Contacts of the helix formed by residues 324 - 351 (chain D) in PDB entry 1RX0
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 324 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C SER 3.8 27.5 - - - +
12C CYS* 4.6 3.1 - - - -
17C MET* 3.6 21.1 - - - +
322D ARG* 2.9 48.5 + - - +
323D LYS* 1.3 78.3 - - - +
325D ALA* 1.3 63.7 + - - +
326D VAL 3.4 2.2 - - - -
327D ALA* 3.4 8.9 + - - +
328D LEU* 3.0 39.6 + - + +
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Residues in contact with ALA 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D ALA* 3.6 37.0 - - - +
318D LEU* 3.8 17.7 - - + +
321D GLU* 4.8 1.8 - - - -
322D ARG 3.1 18.3 + - - +
323D LYS 3.4 0.4 - - - -
324D ASP* 1.3 80.1 + - - +
326D VAL* 1.3 59.4 + - + +
328D LEU* 3.3 1.5 + - - +
329D CYS* 2.9 36.6 + - - -
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Residues in contact with VAL 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D ASN* 4.1 13.9 - - - +
318D LEU* 6.1 1.3 - - + -
322D ARG 4.9 0.2 + - - -
323D LYS 4.9 4.8 + - - +
324D ASP 3.4 0.8 - - - -
325D ALA* 1.3 78.8 - - + +
327D ALA* 1.3 63.1 + - - +
329D CYS* 3.5 3.9 + - - +
330D SER* 3.1 29.5 + - - +
385D LEU* 5.5 8.5 - - + -
400D 2MC 3.6 50.9 - - + +
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Residues in contact with ALA 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C CYS* 3.4 32.1 - - + -
323D LYS 5.6 0.2 + - - -
324D ASP* 3.4 9.7 + - - +
325D ALA 3.3 0.2 - - - -
326D VAL* 1.3 79.8 - - - +
328D LEU* 1.3 58.9 + - - +
330D SER* 3.2 7.5 + - - -
331D MET* 2.9 34.0 + - + +
385D LEU* 5.8 1.6 - - - -
386D ILE* 4.3 7.2 - - - +
389D SER* 4.2 19.1 - - - +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C CYS* 4.3 12.8 - - - +
305C VAL* 4.3 11.2 - - + -
310D MET* 5.1 1.1 - - + +
313D ASN* 3.9 22.7 - - - +
314D ALA* 3.6 14.3 - - + +
317D ALA* 3.6 14.6 - - + -
322D ARG* 3.6 17.3 - - - +
324D ASP* 3.0 41.4 + - + +
325D ALA* 3.7 4.5 - - - +
327D ALA* 1.3 75.6 - - + +
329D CYS* 1.3 59.7 + - - +
331D MET* 3.3 22.0 + - + +
332D ALA* 2.8 31.4 + - - +
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Residues in contact with CYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D ASN* 3.7 26.7 - - + +
255D ARG* 4.7 6.8 - - + +
256D ILE* 3.4 34.4 - - + +
314D ALA* 4.0 10.3 - - - -
318D LEU* 4.1 21.1 - - - -
325D ALA 2.9 25.4 + - - +
326D VAL* 3.8 5.6 - - - +
328D LEU* 1.3 76.0 - - - +
330D SER* 1.3 58.5 + - - +
332D ALA* 3.7 1.6 - - - +
333D LYS* 3.0 30.5 + - - +
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Residues in contact with SER 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D ASN* 5.4 0.7 + - - -
255D ARG* 4.8 4.5 + - - +
326D VAL* 3.1 14.8 + - - +
327D ALA* 3.5 9.8 - - - -
328D LEU 3.2 0.2 - - - -
329D CYS* 1.3 79.8 - - - +
331D MET* 1.3 56.5 + - - +
333D LYS* 3.5 1.7 + - - +
334D LEU* 3.0 30.1 + - - +
382D MET* 3.7 26.6 - - - +
385D LEU* 3.6 26.5 - - - +
386D ILE* 3.8 18.6 - - - -
400D 2MC 5.3 0.3 + - - -
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Residues in contact with MET 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C CYS* 3.9 32.3 - - - +
301C ALA* 3.5 44.2 - - + +
302C THR* 3.5 19.7 - - + +
305C VAL* 3.8 19.5 - - - -
310D MET* 4.0 12.6 - - + -
327D ALA* 2.9 20.3 + - + +
328D LEU* 3.7 15.7 - - + +
330D SER* 1.3 76.7 - - - +
332D ALA* 1.3 58.4 + - - +
334D LEU* 3.7 0.7 - - - +
335D PHE* 2.8 34.3 + - - +
386D ILE* 3.7 20.0 - - + -
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Residues in contact with ALA 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ILE* 5.5 4.0 - - + -
259D ALA* 4.5 3.1 - - + -
310D MET* 3.6 39.4 - - + +
311D VAL* 4.0 8.5 - - + -
314D ALA* 3.7 11.4 - - + -
328D LEU 2.8 18.2 + - - +
329D CYS* 3.7 3.4 - - - +
331D MET* 1.3 74.0 - - - +
333D LYS* 1.3 61.2 + - - +
335D PHE* 4.1 0.2 - - - +
336D ALA* 2.8 36.8 + - - +
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Residues in contact with LYS 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ARG* 3.7 35.8 + - + +
258D ILE* 5.0 3.8 - - + -
259D ALA* 4.1 10.7 - - - +
329D CYS 3.0 17.0 + - - +
330D SER 3.8 3.4 - - - +
332D ALA* 1.3 74.9 - - - +
334D LEU* 1.3 58.3 + - - +
337D THR* 2.6 45.2 + - + +
372D HIS 2.8 28.9 + - - -
373D GLN 3.8 5.1 - - - -
375D LEU 3.2 13.2 + - - -
376D GLU* 4.4 7.9 - - - -
377D GLY 2.6 27.2 + - - +
379D ASN* 2.9 20.2 + - - +
382D MET* 3.9 14.4 - - + -
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C ALA 5.1 0.9 - - - +
299C ASP* 4.1 11.0 - - - +
302C THR* 3.9 16.2 - - + +
330D SER 3.0 18.1 + - - +
331D MET 3.7 2.7 - - - +
333D LYS* 1.3 79.6 - - - +
335D PHE* 1.3 64.6 + - - +
337D THR* 3.5 0.9 + - - -
338D ASP* 3.3 46.4 + - - +
379D ASN* 3.5 33.4 - - + +
382D MET* 4.0 7.2 - - + -
383D ARG* 3.7 32.1 - - + +
386D ILE* 3.8 21.5 - - + -
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Residues in contact with PHE 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C THR* 3.9 13.0 - - + -
303C ARG* 3.3 47.6 - - - +
306C ALA* 4.0 15.3 - - + -
335C PHE* 3.7 24.7 - + - -
303D ARG* 4.4 1.3 - - - -
306D ALA* 3.7 9.0 - - + -
307D ALA* 3.5 34.5 - - - -
310D MET* 3.8 18.8 - - + -
331D MET 2.8 21.1 + - - +
332D ALA 4.1 1.1 - - - +
334D LEU* 1.3 77.2 - - - +
336D ALA* 1.3 59.3 + - - +
338D ASP* 3.8 2.1 - - - +
339D GLU* 2.9 52.7 + - + +
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Residues in contact with ALA 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D ALA* 3.9 15.0 - - + +
262D SER* 4.6 1.1 - - - -
263D LEU* 4.5 2.5 - - + -
307D ALA* 4.1 20.6 - - + +
310D MET* 5.8 0.2 - - + -
311D VAL* 3.6 25.1 - - + -
332D ALA 2.8 23.7 + - - +
335D PHE* 1.3 75.5 - - + +
337D THR* 1.3 57.4 + - - +
340D CYS* 2.8 36.6 + - - +
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Residues in contact with THR 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258D ILE* 4.6 1.6 - - + -
259D ALA* 4.3 15.0 - - - -
262D SER* 3.8 19.4 + - - +
333D LYS* 2.6 32.7 + - + +
336D ALA* 1.3 76.0 - - - +
338D ASP* 1.3 59.6 + - - +
340D CYS* 4.5 0.2 - - - +
341D PHE* 3.3 23.6 + - - +
369D SER 4.8 2.1 - - - +
372D HIS* 3.7 30.5 - - + +
373D GLN* 3.6 12.5 - - - +
379D ASN* 3.0 25.3 + - - -
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Residues in contact with ASP 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ARG* 5.7 2.7 - - - +
334D LEU* 3.3 29.9 + - - +
335D PHE* 3.8 2.9 - - - +
336D ALA 3.2 0.4 - - - -
337D THR* 1.3 80.4 + - - +
339D GLU* 1.3 68.9 + - + +
341D PHE* 3.9 2.9 - - - +
342D ALA* 3.2 22.2 + - - +
373D GLN* 2.7 31.4 + - - +
379D ASN* 2.7 22.4 + - - +
383D ARG* 3.8 11.6 + - - -
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Residues in contact with GLU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ARG* 2.9 31.8 + - - +
303D ARG* 2.6 48.1 + - + +
307D ALA* 4.6 8.3 - - + -
335D PHE* 2.9 49.1 + - + +
336D ALA 4.2 1.6 - - - +
338D ASP* 1.3 80.0 - - + +
340D CYS* 1.3 58.7 + - - +
342D ALA* 3.3 9.1 + - - +
343D ILE* 3.0 33.5 + - + +
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Residues in contact with CYS 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D SER* 3.5 42.4 - - - +
263D LEU* 3.8 22.7 - - - -
266D ALA* 3.7 16.6 - - + -
304D LEU* 4.8 2.5 - - - -
307D ALA* 4.2 9.0 - - - -
336D ALA 2.8 29.1 + - - +
337D THR 4.5 0.2 - - - +
339D GLU* 1.3 71.0 - - - +
341D PHE* 1.3 65.5 + - - +
343D ILE* 3.3 5.3 + - - +
344D CYS* 3.0 28.8 + - - -
369D SER* 4.7 2.0 - - - -
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Residues in contact with PHE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PHE* 5.0 7.9 - + - -
345B ASN* 4.0 22.7 - - - -
337D THR 3.3 19.5 + - - +
338D ASP 3.9 3.6 - - - +
340D CYS* 1.3 77.9 - - - +
342D ALA* 1.3 62.3 + - + +
344D CYS* 3.2 2.4 + - - +
345D ASN* 2.9 49.0 + - + +
366D VAL* 3.6 24.9 - - + -
369D SER* 3.7 22.4 + - - +
370D ARG* 3.6 42.6 - - + -
373D GLN* 3.6 21.5 - - - +
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Residues in contact with ALA 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ASP 3.2 10.9 + - - +
339D GLU* 3.5 12.8 - - - +
341D PHE* 1.3 87.3 - - + +
343D ILE* 1.3 57.8 + - + +
345D ASN* 3.4 5.0 + - - +
346D GLN* 2.9 29.8 + - - +
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Residues in contact with ILE 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D ALA* 4.0 20.6 - - + +
269D SER* 4.8 1.1 - - - -
270D VAL* 3.6 28.5 - - + -
300D MET* 3.4 42.9 - - + +
303D ARG* 4.0 11.4 - - + +
304D LEU* 3.6 25.4 - - + +
339D GLU* 3.0 24.6 + - + +
340D CYS* 3.6 8.1 - - - +
342D ALA* 1.3 77.5 - - + +
344D CYS* 1.3 58.9 + - - +
346D GLN* 3.2 5.1 + - - +
347D ALA* 2.9 26.7 + - - +
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Residues in contact with CYS 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ALA* 3.6 28.0 - - - -
266D ALA* 3.7 5.2 - - - -
269D SER* 3.4 28.3 - - - +
340D CYS 3.0 21.4 + - - +
341D PHE 3.7 3.1 - - - +
343D ILE* 1.3 77.8 - - - +
345D ASN* 1.3 58.1 + - - +
347D ALA* 3.2 3.8 + - - +
348D LEU 3.0 22.0 + - - -
362D VAL* 3.6 1.7 - - - +
365D TYR* 3.9 8.3 - - - -
366D VAL* 3.2 30.8 - - + +
369D SER* 4.1 8.3 - - - +
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Residues in contact with ASN 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PHE* 4.1 18.8 - - - -
370B ARG* 2.8 59.4 + - - +
373B GLN* 5.4 1.0 + - - +
341D PHE* 2.9 38.2 + - + +
342D ALA* 3.8 6.3 - - - +
344D CYS* 1.3 73.2 - - - +
346D GLN* 1.3 66.4 + - - +
348D LEU* 3.3 3.6 + - - +
349D GLN* 3.2 5.0 + - - +
366D VAL* 3.7 18.4 - - + +
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Residues in contact with GLN 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLU* 5.3 0.8 + - - +
292D TYR* 4.9 6.7 + - - -
296D THR* 2.7 37.4 + - + +
300D MET* 3.4 19.1 - - + -
342D ALA 2.9 16.8 + - - +
343D ILE* 3.6 4.7 - - - +
345D ASN* 1.3 74.8 - - - +
347D ALA* 1.3 65.9 + - - +
349D GLN* 3.1 12.8 + - - +
350D MET* 2.7 61.5 + - - +
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Residues in contact with ALA 347 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D SER* 3.7 17.9 - - - +
273D THR* 3.1 24.9 - - - +
300D MET* 3.9 6.3 - - + +
343D ILE 2.9 13.4 + - - +
344D CYS 3.3 9.9 - - - +
346D GLN* 1.3 77.3 - - - +
348D LEU* 1.3 59.7 + - - +
350D MET* 3.2 10.1 + - - +
351D HIS* 2.8 23.8 + - - +
362D VAL* 3.6 14.1 - - + -
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B VAL* 5.2 4.5 - - + -
370B ARG* 3.8 22.0 - - + +
374B ILE* 4.0 18.4 - - + -
344D CYS 3.0 12.7 + - - +
345D ASN* 3.4 15.3 - - - +
347D ALA* 1.3 78.2 - - - +
349D GLN* 1.3 64.1 + - - +
351D HIS* 3.0 15.1 + - - +
352D GLY 3.5 7.6 + - - +
355D GLY* 3.3 31.6 - - - +
356D TYR* 4.2 9.2 - - + +
362D VAL* 3.4 14.1 - - + +
363D GLN* 4.1 11.9 - - + -
366D VAL* 4.0 25.1 - - + -
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Residues in contact with GLN 349 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ARG* 2.9 37.6 + - - +
373B GLN* 3.2 28.1 + - - +
374B ILE* 3.5 14.2 - - - +
378B SER* 4.5 1.4 - - - -
379B ASN* 4.5 2.2 - - - +
380B GLU* 2.9 40.6 + - - +
399B FAD 2.6 25.4 + - - +
345D ASN 3.2 2.9 + - - +
346D GLN* 3.1 22.3 + - - +
348D LEU* 1.3 80.9 - - - +
350D MET* 1.3 57.1 + - + +
352D GLY* 2.9 16.1 + - - -
----------------------------------------------------------
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Residues in contact with MET 350 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B GLU* 4.6 5.2 - - + +
399B FAD 3.5 24.4 - - - +
273D THR* 3.7 29.4 - - + +
276D HIS* 3.3 17.1 - - + -
277D LEU* 4.5 10.5 - - + +
287D LEU* 4.3 2.6 - - - +
292D TYR* 4.9 1.3 - - + -
293D LEU* 3.4 44.4 - - + +
296D THR* 4.5 7.2 - - + -
297D LEU* 5.8 0.7 - - - -
300D MET* 4.8 2.2 - - - +
346D GLN* 2.7 54.3 + - + +
347D ALA 3.2 8.7 + - - +
349D GLN* 1.3 82.9 - - + +
351D HIS* 1.3 59.1 + - - +
352D GLY 3.3 0.2 - - - -
----------------------------------------------------------
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Residues in contact with HIS 351 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B FAD 4.1 4.6 + - - +
272D LEU* 4.0 23.8 + - + +
273D THR* 3.9 30.5 + - - -
276D HIS* 3.7 29.5 + + + +
347D ALA* 2.8 23.9 + - + -
348D LEU 3.0 7.6 + - - +
350D MET* 1.3 79.6 - - - +
352D GLY* 1.3 63.9 + - - +
354D TYR* 3.4 23.7 + - + +
355D GLY* 3.5 18.6 - - - +
360D TYR* 4.1 25.4 - + - -
362D VAL* 4.3 19.3 - - + +
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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