Contacts of the helix formed by residues 321 - 345 (chain D) in PDB entry 1EJI
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 THR 321 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C MSE 3.7 17.3 - - - -
317D LYS* 3.8 12.3 - - + +
318D GLN* 2.8 27.6 + - - +
319D ALA 4.0 1.4 - - - +
320D MSE 1.3 81.6 - - - +
322D THR* 1.3 60.1 + - - +
323D GLU* 3.4 14.6 + - - +
324D PHE* 2.9 18.0 + - - +
325D LYS* 3.2 22.3 + - - +
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Residues in contact with THR 322 (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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14C LEU* 3.2 27.4 - - + -
321D THR* 1.3 72.1 - - - +
323D GLU* 1.3 70.4 + - - +
324D PHE 2.9 2.0 - - - -
325D LYS* 3.2 13.8 + - + +
326D ILE* 2.8 30.4 + - + +
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Residues in contact with GLU 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 4.1 11.2 - - + +
17C SER* 3.2 37.7 + - - -
18C HIS* 3.2 36.9 - - + +
21C MSE 4.2 10.0 - - + +
321D THR* 3.5 16.0 - - - +
322D THR* 1.3 89.1 + - - +
324D PHE* 1.3 57.0 + - - +
326D ILE* 2.8 23.5 - - - +
327D TYR 3.1 7.4 + - - -
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Residues in contact with PHE 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C HIS* 4.8 1.1 - - - -
21C MSE 4.8 1.3 - - + -
234D GLY* 3.9 16.2 - - - -
237D ALA* 4.6 0.9 - - + -
238D ALA* 4.2 10.8 - - + -
258D THR 3.9 11.7 - - - -
259D LEU* 4.2 17.7 - - + -
260D ARG* 3.6 29.2 - - + -
315D ALA 5.9 0.4 - - - -
318D GLN* 3.2 20.9 - - + +
319D ALA* 2.8 45.3 - - + +
321D THR* 2.9 12.4 + - - +
323D GLU* 1.3 75.5 - - - +
325D LYS* 1.3 68.7 + - - +
326D ILE 3.0 1.6 - - - -
327D TYR* 2.9 22.8 + + - +
328D GLN* 2.9 38.6 + - - +
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Residues in contact with LYS 325 (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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238D ALA* 3.0 43.3 + - + +
239D GLY* 4.5 6.7 - - - -
240D VAL* 4.3 2.4 - - + +
321D THR 3.2 10.9 + - - +
322D THR* 3.2 16.1 + - + +
324D PHE* 1.3 78.8 - - - +
326D ILE* 1.3 58.4 + - - +
328D GLN* 3.8 2.9 + - - +
329D LEU* 3.2 38.2 + - + +
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Residues in contact with ILE 326 (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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7C MET* 4.4 9.2 - - + -
11C ASP* 4.0 24.9 - - + +
14C LEU* 4.2 27.6 - - + -
15C TRP* 3.5 37.9 - - + +
18C HIS* 5.2 3.6 - - + -
322D THR* 2.8 20.3 + - + +
323D GLU* 2.8 33.4 - - - +
325D LYS* 1.3 77.1 - - - +
327D TYR* 1.3 64.3 + - - +
329D LEU* 3.1 13.1 + - + +
330D GLN* 3.0 21.3 + - - +
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Residues in contact with TYR 327 (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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15C TRP* 4.7 7.6 - + - -
18C HIS* 3.4 29.6 - + + +
55D ASN* 3.2 14.6 + - - -
258D THR 4.8 2.7 - - - -
260D ARG* 3.5 23.3 - - - -
323D GLU 3.1 10.9 + - - +
324D PHE* 2.9 16.7 + + - +
326D ILE* 1.3 76.5 - - - +
328D GLN* 1.3 98.0 + - - +
330D GLN* 3.0 9.2 + - - +
331D VAL* 2.9 38.5 + - + +
406D PRO* 2.9 28.8 + - - +
409D THR* 3.5 9.4 - - + -
410D SER* 3.0 35.0 + - - -
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Residues in contact with GLN 328 (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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234D GLY 3.9 6.1 - - - -
235D LEU* 2.9 49.8 - - + +
238D ALA* 3.6 23.1 - - + -
240D VAL* 4.1 6.7 - - + -
258D THR* 3.4 17.7 + - - +
324D PHE* 2.9 38.0 + - - +
325D LYS 3.9 1.8 - - - +
327D TYR* 1.3 92.9 + - - +
329D LEU* 1.3 62.1 + - - +
331D VAL* 3.2 21.6 - - - +
332D LEU* 3.1 24.6 + - - +
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Residues in contact with LEU 329 (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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240D VAL* 3.8 22.2 - - + -
325D LYS* 3.2 31.2 + - + +
326D ILE* 3.1 17.1 + - + +
328D GLN* 1.3 74.1 - - - +
330D GLN* 1.3 66.5 + - - +
332D LEU* 3.2 11.8 + - + +
333D ALA* 3.0 22.4 + - - +
336D ARG* 4.8 5.6 + - - +
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Residues in contact with GLN 330 (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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7C MET* 4.0 23.7 - - + +
15C TRP* 3.8 17.1 + - + +
326D ILE 3.0 11.9 + - - +
327D TYR 3.4 8.7 - - - +
329D LEU* 1.3 77.0 - - - +
331D VAL* 1.3 53.8 + - - +
333D ALA* 3.2 5.7 + - - +
334D ASN* 2.6 77.9 + - - +
409D THR* 3.7 8.3 - - + -
414D LEU* 3.3 28.1 - - + +
415D GLU* 3.1 28.0 + - - +
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Residues in contact with VAL 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D LEU* 4.6 2.0 - - + -
327D TYR* 2.9 56.0 + - + +
328D GLN* 3.2 23.6 - - - +
330D GLN* 1.3 76.1 - - - +
332D LEU* 1.3 62.2 + - - +
334D ASN* 3.5 0.9 + - - +
335D CYS* 3.2 11.3 + - - +
357D HIS* 4.0 11.8 - - + -
405D THR* 2.8 35.2 + - - +
406D PRO* 3.8 24.2 - - + -
409D THR* 3.6 12.8 - - + +
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Residues in contact with LEU 332 (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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235D LEU* 4.4 11.9 - - + -
240D VAL* 3.3 46.4 - - + +
241D VAL* 4.3 3.1 - - + -
328D GLN 3.1 9.9 + - - +
329D LEU* 3.6 12.8 - - + +
331D VAL* 1.3 74.2 - - - +
333D ALA* 1.3 69.6 + - - +
335D CYS* 2.9 20.3 + - - +
336D ARG* 3.3 24.9 + - - +
355D ASP 3.7 8.1 - - - +
356D ASN* 3.2 42.4 - - - +
357D HIS* 4.2 1.3 - - - +
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Residues in contact with ALA 333 (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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329D LEU 3.0 13.9 + - - +
330D GLN* 3.4 15.5 - - - +
332D LEU* 1.3 75.7 - - - +
334D ASN* 1.3 63.3 + - - +
336D ARG* 3.1 41.5 + - - +
337D ALA* 3.1 12.1 + - - +
415D GLU* 4.0 22.0 - - + +
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Residues in contact with ASN 334 (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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330D GLN* 2.6 49.6 + - - +
331D VAL 3.7 5.2 - - - +
333D ALA* 1.3 72.6 - - - +
335D CYS* 1.3 62.9 + - - +
337D ALA* 3.4 7.9 - - - +
338D LEU* 3.0 23.7 + - - +
405D THR* 4.1 2.5 - - - -
409D THR* 2.8 23.9 + - - +
413D LEU 3.1 19.0 + - - -
414D LEU 3.3 16.1 - - - -
415D GLU* 3.3 1.8 + - - -
418D PHE* 3.2 29.9 - - + -
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Residues in contact with CYS 335 (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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331D VAL 3.2 7.8 + - - +
332D LEU 2.9 12.2 + - - +
334D ASN* 1.3 76.6 - - - +
336D ARG* 1.3 68.2 + - + +
338D LEU* 3.0 5.6 + - - +
339D SER* 2.8 22.9 + - - -
354D SER* 3.6 20.6 - - - -
356D ASN 3.5 24.0 - - - +
357D HIS* 3.9 10.5 - - - -
358D LEU 3.8 4.0 - - - -
359D ILE* 3.6 24.0 - - - +
405D THR* 3.8 15.2 - - + +
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Residues in contact with ARG 336 (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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329D LEU* 4.8 6.3 + - - +
332D LEU* 3.3 20.7 + - - +
333D ALA* 3.1 36.9 + - - +
335D CYS* 1.3 75.8 - - + +
337D ALA* 1.3 55.7 + - - +
339D SER* 2.9 7.0 + - - -
340D ASP* 2.5 48.9 + - - +
354D SER* 5.4 8.1 - - - +
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Residues in contact with ALA 337 (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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333D ALA 3.1 9.2 + - - +
334D ASN* 3.4 10.5 - - - +
336D ARG* 1.3 79.0 - - - +
338D LEU* 1.3 57.3 + - - +
340D ASP* 3.4 5.4 + - - +
341D ALA* 3.0 32.1 + - - +
415D GLU* 3.9 39.0 - - + +
418D PHE* 4.6 3.1 - - + -
419D GLN* 4.8 8.9 - - + +
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Residues in contact with LEU 338 (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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50D LEU* 4.5 13.0 - - + -
334D ASN 3.0 10.5 + - - +
335D CYS* 3.6 7.6 - - - +
337D ALA* 1.3 80.1 - - - +
339D SER* 1.3 57.1 + - - +
341D ALA* 4.2 2.0 - - - +
342D LEU* 3.0 50.0 + - + +
359D ILE* 4.3 6.1 - - + -
403D LEU* 4.4 21.3 - - + -
405D THR* 4.5 9.2 - - + -
418D PHE* 3.8 37.7 - - + +
421D VAL* 4.8 1.3 - - + -
422D ALA* 3.7 26.2 - - + +
425D ILE* 4.4 7.2 - - + -
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Residues in contact with SER 339 (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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335D CYS* 2.8 13.7 + - - -
336D ARG* 3.5 10.1 - - - -
338D LEU* 1.3 74.7 - - - +
340D ASP* 1.3 60.4 + - - +
342D LEU* 3.8 3.1 - - - +
343D THR* 2.5 38.2 + - - -
349D ILE* 3.7 24.0 - - - +
352D GLY 4.2 2.1 + - - -
353D GLY* 3.8 13.7 - - - -
354D SER* 5.2 2.0 - - - -
359D ILE* 4.0 24.0 - - - +
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Residues in contact with ASP 340 (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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336D ARG* 2.5 42.7 + - - +
337D ALA* 3.7 6.1 - - - +
339D SER* 1.3 73.7 + - - +
341D ALA* 1.3 55.1 + - - +
342D LEU 3.0 1.3 - - - -
343D THR* 3.0 6.2 + - - -
344D GLU* 2.6 38.1 + - - +
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Residues in contact with ALA 341 (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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337D ALA 3.0 17.0 + - - +
338D LEU 4.2 0.7 - - - +
340D ASP* 1.3 75.1 - - - +
342D LEU* 1.3 57.7 + - - +
344D GLU* 3.5 17.8 - - - +
345D LEU* 3.0 33.4 + - + +
419D GLN* 4.4 23.1 - - + +
422D ALA* 3.7 21.5 - - + -
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Residues in contact with LEU 342 (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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338D LEU* 3.0 31.4 + - + +
339D SER* 3.8 4.5 - - - +
340D ASP 3.0 0.8 - - - -
341D ALA* 1.3 75.4 - - - +
343D THR* 1.3 65.4 + - - +
345D LEU* 3.3 12.7 + - + -
346D GLY 3.4 0.5 + - - -
347D TYR* 3.1 34.9 + - + +
349D ILE* 4.6 7.0 - - + -
359D ILE* 3.9 20.4 - - + -
361D MSE 4.0 21.5 - - + -
403D LEU* 4.0 13.9 - - + -
422D ALA* 3.4 41.5 - - + +
425D ILE* 4.9 8.1 - - + -
426D HIS 5.5 0.4 - - - +
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Residues in contact with THR 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D SER* 2.5 26.1 + - - -
340D ASP* 3.5 6.4 - - - -
342D LEU* 1.3 73.0 - - - +
344D GLU* 1.3 59.7 + - - +
346D GLY* 2.6 28.9 + - - -
347D TYR 3.6 15.6 + - - +
349D ILE* 3.7 15.9 - - + +
352D GLY 4.4 7.1 + - - +
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Residues in contact with GLU 344 (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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340D ASP 2.6 21.1 + - - +
341D ALA* 3.5 17.2 - - - +
343D THR* 1.3 74.7 - - - +
345D LEU* 1.3 59.3 + - + +
346D GLY* 2.9 5.7 + - - -
419D GLN* 5.7 1.0 - - - +
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Residues in contact with LEU 345 (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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341D ALA* 3.0 21.8 + - + +
342D LEU* 3.6 11.7 - - + +
343D THR 3.1 0.4 - - - -
344D GLU* 1.3 78.6 - - + +
346D GLY* 1.3 59.9 + - - +
347D TYR* 3.7 15.5 - - + -
366D LYS* 5.4 1.2 + - - -
422D ALA* 4.1 16.8 - - + +
423D HIS* 4.4 10.5 - - + +
426D HIS* 3.3 55.8 + - + +
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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