Contacts of the helix formed by residues 299 - 321 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A LEU 2.7 28.9 + - - -
289A MET 2.8 16.8 + - - -
290A TYR 3.8 11.4 - - - -
291A ASP* 3.5 14.7 - - - +
298A LEU* 1.3 75.7 - - - +
300A ASP* 1.3 60.8 + - - +
301A THR* 3.5 3.9 + - - -
302A ALA* 3.3 13.4 + - - +
303A ARG* 2.9 29.4 + - - +
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ASP* 5.2 5.5 + - - +
299A SER* 1.3 74.9 - - - +
301A THR* 1.3 58.9 + - - +
303A ARG* 2.8 40.8 + - - +
304A HIS* 2.9 50.9 + - + -
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Residues in contact with THR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ILE* 4.6 6.5 - - + -
281A LEU* 4.6 10.5 - - + -
288A LEU* 4.1 22.9 - - + +
289A MET* 5.4 2.9 - - - -
299A SER* 3.3 8.1 + - - -
300A ASP* 1.3 79.2 - - - +
302A ALA* 1.3 56.3 + - - +
304A HIS* 3.4 2.4 + - - -
305A TYR* 2.9 28.1 + - - +
391A ILE* 3.6 37.6 - - + +
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Residues in contact with ALA 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A LEU 4.6 0.4 + - - -
289A MET* 3.5 56.5 - - + +
298A LEU* 3.9 15.5 - - + -
299A SER* 3.3 11.1 + - - +
301A THR* 1.3 76.2 - - - +
303A ARG* 1.3 64.3 + - - +
305A TYR* 3.1 4.9 + - - +
306A ILE* 3.0 29.0 + - + +
365A LEU* 4.5 0.5 - - - +
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A TYR* 6.4 1.8 - - - -
298A LEU* 4.7 12.6 + - + +
299A SER 2.9 14.4 + - - +
300A ASP* 2.8 39.7 + - - +
302A ALA* 1.3 75.2 - - - +
304A HIS* 1.3 65.3 + - - +
306A ILE* 3.3 11.3 + - - +
307A GLY 2.8 22.3 + - - -
342A TYR* 4.0 18.8 - - + +
396A GLU* 2.9 37.5 + - - -
397A PRO* 3.5 27.8 - - + +
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Residues in contact with HIS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ASP* 2.9 38.1 + - + +
301A THR* 3.9 4.2 + - - +
303A ARG* 1.3 80.3 + - - +
305A TYR* 1.3 58.6 + - - +
307A GLY* 3.6 1.0 - - - -
308A GLY 2.9 22.0 + - - -
390A GLY* 3.3 26.2 - - - +
391A ILE* 3.8 12.9 + - + +
394A LYS* 3.5 40.1 - - + +
395A ILE 3.3 19.2 - - - +
396A GLU* 2.8 29.1 + - - -
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Residues in contact with TYR 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PHE* 4.4 3.5 - - - -
279A GLN* 2.7 36.2 + - + +
280A SER 6.5 0.4 - - - -
281A LEU* 3.9 24.4 - - + +
289A MET* 4.8 3.8 - - + -
301A THR 2.9 14.7 + - - +
302A ALA* 3.1 13.7 + - - +
304A HIS* 1.3 75.7 - - - +
306A ILE* 1.3 61.7 + - - +
308A GLY* 3.0 11.4 + - - -
309A LEU* 3.0 26.0 + - + +
365A LEU* 3.5 22.0 - - + -
383A MET 3.5 9.1 + - - -
384A LEU* 3.5 25.3 + - + +
387A GLY* 3.5 37.4 - - - +
388A LEU 4.4 0.2 - - - -
391A ILE* 3.8 14.1 - - + +
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Residues in contact with ILE 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.8 19.5 - - + -
302A ALA 3.0 18.3 + - - +
303A ARG* 3.5 7.9 - - - +
305A TYR* 1.3 73.7 - - - +
307A GLY* 1.3 57.8 + - - +
309A LEU* 3.1 10.3 + - - +
310A LEU* 2.9 40.2 + - + +
342A TYR* 3.8 38.6 - - + -
351A VAL* 4.1 10.1 - - + -
353A ILE* 3.8 28.9 - - + -
365A LEU* 3.7 24.0 - - + -
397A PRO* 4.3 3.8 - - + -
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Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ARG 2.8 12.8 + - - -
304A HIS 3.4 4.7 + - - -
305A TYR 3.2 0.6 - - - -
306A ILE* 1.3 76.7 - - - +
308A GLY* 1.3 55.3 + - - +
310A LEU* 4.1 1.6 - - - +
311A HIS* 2.9 32.7 + - - +
395A ILE* 3.6 25.1 - - - +
397A PRO* 3.9 19.4 - - - +
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Residues in contact with GLY 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A HIS 2.9 11.1 + - - -
305A TYR 3.0 3.3 + - - -
307A GLY* 1.3 71.7 - - - +
309A LEU* 1.3 56.6 + - - +
311A HIS* 3.3 0.4 + - - -
312A HIS* 2.8 44.5 + - - +
386A ALA 3.3 24.7 - - - -
390A GLY* 3.8 13.4 - - - -
395A ILE* 4.5 3.4 - - - -
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLN* 4.4 0.9 - - - +
305A TYR* 3.0 29.1 + - + +
306A ILE* 3.5 10.8 - - - +
308A GLY* 1.3 74.3 - - - +
310A LEU* 1.3 61.3 + - + +
312A HIS 3.8 0.5 - - - -
313A ALA* 2.9 30.1 + - - +
316A LEU* 3.9 25.4 - - + +
351A VAL* 4.6 4.7 - - + -
365A LEU* 3.7 30.1 - - + -
367A PHE* 4.2 31.4 - - + -
383A MET* 3.6 35.2 - - + +
386A ALA* 4.2 2.4 + - + -
387A GLY 4.4 0.4 - - - +
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A ILE* 2.9 33.8 + - + +
307A GLY* 4.4 2.9 - - - +
309A LEU* 1.3 79.1 - - - +
311A HIS* 1.3 62.1 + - - +
313A ALA* 3.5 15.9 - - + +
314A PRO* 4.3 0.3 - - - +
340A LEU* 3.5 46.5 - - + +
341A VAL* 3.7 18.2 - - - -
342A TYR* 3.8 9.2 - - + +
350A CYS* 3.8 30.7 - - + -
351A VAL* 4.0 13.2 - - + -
367A PHE* 4.9 2.0 - - + -
397A PRO* 4.8 8.3 - - + -
398A GLN* 5.7 4.0 - - + +
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Residues in contact with HIS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A GLY 2.9 20.8 + - - +
308A GLY 3.8 1.6 - - - +
310A LEU* 1.3 78.6 - - - +
312A HIS* 1.3 90.6 + + - +
314A PRO* 3.4 12.8 - - - +
395A ILE* 4.0 27.9 - - + +
429A ARG* 5.4 3.2 + - - -
433A ASP* 5.8 1.2 + - - -
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Residues in contact with HIS 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLY* 2.8 29.0 + - - +
309A LEU 3.8 0.4 - - - +
311A HIS* 1.3 95.1 + + - +
313A ALA* 1.3 65.0 + - - +
314A PRO* 3.2 4.4 - - - +
315A SER* 2.9 10.4 + - - -
316A LEU* 2.8 21.4 + - + -
386A ALA* 3.9 29.2 - - + -
389A ASP* 2.7 30.9 + - + +
395A ILE* 4.6 0.6 - - + +
433A ASP* 4.6 11.4 + - - -
436A TYR* 3.4 42.7 - + + -
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Residues in contact with ALA 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU 2.9 16.4 + - - +
310A LEU* 3.5 15.7 - - + +
312A HIS* 1.3 74.3 - - - +
314A PRO* 1.4 69.2 - - + +
315A SER 3.0 1.4 + - - -
316A LEU* 4.0 8.7 - - + -
317A LEU* 3.1 39.1 + - + +
340A LEU* 3.6 27.4 - - + -
367A PHE* 5.6 3.6 - - + -
420A PRO* 5.1 1.6 - - + -
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Residues in contact with PRO 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LEU 4.3 2.2 - - - +
311A HIS 3.4 13.7 - - - +
312A HIS 3.2 6.1 - - - -
313A ALA* 1.4 94.7 - - + +
315A SER* 1.3 56.6 + - - +
340A LEU* 4.6 11.2 - - + -
420A PRO* 4.2 17.2 - - + +
425A ASP 4.9 0.3 - - - -
426A VAL* 3.5 20.8 - - - +
429A ARG* 3.5 53.2 - - + +
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A HIS* 2.9 8.4 + - - +
314A PRO* 1.3 78.1 - - - +
316A LEU* 1.3 64.9 + - - +
317A LEU 3.1 2.2 - - - -
318A ALA* 3.0 24.0 + - - +
319A PHE* 4.4 0.7 + - - -
426A VAL 4.3 4.9 - - - -
429A ARG* 3.9 9.1 - - - +
430A LEU* 3.8 25.5 - - - +
433A ASP* 3.6 20.5 + - - -
436A TYR* 2.7 37.3 + - - -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A LEU* 3.9 42.6 - - + +
312A HIS* 2.8 22.2 + - + +
313A ALA* 4.0 3.4 - - - +
315A SER* 1.3 74.3 + - - +
317A LEU* 1.3 62.4 + - + +
319A PHE* 3.0 16.5 + - - +
320A THR* 3.2 22.9 + - + +
367A PHE* 3.9 17.5 - - + -
382A ALA* 3.4 45.3 - - + +
383A MET* 3.6 3.4 - - - +
386A ALA* 4.0 8.3 - - + -
436A TYR* 3.3 12.3 - - - +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ALA* 3.1 29.8 + - + +
315A SER 3.1 0.6 + - - -
316A LEU* 1.3 77.1 - - + +
318A ALA* 1.3 57.9 + - - +
319A PHE 3.1 0.2 - - - -
320A THR* 3.0 23.3 - - - +
321A ASN* 2.7 40.1 + - - +
327A TYR* 3.5 16.4 - - + +
330A LEU* 4.0 17.3 - - + -
340A LEU* 5.9 1.1 - - + -
367A PHE* 4.3 11.7 - - + -
369A SER* 3.2 30.5 - - - +
419A THR* 4.9 4.7 - - + -
420A PRO* 3.8 25.8 - - + -
426A VAL* 4.1 6.7 - - + -
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A SER 3.0 16.5 + - - +
317A LEU* 1.3 77.2 - - - +
319A PHE* 1.3 57.3 + - + +
322A PRO* 3.3 17.3 - - - +
426A VAL* 3.6 23.2 - - + +
427A ILE* 3.8 17.4 - - + +
430A LEU* 3.8 27.6 - - + -
451A TRP* 3.0 20.8 + - - -
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A SER 5.1 1.1 - - - -
316A LEU* 3.0 6.8 + - - +
318A ALA* 1.3 79.7 - - + +
320A THR* 1.3 62.1 + - - +
321A ASN 3.5 0.7 - - - -
322A PRO* 3.8 11.4 - - - +
375A ASN 4.6 4.3 + - - +
378A LEU* 4.0 28.4 - - + +
379A ALA* 3.5 16.7 + - - +
382A ALA* 3.9 30.7 - - + -
430A LEU* 3.9 29.6 - - + -
437A LEU* 4.0 11.4 - - + -
443A PHE* 3.7 28.5 - + - -
447A LEU* 4.8 3.6 - - + -
448A ILE* 4.6 7.2 - - + -
451A TRP* 3.4 54.7 - + + -
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A MET* 5.3 0.2 - - - +
316A LEU* 3.2 29.8 + - + +
317A LEU* 3.0 24.6 - - - +
319A PHE* 1.3 80.2 - - + +
321A ASN* 1.3 71.3 + - - +
322A PRO* 3.6 3.4 - - - +
367A PHE* 4.2 4.0 - - + -
370A PRO* 3.3 14.4 - - - +
371A ASP 3.1 32.1 + - - +
379A ALA* 4.3 10.3 - - - +
383A MET* 3.8 28.5 - - + -
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A LEU* 2.7 20.4 + - + +
320A THR* 1.3 100.6 + - - +
322A PRO* 1.3 59.5 - - - +
323A THR 3.3 0.3 + - - -
326A SER* 3.3 17.9 + - - -
327A TYR* 2.9 38.6 + - + +
329A ARG* 3.9 3.8 - - - +
330A LEU* 3.8 16.2 - - - +
369A SER* 2.7 42.7 + - - +
371A ASP* 3.6 14.7 + - - -
423A LEU* 4.0 0.5 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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