Contacts of the helix formed by residues 299 - 321 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288F LEU 2.6 28.4 + - - -
289F MET 2.7 17.0 + - - -
290F TYR 3.7 12.1 - - - -
291F ASP* 3.5 13.8 - - - +
298F LEU* 1.3 76.6 - - - +
300F ASP* 1.3 60.0 + - - +
301F THR* 3.4 4.9 + - - -
302F ALA* 3.2 14.6 + - - +
303F ARG* 2.9 28.7 + - - +
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Residues in contact with ASP 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F ASP* 5.1 4.9 + - - +
299F SER* 1.3 74.0 - - - +
301F THR* 1.3 59.2 + - - +
303F ARG* 2.8 41.1 + - - +
304F HIS* 2.8 49.5 + - + -
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Residues in contact with THR 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ILE* 4.6 6.7 - - + -
281F LEU* 4.6 10.8 - - + -
288F LEU* 4.1 22.7 + - + +
289F MET* 5.4 2.2 - - - -
299F SER* 3.3 8.3 + - - -
300F ASP* 1.3 79.1 - - - +
302F ALA* 1.3 56.7 + - - +
304F HIS* 3.5 2.9 + - - -
305F TYR* 2.9 27.9 + - - +
391F ILE* 3.5 36.8 - - + +
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Residues in contact with ALA 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F LEU 4.6 0.4 + - - -
289F MET* 3.5 54.5 - - + +
298F LEU* 3.8 17.7 - - + -
299F SER* 3.2 10.2 + - - +
301F THR* 1.3 78.6 - - - +
303F ARG* 1.3 58.1 + - - +
305F TYR* 3.0 5.1 + - - +
306F ILE* 3.0 33.1 + - + +
365F LEU* 4.5 0.3 - - - +
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Residues in contact with ARG 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295F TYR* 6.3 2.0 - - - -
298F LEU* 4.7 12.4 + - + +
299F SER 2.9 15.3 + - - +
300F ASP* 2.8 39.6 + - - +
302F ALA* 1.3 74.9 - - - +
304F HIS* 1.3 64.7 + - - +
306F ILE* 3.4 10.1 + - - +
307F GLY 2.9 21.3 + - - -
342F TYR* 4.0 19.3 - - + +
396F GLU* 2.9 38.0 + - - -
397F PRO* 3.4 31.2 - - + +
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Residues in contact with HIS 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F ASP* 2.8 39.1 + - + +
301F THR* 3.9 3.8 + - - +
303F ARG* 1.3 77.9 + - - +
305F TYR* 1.3 60.0 + - - +
307F GLY* 3.2 1.6 + - - -
308F GLY 3.0 22.9 + - - -
390F GLY* 3.4 25.3 - - - +
391F ILE* 3.8 13.6 + - + +
394F LYS* 3.5 40.6 - - + +
395F ILE 3.4 18.7 - - - +
396F GLU* 2.8 29.5 + - - -
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Residues in contact with TYR 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F ALA* 5.7 0.2 - - - +
130F PHE* 4.4 3.1 - - - -
279F GLN* 2.8 38.4 + - + +
280F SER 6.4 0.4 - - - -
281F LEU* 3.9 24.6 - - + +
289F MET* 4.8 4.7 - - + -
301F THR 2.9 15.1 + - - +
302F ALA* 3.0 12.5 + - - +
304F HIS* 1.3 72.6 - - - +
306F ILE* 1.3 64.9 + - - +
308F GLY* 3.1 3.8 + - - -
309F LEU* 3.1 33.8 + - + +
365F LEU* 3.5 22.0 - - + -
383F MET 3.6 0.8 + - - -
384F LEU* 3.5 33.4 - - + +
387F GLY* 3.6 37.2 - - - +
388F LEU* 4.4 0.4 - - + -
391F ILE* 3.8 12.9 - - + +
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Residues in contact with ILE 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F LEU* 3.7 19.3 - - + -
302F ALA 3.0 18.0 + - - +
303F ARG* 3.6 8.1 - - - +
305F TYR* 1.3 74.3 - - - +
307F GLY* 1.3 64.8 + - - +
309F LEU* 3.1 10.1 + - - +
310F LEU* 2.9 34.3 + - + +
342F TYR* 3.8 38.1 - - + -
351F VAL* 4.1 9.6 - - + -
353F ILE* 3.7 29.8 - - + -
365F LEU* 3.7 24.7 - - + -
397F PRO* 4.3 3.6 - - + -
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Residues in contact with GLY 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303F ARG 2.9 12.9 + - - -
304F HIS 3.2 5.5 + - - -
306F ILE* 1.3 75.5 - - - +
308F GLY* 1.3 56.8 + - - +
310F LEU* 4.3 1.6 - - - +
311F HIS* 2.9 33.4 + - - +
395F ILE* 3.6 24.4 - - - +
397F PRO* 3.9 19.8 - - - +
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Residues in contact with GLY 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304F HIS 3.0 11.3 + - - -
305F TYR 3.1 3.1 + - - -
307F GLY* 1.3 73.7 - - - +
309F LEU* 1.3 59.0 + - - +
311F HIS* 4.5 2.0 - - - -
312F HIS* 2.8 40.6 + - - +
386F ALA 3.3 24.9 - - - -
390F GLY* 3.8 12.9 - - - -
395F ILE* 4.5 1.6 - - - -
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Residues in contact with LEU 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279F GLN* 4.4 1.1 - - - +
305F TYR* 3.1 29.5 + - + +
306F ILE* 3.1 8.3 + - - +
308F GLY* 1.3 72.7 - - - +
310F LEU* 1.3 62.5 + - + +
312F HIS 3.8 0.2 - - - -
313F ALA* 2.9 29.8 + - - +
316F LEU* 3.8 26.4 - - + +
351F VAL* 4.4 7.2 - - + -
365F LEU* 3.7 30.5 - - + -
367F PHE* 4.1 30.2 - - + -
383F MET* 3.6 35.9 - - + +
386F ALA* 4.3 2.2 + - + -
387F GLY 4.5 0.2 - - - +
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Residues in contact with LEU 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ILE* 2.9 32.7 + - + +
307F GLY* 4.3 3.4 - - - +
309F LEU* 1.3 80.2 - - + +
311F HIS* 1.3 62.4 + - - +
313F ALA* 3.5 13.6 - - + +
340F LEU* 3.5 48.7 - - + +
341F VAL* 3.8 0.7 - - - -
342F TYR* 3.8 26.9 - - + +
350F CYS* 3.8 31.4 - - + -
351F VAL* 4.1 12.6 - - + -
367F PHE* 5.0 1.1 - - + -
397F PRO* 4.7 9.2 - - + -
398F GLN* 5.6 4.3 - - + +
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Residues in contact with HIS 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307F GLY 2.9 21.1 + - - +
308F GLY 3.9 1.8 - - - +
310F LEU* 1.3 78.0 - - - +
312F HIS* 1.3 88.8 + + - +
314F PRO* 3.4 16.6 - - - +
395F ILE* 3.9 28.5 - - + +
429F ARG* 5.4 2.6 + - - -
433F ASP* 5.8 1.4 + - - -
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Residues in contact with HIS 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308F GLY* 2.8 29.3 + - - +
311F HIS* 1.3 93.0 + + - +
313F ALA* 1.3 65.2 + - - +
314F PRO* 3.2 4.5 - - - -
315F SER* 2.8 11.0 + - - -
316F LEU* 2.8 21.0 + - + -
386F ALA* 4.0 25.1 - - + -
389F ASP* 2.8 30.3 + - + -
395F ILE* 4.6 0.4 - - + +
433F ASP* 4.6 12.5 + - - -
436F TYR* 3.5 48.9 - + + +
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Residues in contact with ALA 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F LEU 2.9 19.0 + - - +
310F LEU* 3.5 12.6 - - + +
312F HIS* 1.3 75.1 - - - +
314F PRO* 1.4 68.9 - - + +
315F SER 3.0 1.0 + - - -
316F LEU* 3.9 9.6 - - + -
317F LEU* 3.1 39.5 + - + +
340F LEU* 3.7 26.5 - - + -
350F CYS* 6.0 0.2 - - - -
367F PHE* 5.6 3.4 - - + -
420F PRO* 5.2 1.1 - - + -
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Residues in contact with PRO 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F LEU 4.3 2.7 - - - +
311F HIS 3.4 12.8 - - - +
312F HIS 3.3 6.1 - - - -
313F ALA* 1.4 91.9 - - + +
315F SER* 1.3 56.3 + - - +
340F LEU* 4.6 11.4 - - + -
420F PRO* 4.3 16.3 - - + +
425F ASP 5.0 0.2 - - - -
426F VAL* 3.5 21.2 - - - +
429F ARG* 3.5 53.3 - - + +
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Residues in contact with SER 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312F HIS* 2.8 10.6 + - - +
314F PRO* 1.3 80.2 - - - +
316F LEU* 1.3 63.0 + - - -
317F LEU 3.2 2.2 - - - -
318F ALA* 3.0 24.0 + - - +
319F PHE* 4.4 1.0 + - - -
426F VAL 4.3 4.0 - - - -
429F ARG* 3.9 11.2 - - - +
430F LEU* 3.8 22.6 - - - +
433F ASP* 3.6 19.6 + - - -
436F TYR* 2.7 36.9 + - - -
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Residues in contact with LEU 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309F LEU* 3.8 32.1 - - + +
312F HIS* 2.8 22.7 + - + +
313F ALA* 3.9 3.8 - - - +
315F SER* 1.3 73.1 + - - +
317F LEU* 1.3 56.7 + - + +
318F ALA 3.1 0.2 - - - -
319F PHE* 3.0 21.3 + - - +
320F THR* 3.2 21.2 + - + +
367F PHE* 3.8 28.7 - - + -
382F ALA* 3.5 43.7 - - + +
383F MET* 3.7 3.1 - - - +
386F ALA* 4.0 9.6 - - + -
436F TYR* 3.4 11.7 - - - +
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Residues in contact with LEU 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F ALA* 3.1 31.8 + - + +
315F SER 3.2 0.4 - - - -
316F LEU* 1.3 71.5 - - + +
318F ALA* 1.3 60.1 + - - +
319F PHE 3.0 2.5 - - - -
320F THR* 3.1 20.2 - - - +
321F ASN* 2.7 38.6 + - - +
327F TYR* 3.5 15.3 - - - +
330F LEU* 4.1 17.5 - - + -
340F LEU* 5.9 0.9 - - + -
367F PHE* 4.3 11.0 - - + -
369F SER* 3.3 29.2 - - - +
419F THR* 5.0 4.3 - - + -
420F PRO* 3.7 26.9 - - + -
426F VAL* 4.1 6.7 - - + -
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Residues in contact with ALA 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F SER 3.0 17.0 + - - +
317F LEU* 1.3 77.4 - - - +
319F PHE* 1.3 59.4 + - + +
322F PRO* 3.4 15.8 - - - +
423F LEU* 5.0 0.2 - - - -
426F VAL* 3.6 28.3 - - + +
427F ILE* 3.9 12.7 - - + +
430F LEU* 3.8 26.2 - - + -
451F TRP* 2.9 20.6 + - - -
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Residues in contact with PHE 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F SER 5.0 0.7 - - - -
316F LEU* 3.0 9.9 + - - +
318F ALA* 1.3 80.1 - - + +
320F THR* 1.3 62.1 - - - +
321F ASN 3.4 1.1 - - - -
322F PRO* 3.9 11.8 - - - +
375F ASN 4.7 4.5 + - - +
378F LEU* 3.9 26.0 - - + +
379F ALA* 3.6 16.9 + - - +
382F ALA* 3.9 28.5 - - + -
430F LEU* 3.8 30.5 - - + -
437F LEU* 4.0 11.2 - - + -
443F PHE* 3.8 28.0 - + - -
447F LEU* 4.8 3.8 - - + -
448F ILE* 4.6 7.4 - - + -
451F TRP* 3.4 56.6 - + + -
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Residues in contact with THR 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F MET* 5.4 0.2 - - - +
316F LEU* 3.2 20.8 + - + +
317F LEU* 3.1 23.9 - - - +
319F PHE* 1.3 79.9 - - - +
321F ASN* 1.3 76.3 + - - +
322F PRO* 3.6 4.0 - - - +
367F PHE* 4.2 4.4 - - + -
370F PRO* 3.3 14.9 - - - +
371F ASP 3.0 33.1 + - - +
379F ALA* 4.3 9.9 - - + +
383F MET* 3.8 37.5 - - + -
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Residues in contact with ASN 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F LEU* 2.7 20.4 + - + +
320F THR* 1.3 103.9 + - - +
322F PRO* 1.3 59.3 - - - +
323F THR 3.3 0.7 + - - -
326F SER* 3.3 18.1 + - - -
327F TYR* 3.0 37.9 + - + +
329F ARG* 3.9 4.4 - - - +
330F LEU* 3.9 15.9 - - - +
369F SER* 2.7 39.6 + - - +
370F PRO* 3.6 0.3 - - - +
371F ASP* 3.4 15.6 + - - -
423F LEU* 4.0 0.9 - - - +
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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
------------------------------------------------------------
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