Contacts of the helix formed by residues 332 - 356 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLN* 5.5 1.7 + - - -
275A LYS* 5.6 4.0 + - - -
277A PHE* 6.0 3.1 - - - -
331A ALA* 1.3 80.3 + - + +
333A PRO* 1.3 95.3 - - - +
334A TYR* 3.3 27.0 + - - +
335A GLU* 2.7 35.5 + - + +
336A ILE* 2.9 13.8 + - - +
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Residues in contact with PRO 333 (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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325A LYS* 5.4 14.4 - - - -
331A ALA* 4.5 7.4 - - + -
332A ASP* 1.3 91.1 - - - +
334A TYR* 1.3 64.6 + - + +
336A ILE* 3.2 15.5 + - + +
337A ILE* 2.8 39.6 + - + +
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Residues in contact with TYR 334 (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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92A PRO 5.3 4.3 + - - -
94A GLN* 3.1 58.1 - - + +
332A ASP* 2.9 19.8 + - - +
333A PRO* 1.3 84.1 - - + +
335A GLU* 1.3 58.2 + - - +
337A ILE* 3.3 18.0 + - + +
338A GLU* 2.8 35.5 + - - +
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LYS* 5.8 2.1 + - - -
278A THR 4.4 2.2 - - - +
279A PRO* 3.7 17.7 - - + +
280A SER* 3.1 29.1 + - - -
283A ILE* 3.6 24.8 - - + +
331A ALA 4.5 1.9 - - - +
332A ASP* 2.7 34.2 + - + +
334A TYR* 1.3 72.7 - - - +
336A ILE* 1.3 58.0 + - - +
338A GLU* 3.5 14.0 - - - +
339A SER* 2.9 28.4 + - - -
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 4.9 11.0 - - + -
321A GLU* 3.9 25.5 - - + +
324A LEU* 3.6 30.6 - - + +
325A LYS* 3.8 39.3 - - + +
328A PHE* 4.5 10.3 - - + +
331A ALA* 4.8 3.6 - - - +
332A ASP 2.9 27.4 + - - +
333A PRO* 3.4 11.4 - - + +
335A GLU* 1.3 77.0 - - + +
337A ILE* 1.3 64.0 + - + +
339A SER* 3.3 7.2 + - - -
340A PHE* 3.3 21.5 + - - +
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Residues in contact with ILE 337 (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 ARG* 5.9 2.9 - - - +
321A GLU* 3.2 29.3 - - - +
333A PRO* 2.8 25.1 + - + +
334A TYR* 3.4 22.9 - - + +
336A ILE* 1.3 74.7 - - + +
338A GLU* 1.3 66.6 + - + +
339A SER 3.2 0.3 + - - -
340A PHE* 3.3 4.5 + - - +
341A ASN* 3.2 35.8 + - - +
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Residues in contact with GLU 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN* 4.2 12.4 + - + +
147A PHE* 3.8 14.5 - - + -
277A PHE* 3.2 40.8 - - - +
278A THR 3.8 0.7 - - - -
279A PRO* 3.3 27.8 - - + +
334A TYR* 2.8 30.4 + - + +
335A GLU* 3.4 17.1 + - - +
337A ILE* 1.3 73.7 - - + +
339A SER* 1.3 58.0 + - - +
341A ASN* 3.3 9.0 + - - +
342A VAL* 2.9 33.1 + - + +
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 4.1 13.7 - - - -
283A ILE* 3.2 20.1 + - - -
284A VAL* 3.2 34.3 + - - +
287A THR* 3.3 9.8 + - - -
324A LEU* 5.8 0.2 - - - -
335A GLU 2.9 17.9 + - - -
336A ILE 3.6 6.1 - - - -
337A ILE 3.1 0.2 - - - -
338A GLU* 1.3 76.8 - - - +
340A PHE* 1.3 62.6 + - - +
342A VAL* 3.3 2.6 + - - +
343A VAL* 3.0 28.6 + - - +
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 4.0 13.8 - - + +
291A ALA* 4.2 7.2 - - + -
295A LEU* 3.9 20.6 - - + -
313A VAL* 3.6 14.8 - - + -
316A ILE* 3.9 7.9 - - + -
317A ARG* 3.5 67.3 - - + -
320A THR* 3.7 32.5 - - + -
321A GLU* 4.5 11.7 - - + +
324A LEU* 5.9 0.7 - - + -
336A ILE 3.3 10.3 + - - +
337A ILE 3.3 6.7 + - - +
339A SER* 1.3 77.7 - - - +
341A ASN* 1.3 58.1 + - - +
343A VAL* 3.2 1.8 + - + +
344A ALA* 2.8 38.8 + - + +
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Residues in contact with ASN 341 (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 ARG* 4.1 21.5 + - - -
337A ILE* 3.2 29.4 + - - +
338A GLU* 3.6 9.6 - - - +
339A SER 3.3 0.2 - - - -
340A PHE* 1.3 79.8 - - - +
342A VAL* 1.3 59.6 + - - +
344A ALA* 3.9 5.7 - - - +
345A LYS* 2.9 31.4 + - - +
540A ASN* 5.0 0.9 - - - +
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Residues in contact with VAL 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 4.0 19.3 - - + -
284A VAL* 4.2 23.1 - - + -
338A GLU* 2.9 19.5 + - + +
339A SER* 3.6 9.2 - - - +
341A ASN* 1.3 75.4 - - + +
343A VAL* 1.3 57.6 + - - +
345A LYS* 3.4 8.2 + - - +
346A GLU* 3.0 29.8 + - + +
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL* 3.6 37.0 - - + +
287A THR* 3.8 18.6 - - + +
288A HIS* 3.7 29.8 - - + +
291A ALA* 5.0 0.9 - - + -
292A MET 5.1 0.7 - - - +
295A LEU* 4.1 16.2 - - + -
339A SER 3.0 17.4 + - - +
340A PHE* 3.2 3.6 + - + +
342A VAL* 1.3 74.4 - - + +
344A ALA* 1.3 65.0 + - - +
346A GLU* 3.2 5.1 + - - +
347A VAL* 2.9 34.1 + - + +
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Residues in contact with ALA 344 (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 LEU* 3.8 22.1 - - + +
299A PHE* 3.6 12.5 - - + -
313A VAL* 5.2 4.5 - - + -
317A ARG* 5.9 0.9 - - - +
340A PHE* 2.8 39.3 + - + +
341A ASN* 3.9 6.7 - - - +
343A VAL* 1.3 72.2 - - - +
345A LYS* 1.3 62.7 + - - +
347A VAL* 4.8 0.2 - - - -
348A PHE* 3.0 26.4 + - - +
540A ASN* 4.9 4.9 - - - +
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Residues in contact with LYS 345 (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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341A ASN 2.9 19.5 + - - +
342A VAL* 3.5 8.3 - - - +
344A ALA* 1.3 78.5 - - - +
346A GLU* 1.3 58.6 + - - +
348A PHE* 3.4 1.2 + - - +
349A ARG* 2.9 60.6 + - - +
539A TYR 4.6 8.7 + - - +
540A ASN* 3.6 45.3 + - - +
541A GLY 4.7 5.9 + - - -
542A ASP* 5.0 2.4 + - - -
562A LYS* 5.9 1.0 - - - +
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Residues in contact with GLU 346 (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 HIS* 5.2 14.6 - - + +
342A VAL* 3.0 19.6 + - + +
343A VAL* 3.2 6.3 + - - +
345A LYS* 1.3 73.5 - - - +
347A VAL* 1.3 61.8 + - - +
349A ARG* 3.3 13.5 + - - +
350A SER* 2.9 43.2 + - - -
353A LEU* 5.8 2.4 - - - +
516A LYS* 6.0 0.2 + - - -
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Residues in contact with VAL 347 (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 HIS* 4.6 7.6 - - + +
292A MET* 3.9 33.4 - - + +
295A LEU* 4.0 12.3 - - + -
296A TYR* 3.7 37.5 - - + +
299A PHE* 4.3 3.4 - - + -
343A VAL* 2.9 33.8 + - + +
344A ALA 4.0 2.7 - - - +
346A GLU* 1.3 74.7 - - - +
348A PHE* 1.3 66.2 + - - +
350A SER* 2.7 24.5 + - - +
351A ILE* 3.3 12.2 + - + +
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Residues in contact with PHE 348 (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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299A PHE* 3.7 35.8 - + + -
344A ALA 3.0 19.6 + - - +
345A LYS 3.4 3.6 - - - +
347A VAL* 1.3 79.0 - - - +
349A ARG* 1.3 69.0 + - + +
351A ILE* 3.5 12.7 + - - +
352A VAL* 3.7 23.4 + - + +
359A CYS* 3.7 29.8 - - + -
514A VAL* 5.4 5.8 - - + -
536A ILE* 3.9 19.7 - - + -
537A GLU* 3.6 37.0 - - + -
540A ASN* 3.7 33.7 - - + +
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Residues in contact with ARG 349 (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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345A LYS* 2.9 47.6 + - - +
346A GLU* 3.9 13.4 + - - +
348A PHE* 1.3 81.8 - - + +
350A SER* 1.3 66.9 + - - +
352A VAL* 3.1 7.8 + - - +
353A LEU* 3.0 29.5 + - + +
514A VAL* 3.7 23.5 - - + +
515A THR* 2.7 32.1 + - - +
540A ASN 2.9 33.3 + - - +
541A GLY* 4.0 2.8 - - - -
542A ASP* 2.9 40.5 + - - -
563A LEU* 5.5 1.0 - - - +
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Residues in contact with SER 350 (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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292A MET* 5.8 3.3 - - - +
296A TYR* 5.8 0.7 - - - -
346A GLU* 2.9 32.7 + - - -
347A VAL* 2.7 25.5 + - - +
349A ARG* 1.3 71.8 - - - +
351A ILE* 1.3 54.7 + - - +
353A LEU* 4.4 8.7 - - - -
354A ASN* 2.7 54.1 + - - +
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Residues in contact with ILE 351 (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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296A TYR* 3.7 40.2 - - + -
299A PHE* 3.6 34.3 - - + +
300A THR* 4.1 16.4 - - + -
347A VAL* 3.3 16.1 + - + +
348A PHE 3.7 7.0 - - - +
349A ARG 3.1 0.6 - - - -
350A SER* 1.3 77.0 + - - +
352A VAL* 1.3 61.1 + - + +
354A ASN* 4.9 0.4 - - - -
355A GLU* 2.9 51.8 + - + +
356A TYR 3.6 1.0 + - - -
357A LYS* 3.8 16.2 - - + +
358A ARG 5.7 2.2 - - - -
359A CYS 5.9 0.2 - - - +
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Residues in contact with VAL 352 (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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348A PHE* 3.7 26.2 + - + +
349A ARG* 3.1 7.5 + - - +
351A ILE* 1.3 77.2 - - + +
353A LEU* 1.3 59.7 + - - +
356A TYR* 3.0 25.5 + - - -
357A LYS 3.5 16.4 - - - +
358A ARG* 4.6 13.0 - - + -
359A CYS 5.6 0.9 - - - +
364A LEU* 4.3 6.3 - - + -
514A VAL* 4.3 20.4 - - + -
528A ARG* 3.5 31.6 + - + -
530A LEU* 4.1 18.4 - - + -
537A GLU* 5.4 0.7 - - - +
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Residues in contact with LEU 353 (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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346A GLU* 5.8 2.2 - - - +
349A ARG* 3.0 23.3 + - + +
350A SER* 3.7 7.9 - - - +
352A VAL* 1.3 77.9 - - - +
354A ASN* 1.3 67.7 + - - +
356A TYR* 3.5 5.2 - - - -
514A VAL* 3.9 23.1 - - + +
515A THR 4.0 11.0 - - - +
516A LYS* 3.8 33.9 - - + +
526A ASP* 4.5 3.8 - - - +
527A TYR* 4.3 10.3 - - - +
528A ARG* 2.8 57.4 + - + +
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Residues in contact with ASN 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A SER* 2.7 36.1 + - - +
351A ILE* 4.9 0.9 - - - -
353A LEU* 1.3 81.9 - - - +
355A GLU* 1.3 69.3 + - + +
356A TYR* 3.7 9.2 - - - -
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Residues in contact with GLU 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TYR* 2.6 39.9 + - - -
300A THR* 4.7 4.9 - - - +
302A TYR* 5.5 2.3 + - - -
351A ILE* 2.9 28.8 + - + +
354A ASN* 1.3 87.3 - - + +
356A TYR* 1.3 75.5 + - - +
357A LYS* 3.0 19.1 + - + +
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Residues in contact with TYR 356 (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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352A VAL 3.0 15.8 + - - -
353A LEU 3.5 16.4 - - - -
354A ASN 4.0 9.2 - - - -
355A GLU* 1.3 81.8 - - - +
357A LYS* 1.3 68.2 - - - +
362A ARG 4.4 0.2 - - - +
363A ASP* 4.5 1.2 - - - +
364A LEU* 4.0 37.6 + - + +
526A ASP* 4.7 0.5 + - - -
528A ARG* 2.9 46.3 + - - -
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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