Contacts of the helix formed by residues 299 - 321 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288E LEU 2.5 29.2 + - - -
289E MET 2.7 18.1 + - - -
290E TYR 3.8 11.7 - - - -
291E ASP* 3.5 13.8 - - - +
298E LEU* 1.3 75.5 - - - +
300E ASP* 1.3 60.3 + - - +
301E THR* 3.5 5.0 + - - -
302E ALA 3.3 12.3 + - - -
303E ARG* 2.9 30.0 + - - +
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Residues in contact with ASP 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291E ASP* 5.1 4.8 + - - +
299E SER* 1.3 72.2 - - - +
301E THR* 1.3 60.4 + - - +
303E ARG* 2.7 41.2 + - - +
304E HIS* 2.9 50.6 + - + -
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Residues in contact with THR 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ILE* 4.6 7.4 - - + -
281E LEU* 4.5 11.4 - - + -
288E LEU* 4.1 23.1 + - + +
289E MET* 5.4 2.7 - - - -
299E SER* 3.3 9.3 + - - -
300E ASP* 1.3 79.1 - - - +
302E ALA* 1.3 56.0 + - - +
304E HIS* 4.7 2.7 - - - -
305E TYR* 3.0 27.3 + - - +
391E ILE* 3.5 37.5 - - + +
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Residues in contact with ALA 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E MET* 3.4 56.5 - - + +
298E LEU* 3.9 15.3 - - + -
299E SER* 3.3 11.5 + - - +
301E THR* 1.3 75.1 - - - +
303E ARG* 1.3 64.6 + - - +
305E TYR* 3.0 4.6 + - - +
306E ILE* 3.0 28.1 + - + +
365E LEU* 4.6 0.3 - - - +
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Residues in contact with ARG 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E TYR* 6.4 1.6 - - - -
298E LEU* 4.7 11.9 + - + +
299E SER 2.9 14.8 + - - +
300E ASP* 2.7 39.9 + - - +
302E ALA* 1.3 75.7 - - - +
304E HIS* 1.3 63.4 + - - +
306E ILE* 3.2 12.7 + - - +
307E GLY 2.8 22.3 + - - -
342E TYR* 4.1 19.1 - - + +
396E GLU* 2.9 37.6 + - - -
397E PRO* 3.5 23.8 - - + +
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Residues in contact with HIS 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300E ASP* 2.9 37.9 + - + +
301E THR* 3.9 4.2 + - - +
303E ARG* 1.3 78.4 + - - +
305E TYR* 1.3 61.1 + - - +
307E GLY* 3.2 1.0 + - - -
308E GLY 2.9 23.9 + - - -
390E GLY* 3.3 24.7 - - - +
391E ILE* 3.8 13.0 + - + +
394E LYS* 3.5 42.0 - - + +
395E ILE 3.4 17.7 - - - +
396E GLU* 2.8 30.2 + - - -
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Residues in contact with TYR 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PHE* 4.4 3.1 - - - -
279E GLN* 2.7 39.1 + - + +
280E SER 6.5 0.2 - - - -
281E LEU* 3.9 23.9 - - + +
289E MET* 4.9 4.5 - - + -
301E THR 3.0 15.9 + - - +
302E ALA* 3.0 12.3 + - - +
304E HIS* 1.3 71.7 - - - +
306E ILE* 1.3 64.7 + - - +
308E GLY* 3.2 3.1 + - - -
309E LEU* 3.0 37.1 + - + +
365E LEU* 3.5 20.6 - - + -
383E MET 3.7 1.1 + - - -
384E LEU* 3.5 33.9 + - + +
387E GLY* 3.6 34.4 - - - +
388E LEU 4.4 0.2 - - - -
391E ILE* 3.8 14.3 - - + +
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Residues in contact with ILE 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E LEU* 3.8 18.6 - - + -
302E ALA 3.0 17.7 + - - +
303E ARG* 3.5 8.5 - - - +
305E TYR* 1.3 71.9 - - - +
307E GLY* 1.3 66.6 + - - +
309E LEU* 3.1 8.8 + - + +
310E LEU* 2.9 36.7 + - + +
342E TYR* 3.8 37.0 - - + -
351E VAL* 4.1 9.6 - - + -
353E ILE* 3.7 29.6 - - + -
365E LEU* 3.7 24.7 - - + -
397E PRO* 4.3 4.3 - - + -
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Residues in contact with GLY 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E ARG 2.8 12.1 + - - -
304E HIS 3.2 5.1 + - - -
306E ILE* 1.3 76.8 - - - +
308E GLY* 1.3 54.2 + - - +
310E LEU* 4.1 1.1 - - - +
311E HIS* 2.9 33.3 + - - +
395E ILE* 3.5 24.7 - - - +
397E PRO* 3.9 19.6 - - - +
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Residues in contact with GLY 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E HIS 2.9 11.5 + - - -
305E TYR 3.2 2.6 + - - -
307E GLY* 1.3 72.4 - - - +
309E LEU* 1.3 55.6 + - - +
311E HIS* 4.5 3.6 - - - -
312E HIS* 2.8 41.4 + - - +
386E ALA 3.3 25.4 - - - -
390E GLY* 3.7 13.8 - - - -
395E ILE* 4.5 3.8 - - - -
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Residues in contact with LEU 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E GLN* 4.4 1.1 - - - +
305E TYR* 3.0 30.7 + - + +
306E ILE* 3.1 11.6 + - - +
308E GLY* 1.3 73.2 - - - +
310E LEU* 1.3 62.5 + - + +
312E HIS 3.8 0.3 - - - -
313E ALA* 2.9 29.8 + - - +
316E LEU* 3.8 26.4 - - + +
351E VAL* 4.6 4.5 - - + -
365E LEU* 3.7 30.1 - - + -
367E PHE* 4.2 30.3 - - + -
383E MET* 3.6 34.5 - - + +
386E ALA* 4.2 3.3 + - + -
387E GLY 4.4 0.2 - - - +
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Residues in contact with LEU 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306E ILE* 2.9 35.3 + - + +
307E GLY* 4.3 2.7 - - - +
309E LEU* 1.3 79.5 - - - +
311E HIS* 1.3 62.6 + - - +
313E ALA* 3.4 15.1 - - + +
314E PRO* 4.2 0.5 - - - +
340E LEU* 3.6 48.5 - - + +
341E VAL* 3.9 0.2 - - - -
342E TYR* 3.8 26.5 - - + +
350E CYS* 3.9 28.7 - - + -
351E VAL* 4.1 13.0 - - + -
367E PHE* 4.9 2.2 - - + -
397E PRO* 4.7 9.4 - - + -
398E GLN* 5.7 3.6 - - + +
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Residues in contact with HIS 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E GLY 2.9 20.5 + - - +
308E GLY 3.8 1.6 - - - +
310E LEU* 1.3 79.0 - - - +
312E HIS* 1.3 90.2 + + - +
314E PRO* 3.4 12.5 - - - +
395E ILE* 3.9 29.1 - - + +
429E ARG* 5.3 3.7 + - - -
433E ASP* 5.8 1.2 + - - -
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Residues in contact with HIS 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308E GLY* 2.8 29.2 + - - +
309E LEU 3.8 0.4 - - - -
311E HIS* 1.3 95.9 + + - +
313E ALA* 1.3 64.6 + - - +
314E PRO* 3.2 3.8 - - - -
315E SER* 2.9 9.7 + - - -
316E LEU* 2.8 20.7 + - + -
386E ALA* 3.9 23.8 - - + -
389E ASP* 2.7 30.1 + - + -
395E ILE* 5.1 0.2 - - + -
433E ASP* 4.6 12.1 + - - -
436E TYR* 3.4 52.2 - + + +
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Residues in contact with ALA 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E LEU 2.9 13.9 + - - +
310E LEU* 3.4 16.6 - - + +
311E HIS 3.3 0.2 - - - -
312E HIS* 1.3 75.3 - - - +
314E PRO* 1.4 69.2 - - + +
315E SER 3.0 1.9 + - - -
316E LEU* 3.9 8.1 - - - -
317E LEU* 3.0 40.0 + - + +
340E LEU* 3.6 27.6 - - + -
350E CYS* 5.9 0.2 - - - -
367E PHE* 5.6 3.6 - - + -
420E PRO* 5.2 1.3 - - + -
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Residues in contact with PRO 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310E LEU 4.2 2.5 - - - +
311E HIS 3.4 13.7 - - - +
312E HIS 3.3 5.2 - - - -
313E ALA* 1.4 94.3 - - + +
315E SER* 1.3 56.7 + - - +
340E LEU* 4.5 10.8 - - + -
420E PRO* 4.3 15.4 - - + +
426E VAL* 3.5 29.1 - - - +
429E ARG* 3.5 45.6 - - + +
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Residues in contact with SER 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312E HIS* 2.9 7.4 + - - -
314E PRO* 1.3 76.7 - - - +
316E LEU* 1.3 67.5 + - - +
317E LEU 3.1 2.5 - - - -
318E ALA* 3.0 23.4 + - - +
319E PHE* 4.5 1.0 + - - -
426E VAL 4.3 4.3 - - - -
429E ARG* 3.9 11.0 - - - +
430E LEU* 3.8 22.3 - - - +
433E ASP* 3.6 20.4 + - - -
436E TYR* 2.7 37.3 + - - -
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Residues in contact with LEU 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E LEU* 3.8 41.1 - - + +
312E HIS* 2.8 18.9 + - + +
313E ALA* 3.9 3.4 - - - +
315E SER* 1.3 77.6 + - - +
317E LEU* 1.3 57.7 + - + +
319E PHE* 2.9 22.4 + - - +
320E THR* 3.2 22.5 + - + +
367E PHE* 3.9 17.9 - - + -
382E ALA* 3.5 43.3 - - + +
383E MET* 3.6 4.0 - - - +
386E ALA* 3.9 10.8 - - + -
436E TYR* 3.3 11.9 - - - +
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Residues in contact with LEU 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E ALA* 3.0 30.5 + - + +
315E SER 3.1 0.4 - - - -
316E LEU* 1.3 77.1 - - + +
318E ALA* 1.3 59.4 + - - +
319E PHE 3.1 0.4 - - - -
320E THR* 3.1 19.1 - - - +
321E ASN* 2.7 40.3 + - - +
327E TYR* 3.6 15.3 - - + +
330E LEU* 4.0 17.0 - - + -
340E LEU* 5.9 1.3 - - + -
350E CYS* 6.2 0.4 - - - -
367E PHE* 4.3 11.0 - - + -
369E SER* 3.3 30.7 - - - +
419E THR* 5.0 4.0 - - + -
420E PRO* 3.7 26.2 - - + -
426E VAL* 4.1 7.0 - - + -
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Residues in contact with ALA 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E SER 3.0 16.6 + - - +
316E LEU 3.0 0.4 + - - -
317E LEU* 1.3 78.0 - - - +
319E PHE* 1.3 57.8 + - + +
321E ASN 4.9 0.7 - - - -
322E PRO* 3.3 17.2 - - - +
426E VAL* 3.7 28.2 - - + +
427E ILE* 4.0 13.0 - - + +
430E LEU* 3.8 26.9 - - + -
451E TRP* 3.0 19.7 + - - -
455E LYS* 5.3 0.2 - - - -
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Residues in contact with PHE 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E SER 5.0 1.1 - - - -
316E LEU* 2.9 7.5 + - - +
318E ALA* 1.3 79.5 - - + +
320E THR* 1.3 61.9 + - - +
321E ASN 3.5 0.7 - - - -
322E PRO* 3.9 10.9 - - - +
375E ASN 4.7 4.0 + - - +
378E LEU* 3.9 25.9 - - + +
379E ALA* 3.5 16.4 + - - +
382E ALA* 3.9 31.2 - - + -
430E LEU* 3.9 31.9 - - + -
437E LEU* 3.9 11.0 - - + -
443E PHE* 3.7 27.4 - + - -
447E LEU* 4.8 3.8 - - + -
448E ILE* 4.6 7.2 - - + -
451E TRP* 3.4 56.6 - + + -
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Residues in contact with THR 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E MET* 5.4 0.3 - - - +
316E LEU* 3.2 21.0 + - + -
317E LEU* 3.1 24.6 - - - +
319E PHE* 1.3 80.3 - - - +
321E ASN* 1.3 75.4 + - - +
322E PRO* 3.5 6.9 - - - +
367E PHE* 4.3 3.6 - - + -
370E PRO* 3.4 13.8 - - - +
371E ASP 3.1 29.8 + - - +
379E ALA* 4.2 9.6 - - - +
383E MET* 3.7 38.4 - - + -
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Residues in contact with ASN 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E LEU* 2.7 19.0 + - + +
320E THR* 1.3 101.6 + - - +
322E PRO* 1.3 58.0 - - - +
323E THR 3.3 0.2 + - - -
326E SER* 3.3 19.3 + - - -
327E TYR* 2.9 38.4 + - + +
329E ARG* 3.9 4.4 - - - +
330E LEU* 3.8 17.6 - - - +
369E SER* 2.8 42.2 + - - +
371E ASP* 3.5 14.6 + - - -
423E LEU* 3.9 1.2 - - - +
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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