 + - - +
336s THR* 2.4 27.3 + - - -
337s GLY* 2.9 10.9 + - - -
372s TYR* 3.7 16.1 - - + +
374s LEU* 4.0 17.7 - - + -
377s LEU* 4.8 3.1 - - + -
379s LEU* 4.5 12.6 - - + -
391s ASN* 5.3 0.2 - - - -
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Residues in contact with ALA 334 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206s VAL* 4.3 12.6 - - + -
208s PHE* 3.4 36.3 - - + +
233s ILE* 3.7 25.8 - - + -
330s ALA 2.9 12.7 + - - +
331s SER* 3.3 9.0 - - - +
333s PHE* 1.3 78.4 - - - +
335s TRP* 1.3 56.7 + - - +
337s GLY 3.2 1.0 + - - -
338s ALA* 2.9 27.0 + - - +
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Residues in contact with TRP 335 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206s VAL* 4.1 13.8 - - + +
240s GLN* 3.2 47.0 + - + +
241s ILE 4.3 4.0 - - - -
242s ARG* 4.5 5.1 - - + +
284s VAL* 3.2 35.2 - - + +
295s GLY* 4.1 11.0 - - - -
296s HIS 4.0 15.3 - - - -
297s THR 4.0 4.3 - - - -
298s GLN* 3.1 49.8 - - + +
331s SER 2.9 11.9 + - - +
332s LEU* 3.2 13.7 - - + +
334s ALA* 1.3 75.7 - - - +
336s THR* 1.3 58.9 - - - +
338s ALA* 3.2 4.9 + - - +
339s GLN* 2.9 44.7 + - - +
357s SER* 3.8 23.6 - - - +
358s GLN 3.7 8.3 - - - -
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Residues in contact with THR 336 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332s LEU 2.9 10.9 + - - +
333s PHE* 2.4 31.5 + - - -
335s TRP* 1.3 76.5 - - - +
337s GLY* 1.3 56.8 + - - +
339s GLN* 3.2 14.0 + - - +
340s ALA* 2.9 28.8 + - - +
355s PHE* 4.0 20.5 - - - +
356s VAL 4.5 0.2 - - - -
357s SER* 3.1 30.5 - - - +
372s TYR* 3.8 16.8 - - + -
374s LEU* 3.3 28.2 - - - +
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Residues in contact with GLY 337 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208s PHE* 3.5 26.7 - - - -
333s PHE* 2.9 13.2 + - - -
334s ALA 3.2 3.8 + - - -
336s THR* 1.3 76.8 + - - +
338s ALA* 1.3 57.6 + - - +
340s ALA* 3.2 3.6 + - - +
341s MET* 2.9 33.3 + - - +
374s LEU* 4.5 0.4 - - - +
377s LEU* 3.9 15.2 - - - +
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Residues in contact with ALA 338 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206s VAL* 5.4 0.4 - - + -
207s HIS 4.4 2.9 - - - +
208s PHE* 3.7 1.6 - - - -
282s ILE* 4.2 11.9 - - - -
283s PHE 4.0 24.2 - - - +
284s VAL* 3.7 22.0 - - + -
334s ALA 2.9 13.0 + - - +
335s TRP* 3.3 11.7 - - - +
337s GLY* 1.3 75.7 - - - +
339s GLN* 1.3 53.8 + - - +
341s MET* 3.2 2.4 + - - +
342s TYR* 2.8 39.1 + - + -
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Residues in contact with GLN 339 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284s VAL* 4.5 6.7 - - + +
293s CYS 3.5 22.0 + - - +
294s TYR* 3.4 10.2 - - + +
295s GLY* 3.0 39.8 + - - +
335s TRP* 2.9 31.6 + - - +
336s THR* 3.3 30.0 + - - +
338s ALA* 1.3 77.1 - - - +
340s ALA* 1.3 61.0 + - - +
342s TYR* 3.2 6.9 + - - +
343s GLN* 3.1 27.2 + - - +
355s PHE* 3.7 19.0 - - + +
356s VAL 4.3 5.1 + - - +
357s SER* 4.1 6.9 - - - -
----------------------------------------------------------
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Residues in contact with ALA 340 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336s THR 2.9 13.2 + - - +
337s GLY* 3.2 9.6 + - - +
339s GLN* 1.3 75.0 - - - +
341s MET* 1.3 55.9 + - - +
343s GLN 3.0 15.4 + - - -
344s GLY 2.6 22.4 - - - +
345s PHE* 3.4 3.8 - - - -
351s VAL* 3.8 20.0 - - + -
355s PHE* 3.7 17.4 - - + -
374s LEU* 4.6 1.6 - - + -
377s LEU* 3.5 24.9 - - + -
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Residues in contact with MET 341 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76s VAL* 3.2 13.2 - - - +
80s LEU* 3.5 21.8 - - + +
83s LEU* 3.6 30.7 - - + -
208s PHE* 3.8 13.2 - - + -
209s TYR 4.9 4.0 - - - +
282s ILE* 3.3 45.8 - - + -
337s GLY 2.9 18.4 + - - +
338s ALA 3.2 7.4 + - - +
340s ALA* 1.3 76.2 - - - +
342s TYR* 1.3 61.8 + - + +
344s GLY* 2.9 22.8 + - - +
345s PHE 3.2 23.1 - - - +
346s TRP* 4.6 4.0 - - - -
377s LEU* 4.3 8.7 - - + -
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Residues in contact with TYR 342 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76s VAL* 3.6 22.0 - - - +
80s LEU* 4.8 6.5 - - + -
282s ILE* 3.9 9.8 + - + -
283s PHE* 3.6 26.7 - - - -
284s VAL* 3.0 31.0 - - + -
286s SER 2.9 21.2 + - - -
287s LYS* 3.6 8.0 - - - -
288s THR* 3.3 51.2 + - + +
293s CYS* 5.0 14.4 - - + -
338s ALA 2.8 28.5 + - - +
339s GLN* 3.2 7.2 + - - +
341s MET* 1.3 78.5 - - + +
343s GLN* 1.3 73.6 + - - +
344s GLY 3.6 0.3 + - - -
----------------------------------------------------------
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Residues in contact with GLN 343 (chain s).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76s VAL* 4.9 1.6 - - - -
293s CYS* 3.5 28.9 - - - +
294s TYR* 3.1 44.5 + - + +
339s GLN 3.1 11.9 + - - +
340s ALA 3.0 10.2 + - - +
342s TYR* 1.3 85.5 + - - +
344s GLY* 1.3 53.3 + - - -
345s PHE* 3.0 22.9 + - - -
353s ARG* 4.1 16.8 + - - +
355s PHE* 4.0 13.0 - - + -
----------------------------------------------------------
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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