Contacts of the helix formed by residues 332 - 356 (chain D) in PDB entry 3U1K
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 ASP 332 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275D LYS* 5.4 10.1 + - - +
277D PHE* 5.6 6.1 - - - -
330D GLU 3.5 2.9 + - - -
331D ALA* 1.3 72.2 - - - +
333D PRO* 1.3 81.8 - - - +
334D TYR* 3.0 45.3 + - - +
335D GLU* 2.7 44.0 + - + +
336D ILE* 3.2 7.0 + - - +
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Residues in contact with PRO 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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325D LYS* 4.7 14.8 - - - +
331D ALA 3.6 5.8 - - - +
332D ASP* 1.3 93.7 - - - +
334D TYR* 1.3 67.1 + - + +
336D ILE* 3.2 13.2 + - + +
337D ILE* 3.0 36.9 + - + +
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Residues in contact with TYR 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLN* 2.9 49.7 + - + +
277D PHE* 6.2 5.4 - + + -
332D ASP* 3.0 31.3 - - - +
333D PRO* 1.3 83.0 - - + +
335D GLU* 1.3 60.0 + - - +
337D ILE* 3.2 17.1 + - + +
338D GLU* 2.8 34.7 + - + +
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Residues in contact with GLU 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D LYS* 4.9 14.0 + - - +
278D THR 4.0 5.0 - - - +
279D PRO* 3.9 13.9 - - + +
280D SER* 3.0 33.8 + - - -
283D ILE* 3.8 23.6 - - + +
331D ALA* 4.4 3.5 - - - +
332D ASP* 2.7 35.7 + - + +
334D TYR* 1.3 75.3 - - - +
336D ILE* 1.3 56.1 + - + +
338D GLU* 3.8 5.6 - - - +
339D SER* 2.8 31.4 + - - -
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Residues in contact with ILE 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D ILE* 4.9 7.6 - - + -
321D GLU* 3.5 38.1 - - + +
324D LEU* 3.9 30.2 - - + +
325D LYS* 4.5 18.6 - - + +
328D PHE* 4.7 5.4 - - + +
331D ALA* 3.7 32.1 - - + +
332D ASP 3.2 18.1 + - - +
333D PRO* 3.4 11.2 - - + +
335D GLU* 1.3 76.7 - - + +
337D ILE* 1.3 59.0 + - + +
339D SER* 3.3 7.3 + - - -
340D PHE* 3.0 26.2 + - - +
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Residues in contact with ILE 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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94D GLN* 5.6 0.9 - - - +
317D ARG* 5.2 6.3 - - - +
321D GLU* 3.3 28.5 - - - +
333D PRO* 3.0 22.3 + - + +
334D TYR* 3.2 19.9 + - + +
336D ILE* 1.3 74.6 - - + +
338D GLU* 1.3 66.1 + - - +
340D PHE* 3.1 5.0 + - - +
341D ASN* 3.0 41.2 + - - +
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Residues in contact with GLU 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D GLN* 5.6 3.6 - - + +
95D PHE* 6.5 1.1 - - - -
145D GLY 5.8 0.3 + - - -
147D PHE* 4.2 19.4 - - + -
277D PHE* 3.6 22.3 - - + +
278D THR* 5.7 0.7 - - - +
279D PRO* 4.3 17.4 - - + +
334D TYR* 2.8 22.4 + - + +
335D GLU* 3.8 6.7 - - - +
337D ILE* 1.3 72.4 - - - +
339D SER* 1.3 63.9 + - - +
341D ASN* 3.1 20.0 + - - +
342D VAL* 2.9 26.4 + - - +
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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
----------------------------------------------------------
279D PRO* 3.7 9.4 - - - +
283D ILE* 3.2 15.6 - - - +
284D VAL* 3.2 25.6 + - - +
287D THR* 3.1 18.7 + - - -
324D LEU* 4.9 0.2 - - - -
335D GLU 2.8 20.0 + - - -
336D ILE 3.5 5.2 - - - -
337D ILE 3.2 0.2 - - - -
338D GLU* 1.3 77.6 - - - +
340D PHE* 1.3 59.5 + - - +
342D VAL* 2.8 25.7 - - - +
343D VAL* 3.2 13.2 + - - +
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Residues in contact with PHE 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D THR* 3.9 16.5 - - + +
291D ALA* 4.2 7.2 - - + -
295D LEU* 4.0 21.1 - - + -
313D VAL* 3.9 17.0 - - + -
316D ILE* 4.0 5.6 - - + -
317D ARG* 3.4 70.7 - - + -
320D THR* 3.3 29.8 - - + +
321D GLU* 4.1 11.9 - - + +
324D LEU* 5.4 0.7 - - + -
336D ILE 3.0 12.8 + - - +
337D ILE 3.1 6.7 + - - +
339D SER* 1.3 75.3 - - - +
341D ASN* 1.3 58.2 - - - +
343D VAL* 3.1 3.3 + - - +
344D ALA* 2.8 32.2 + - + -
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Residues in contact with ASN 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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95D PHE* 6.0 5.7 - - - -
317D ARG* 2.9 28.6 + - - -
337D ILE* 3.0 35.1 + - - +
338D GLU* 3.1 19.5 + - - +
340D PHE* 1.3 77.2 - - - +
342D VAL* 1.3 57.6 + - - +
344D ALA* 3.3 4.5 + - - +
345D LYS* 2.8 31.6 + - - +
540D ASN* 5.2 0.2 - - - +
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Residues in contact with VAL 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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279D PRO* 3.6 21.3 - - + -
284D VAL* 4.2 17.7 - - + -
338D GLU* 2.9 16.7 + - - +
339D SER* 2.8 33.0 - - - +
341D ASN* 1.3 72.0 - - - +
343D VAL* 1.3 57.5 + - - +
345D LYS* 3.4 9.3 + - + +
346D GLU* 3.0 34.8 + - + +
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Residues in contact with VAL 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D VAL* 3.5 30.3 - - + +
287D THR* 3.4 24.9 - - + +
288D HIS* 3.8 26.9 - - + +
291D ALA* 4.8 1.3 - - + -
292D MET 5.2 0.7 - - - +
295D LEU* 3.8 19.5 - - + -
339D SER 3.2 13.2 + - - +
340D PHE* 3.1 8.6 + - + +
342D VAL* 1.3 76.0 - - - +
344D ALA* 1.3 66.7 + - - +
346D GLU* 3.2 6.1 + - - +
347D VAL* 3.0 30.0 + - + +
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Residues in contact with ALA 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D LEU* 3.9 22.0 - - + -
299D PHE* 3.7 11.7 - - + -
313D VAL* 4.9 5.4 - - + -
340D PHE* 2.8 36.8 + - + +
341D ASN* 3.8 5.8 - - - +
343D VAL* 1.3 73.7 - - - +
345D LYS* 1.3 62.9 + - - +
347D VAL* 3.5 0.4 + - - -
348D PHE* 3.0 26.5 + - - +
540D ASN* 4.9 3.8 - - - +
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Residues in contact with LYS 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 ASN 2.8 19.4 + - - +
342D VAL* 3.6 8.3 - - - +
344D ALA* 1.3 77.6 - - - +
346D GLU* 1.3 57.4 + - - +
348D PHE* 3.6 1.4 + - - +
349D ARG* 3.0 58.7 + - - +
539D TYR 4.6 5.5 + - - +
540D ASN* 3.6 49.1 + - - +
541D GLY 4.7 6.4 + - - -
542D ASP* 5.1 2.4 + - - -
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Residues in contact with GLU 346 (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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288D HIS* 5.6 9.3 - - + +
342D VAL* 3.0 23.2 + - + +
343D VAL* 3.2 6.9 + - - +
345D LYS* 1.3 73.4 - - - +
347D VAL* 1.3 67.5 + - + +
349D ARG* 3.2 15.4 + - - +
350D SER* 2.9 29.9 + - - -
353D LEU* 6.0 1.7 - - - +
516D LYS* 5.5 8.9 - - - +
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Residues in contact with VAL 347 (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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288D HIS* 4.7 10.3 - - + -
292D MET* 4.2 22.2 - - + +
295D LEU* 4.1 22.2 - - + -
296D TYR* 3.8 37.0 - - + +
299D PHE* 4.2 6.7 - - + -
343D VAL* 3.0 23.5 + - + +
344D ALA 4.0 2.9 - - - +
346D GLU* 1.3 74.7 - - - +
348D PHE* 1.3 66.2 + - - +
350D SER* 2.6 26.6 + - - +
351D ILE* 3.3 11.2 + - + +
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Residues in contact with PHE 348 (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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299D PHE* 3.7 32.6 - + + -
344D ALA 3.0 18.6 + - - +
345D LYS 3.6 3.6 - - - +
347D VAL* 1.3 78.6 - - - +
349D ARG* 1.3 69.6 + - + +
351D ILE* 3.5 16.2 + - - +
352D VAL* 3.7 18.8 + - + +
359D CYS* 3.6 32.8 - - + -
514D VAL* 5.6 6.1 - - + -
530D LEU* 6.0 0.4 - - + -
536D ILE* 3.7 29.8 - - + -
537D GLU* 3.7 34.3 - - + -
540D ASN* 3.6 28.7 - - + +
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Residues in contact with ARG 349 (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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345D LYS* 3.0 41.3 + - - +
346D GLU* 3.2 15.9 + - - +
348D PHE* 1.3 83.6 - - + +
350D SER* 1.3 65.6 + - - +
352D VAL* 3.1 8.6 + - - +
353D LEU* 3.0 29.4 + - + +
514D VAL* 3.7 22.6 - - + +
515D THR* 3.1 33.0 + - - +
540D ASN 2.8 38.9 + - - +
541D GLY* 3.7 5.1 - - - -
542D ASP* 2.9 41.1 + - - -
563D LEU* 5.2 1.8 - - - +
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Residues in contact with SER 350 (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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296D TYR* 5.6 1.9 - - - -
346D GLU* 2.9 21.7 + - - -
347D VAL* 2.6 25.9 + - - +
349D ARG* 1.3 76.6 - - - +
351D ILE* 1.3 59.8 + - - +
353D LEU* 3.1 8.6 + - - -
354D ASN* 2.8 51.5 + - - +
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Residues in contact with ILE 351 (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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296D TYR* 4.2 24.0 - - + +
299D PHE* 3.4 39.0 - - + +
300D THR* 3.9 27.1 - - + -
302D TYR* 6.2 0.2 - - - +
347D VAL* 3.4 16.2 - - + +
348D PHE 3.6 6.7 - - - +
350D SER* 1.3 78.4 + - - +
352D VAL* 1.3 59.1 + - + +
354D ASN* 5.1 0.4 - - - -
355D GLU* 2.9 50.3 + - + +
356D TYR 3.7 0.7 + - - -
357D LYS* 3.9 16.6 - - + +
358D ARG 5.5 3.6 - - - +
359D CYS 5.8 0.2 - - - +
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Residues in contact with VAL 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D PHE* 3.7 29.6 - - + +
349D ARG* 3.1 8.9 + - - +
351D ILE* 1.3 76.5 - - + +
353D LEU* 1.3 62.4 + - - +
356D TYR* 3.2 17.5 + - - -
357D LYS 3.4 17.9 - - - +
358D ARG* 4.7 11.9 - - + -
359D CYS 5.6 0.7 - - - +
364D LEU* 4.3 6.5 - - + -
514D VAL* 4.3 16.6 - - + -
528D ARG* 3.2 33.0 + - + -
530D LEU* 4.0 20.4 - - + -
537D GLU* 5.5 0.7 - - - +
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Residues in contact with LEU 353 (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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346D GLU* 6.0 1.6 - - - +
349D ARG* 3.0 26.3 + - + +
350D SER* 3.7 7.6 - - - +
352D VAL* 1.3 78.7 - - - +
354D ASN* 1.3 68.3 + - - +
356D TYR* 3.7 2.4 - - - -
514D VAL* 3.9 24.0 - - + +
515D THR 3.9 22.9 - - - +
516D LYS* 4.2 24.2 - - + +
526D ASP* 4.3 7.6 - - - +
527D TYR* 4.5 6.1 - - - +
528D ARG* 2.1 60.5 + - + +
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Residues in contact with ASN 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D SER* 2.8 38.3 + - - +
353D LEU* 1.3 80.7 - - - +
355D GLU* 1.3 69.1 + - + +
356D TYR* 3.7 9.2 - - - -
516D LYS* 5.8 1.6 + - - -
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Residues in contact with GLU 355 (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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296D TYR* 2.6 38.1 + - - -
300D THR* 5.0 3.6 - - - +
302D TYR* 5.4 2.6 + - - -
351D ILE* 2.9 28.1 + - + +
354D ASN* 1.3 87.2 - - + +
356D TYR* 1.3 74.3 + - - +
357D LYS* 2.9 20.2 + - + +
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Residues in contact with TYR 356 (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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352D VAL 3.2 16.1 + - - -
353D LEU 3.7 4.7 - - - -
354D ASN 4.2 8.3 - - - -
355D GLU* 1.3 81.0 - - - +
357D LYS* 1.3 60.5 + - - +
363D ASP* 4.2 11.6 - - - +
364D LEU* 4.0 30.0 + - + +
526D ASP* 4.5 0.9 + - - -
528D ARG* 3.0 53.0 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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