Contacts of the helix formed by residues 299 - 321 (chain D) in PDB entry 3ZXR
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 SER 299 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288D LEU 2.6 28.6 + - - -
289D MET 2.7 17.2 + - - -
290D TYR 3.8 11.9 - - - -
291D ASP* 3.5 13.9 - - - +
298D LEU* 1.3 75.3 - - - +
300D ASP* 1.3 60.7 + - - +
301D THR* 3.4 4.2 + - - -
302D ALA* 3.2 12.7 + - - +
303D ARG* 2.9 29.5 + - - +
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Residues in contact with ASP 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D ASP* 5.2 4.8 + - - +
299D SER* 1.3 72.8 - - - +
301D THR* 1.3 66.7 + - - +
303D ARG* 2.8 38.9 + - - +
304D HIS* 3.0 44.7 + - + -
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Residues in contact with THR 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ILE* 4.6 7.0 - - + -
281D LEU* 4.5 10.3 - - + -
288D LEU* 4.1 23.2 + - + +
289D MET* 5.4 2.5 - - - -
299D SER* 3.3 8.3 + - - -
300D ASP* 1.3 80.1 - - - +
302D ALA* 1.3 56.9 + - - +
304D HIS* 3.5 2.4 + - - -
305D TYR* 3.0 27.0 + - - +
391D ILE* 3.6 37.4 - - + +
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Residues in contact with ALA 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D LEU 4.6 0.6 + - - -
289D MET* 3.4 55.6 - - + +
298D LEU* 3.8 17.7 - - + -
299D SER* 3.2 9.9 + - - +
301D THR* 1.3 78.6 - - - +
303D ARG* 1.3 63.0 + - - +
305D TYR* 3.0 5.5 + - - +
306D ILE* 3.0 28.5 + - + +
365D LEU* 4.5 0.5 - - - +
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Residues in contact with ARG 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D GLY* 6.0 2.4 - - - -
295D TYR* 6.4 1.1 - - - -
298D LEU* 4.7 12.7 + - + +
299D SER 2.9 14.6 + - - +
300D ASP* 2.8 40.0 + - - +
302D ALA* 1.3 74.9 - - - +
304D HIS* 1.3 64.7 + - - +
306D ILE* 3.3 10.8 + - - +
307D GLY 2.8 22.2 + - - -
342D TYR* 4.0 18.6 - - + +
396D GLU* 2.9 37.0 + - - -
397D PRO* 3.5 29.0 - - + +
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Residues in contact with HIS 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D ASP* 3.0 38.6 + - + +
301D THR* 3.9 3.8 + - - +
303D ARG* 1.3 77.7 + - - +
305D TYR* 1.3 61.3 + - - +
307D GLY* 3.3 0.9 + - - -
308D GLY 2.9 22.2 + - - -
390D GLY* 3.3 25.7 - - - +
391D ILE* 3.8 13.6 + - + +
394D LYS* 3.5 41.2 + - + +
395D ILE 3.4 19.4 - - - +
396D GLU* 2.8 29.5 + - - -
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Residues in contact with TYR 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ALA* 5.7 0.2 - - - +
130D PHE* 4.4 3.5 - - - -
279D GLN* 2.8 38.3 + - + +
280D SER 6.2 0.4 - - - -
281D LEU* 3.9 24.7 - - + +
289D MET* 5.0 4.9 - - + -
301D THR 3.0 14.1 + - - +
302D ALA* 3.0 13.2 + - - +
304D HIS* 1.3 71.9 - - - +
306D ILE* 1.3 65.7 + - - +
308D GLY* 3.1 3.8 + - - -
309D LEU* 3.0 33.6 + - + +
365D LEU* 3.5 23.1 - - + -
383D MET 4.0 0.7 - - - -
384D LEU* 3.5 32.7 - - + +
387D GLY* 3.6 39.6 - - - -
388D LEU 4.4 0.2 - - - -
391D ILE* 3.9 13.9 - - + +
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Residues in contact with ILE 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D LEU* 3.8 17.9 - - + -
302D ALA 3.0 18.3 + - - +
303D ARG* 3.5 9.2 - - - +
305D TYR* 1.3 74.7 - - - +
307D GLY* 1.3 58.3 + - - +
309D LEU* 3.1 9.3 + - - +
310D LEU* 2.9 39.7 + - + +
342D TYR* 3.8 39.7 - - + -
351D VAL* 4.1 10.1 - - + -
353D ILE* 3.7 30.1 - - + -
365D LEU* 3.7 23.3 - - + -
397D PRO* 4.4 4.0 - - + -
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Residues in contact with GLY 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ARG 2.8 12.3 + - - -
304D HIS 3.5 4.7 - - - -
305D TYR 3.2 0.6 - - - -
306D ILE* 1.3 76.6 - - - +
308D GLY* 1.3 55.3 + - - +
310D LEU* 4.4 1.4 - - - +
311D HIS* 3.0 32.4 + - - +
395D ILE* 3.5 25.7 - - - +
397D PRO* 3.9 19.6 - - - +
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Residues in contact with GLY 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D HIS 2.9 10.9 + - - -
305D TYR 3.1 3.5 + - - -
307D GLY* 1.3 73.7 - - - +
309D LEU* 1.3 55.5 - - - +
311D HIS* 3.7 2.0 - - - -
312D HIS* 2.8 44.9 + - - +
386D ALA 3.3 25.6 - - - -
390D GLY* 3.8 12.9 - - - -
395D ILE* 4.5 1.3 - - - -
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Residues in contact with LEU 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D GLN* 4.4 1.1 - - - +
305D TYR* 3.0 29.3 + - + +
306D ILE* 3.1 9.2 + - - +
308D GLY* 1.3 73.4 - - - +
310D LEU* 1.3 63.3 + - + +
312D HIS 3.8 0.7 - - - -
313D ALA* 2.9 30.5 + - - +
316D LEU* 3.8 25.5 - - + +
351D VAL* 4.5 6.5 - - + -
365D LEU* 3.7 30.7 - - + -
367D PHE* 4.1 30.8 - - + -
383D MET* 3.7 34.1 - - + +
386D ALA* 4.2 2.0 + - + -
387D GLY 4.5 0.4 - - - +
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Residues in contact with LEU 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D ILE* 2.9 33.6 + - + +
307D GLY* 4.4 2.9 - - - +
309D LEU* 1.3 78.4 - - - +
311D HIS* 1.3 62.1 + - - +
313D ALA* 3.5 14.0 - - + +
314D PRO* 4.2 0.5 - - - +
340D LEU* 3.6 47.3 - - + +
341D VAL* 3.7 0.9 - - - -
342D TYR* 3.7 26.9 - - + +
350D CYS* 3.7 32.1 - - + -
351D VAL* 4.0 12.1 - - + -
367D PHE* 4.9 1.3 - - + -
397D PRO* 4.7 8.5 - - + -
398D GLN* 5.7 3.6 - - + +
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Residues in contact with HIS 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307D GLY 3.0 21.3 + - - +
308D GLY 3.8 1.8 - - - +
310D LEU* 1.3 79.1 - - - +
312D HIS* 1.3 92.5 + + - +
314D PRO* 3.4 12.3 - - - +
395D ILE* 3.9 28.1 - - + +
429D ARG* 5.3 4.1 + - - -
433D ASP* 5.8 1.0 + - - -
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Residues in contact with HIS 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D GLY* 2.8 27.8 + - - +
309D LEU 4.4 0.2 - - - +
311D HIS* 1.3 95.3 + + - +
313D ALA* 1.3 65.0 + - - +
314D PRO* 3.2 4.7 - - - -
315D SER* 2.9 8.8 + - - -
316D LEU* 2.8 22.1 + - + -
386D ALA* 3.9 26.2 - - + -
389D ASP* 2.7 30.7 + - + -
395D ILE* 4.6 0.2 - - - +
433D ASP* 4.6 11.8 + - - -
436D TYR* 3.5 48.5 - + + +
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Residues in contact with ALA 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D LEU 2.9 18.4 + - - +
310D LEU* 3.5 12.6 - - + +
312D HIS* 1.3 75.1 - - - +
314D PRO* 1.4 71.2 - - + +
315D SER 3.0 1.0 + - - -
316D LEU* 3.9 9.2 - - + -
317D LEU* 3.1 38.7 + - + +
340D LEU* 3.7 26.9 - - + -
367D PHE* 5.6 3.8 - - + -
420D PRO* 5.2 1.1 - - + -
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Residues in contact with PRO 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310D LEU 4.2 2.7 - - - +
311D HIS 3.4 14.4 - - - +
312D HIS 3.3 5.4 - - - +
313D ALA* 1.4 92.8 - - + +
315D SER* 1.3 56.2 + - - +
340D LEU* 4.5 11.0 - - + -
420D PRO* 4.3 14.9 - - + +
426D VAL* 3.5 29.3 - - - +
429D ARG* 3.6 45.3 - - + +
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Residues in contact with SER 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D HIS* 2.9 6.9 + - - +
314D PRO* 1.3 77.1 - - - +
316D LEU* 1.3 67.6 + - - +
317D LEU 3.1 2.5 - - - -
318D ALA* 3.0 24.3 + - - +
319D PHE* 5.1 0.9 - - - -
426D VAL 4.3 4.7 - - - -
429D ARG* 3.8 11.6 - - - +
430D LEU* 3.8 22.6 - - - +
433D ASP* 3.6 20.4 + - - -
436D TYR* 2.7 38.7 + - - -
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Residues in contact with LEU 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D LEU* 3.8 32.1 - - + +
312D HIS* 2.8 25.9 + - + +
313D ALA* 3.9 3.6 - - - -
315D SER* 1.3 73.5 + - - +
317D LEU* 1.3 56.3 + - + +
318D ALA 3.1 0.2 - - - -
319D PHE* 3.0 23.0 + - - +
320D THR* 3.2 21.0 + - + +
367D PHE* 3.8 28.9 - - + -
382D ALA* 3.5 44.2 - - + +
383D MET* 3.6 3.1 - - - +
386D ALA* 4.0 8.3 - - + -
436D TYR* 3.4 11.0 - - - +
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Residues in contact with LEU 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D ALA* 3.1 29.4 + - + +
315D SER 3.0 0.6 + - - -
316D LEU* 1.3 75.7 - - + +
318D ALA* 1.3 58.6 + - - +
319D PHE 3.1 0.2 - - - -
320D THR* 3.0 25.8 - - - +
321D ASN* 2.7 42.9 + - - +
327D TYR* 3.6 14.6 - - + +
330D LEU* 4.1 16.6 - - + -
340D LEU* 5.9 1.1 - - + -
367D PHE* 4.3 11.2 - - + -
369D SER* 3.3 30.7 - - - +
419D THR* 5.0 4.5 - - + -
420D PRO* 3.8 26.9 - - + -
426D VAL* 4.2 6.5 - - + -
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Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D SER 3.0 16.6 + - - +
317D LEU* 1.3 78.8 - - - +
319D PHE* 1.3 58.3 + - + +
321D ASN 4.8 0.7 - - - -
322D PRO* 3.2 17.4 - - - +
423D LEU* 4.9 0.2 - - - -
426D VAL* 3.6 27.9 - - + +
427D ILE* 3.9 13.2 - - + +
430D LEU* 3.8 27.4 - - + -
451D TRP* 3.0 19.3 + - - +
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Residues in contact with PHE 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D SER 5.1 0.7 - - - -
316D LEU* 3.0 7.4 + - - +
318D ALA* 1.3 80.5 - - + +
320D THR* 1.3 61.6 + - - +
321D ASN 3.4 0.7 - - - -
322D PRO* 3.9 11.3 - - - +
374D GLY* 5.5 0.2 - - - -
375D ASN 4.6 4.7 + - - +
378D LEU* 4.0 29.3 - - + +
379D ALA* 3.6 15.6 + - - +
382D ALA* 3.9 31.2 - - + -
430D LEU* 3.8 31.0 - - + -
437D LEU* 3.9 11.0 - - + -
443D PHE* 3.7 28.3 - + - -
447D LEU* 4.7 3.4 - - + -
448D ILE* 4.6 7.6 - - + -
451D TRP* 3.5 52.5 - + + -
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Residues in contact with THR 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D MET* 5.3 0.5 - - - +
316D LEU* 3.2 30.4 + - + +
317D LEU* 3.0 24.4 - - - +
319D PHE* 1.3 80.7 - - - +
321D ASN* 1.3 76.9 + - - +
322D PRO* 3.6 4.0 - - - +
367D PHE* 4.2 3.6 - - + -
370D PRO* 3.4 14.5 - - - +
371D ASP 3.1 32.4 + - - +
379D ALA* 4.3 9.3 - - - +
383D MET* 3.8 28.0 - - + -
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Residues in contact with ASN 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D LEU* 2.7 20.1 + - + +
320D THR* 1.3 102.1 + - - +
322D PRO* 1.3 62.2 - - - +
323D THR 3.4 2.5 - - - -
326D SER* 3.4 13.5 + - - -
327D TYR* 2.8 38.2 + - + +
329D ARG* 3.9 4.6 - - - +
330D LEU* 3.9 16.4 - - - +
369D SER* 2.7 42.2 + - - +
371D ASP* 3.4 16.9 + - - -
423D LEU* 4.0 1.0 - - - +
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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) + - + + + + + -
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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