Contacts of the helix formed by residues 332 - 356 (chain B) in PDB entry 5ZF6
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLN* 5.4 1.9 + - - -
277B PHE* 5.7 7.0 - - - -
330B GLU 3.9 1.4 + - - -
331B ALA* 1.3 74.2 - - - +
333B PRO* 1.3 78.0 - - - +
334B TYR* 2.6 39.3 + - - +
335B GLU* 3.1 33.5 + - + +
336B ILE* 3.3 12.6 + - - +
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Residues in contact with PRO 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B LYS* 4.5 20.1 + - - +
331B ALA 3.5 5.8 - - - +
332B ASP* 1.3 91.6 - - - +
334B TYR* 1.3 60.3 + - - +
336B ILE* 3.5 17.4 + - + +
337B ILE* 3.6 15.2 + - - +
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Residues in contact with TYR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLN* 3.1 50.6 + - + +
147B PHE* 3.2 43.1 - + - -
277B PHE* 4.4 18.2 + + + -
332B ASP* 2.6 22.0 + - - +
333B PRO* 1.3 70.4 - - + +
335B GLU* 1.3 67.5 + - - +
336B ILE 3.1 1.8 - - - -
337B ILE* 3.0 25.8 + - + +
338B GLU* 3.1 38.8 + - + +
341B ASN* 5.9 1.3 - - - -
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LYS* 5.7 4.5 + - - -
278B THR 4.8 1.5 - - - +
279B PRO* 4.3 16.7 - - + +
280B SER* 3.3 27.4 + - - -
283B ILE* 3.4 29.8 - - + +
331B ALA* 4.0 3.5 - - - -
332B ASP* 3.1 36.3 + - + +
334B TYR* 1.3 84.3 - - + +
336B ILE* 1.3 56.8 + - - +
338B GLU* 4.1 3.5 - - - +
339B SER* 3.1 32.9 + - - -
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 4.5 11.7 - - + -
321B GLU* 3.5 37.7 - - + +
324B LEU* 3.7 38.4 - - + +
325B LYS* 4.6 16.6 - - - +
328B PHE* 4.6 2.7 - - + +
331B ALA* 3.7 24.9 - - + +
332B ASP 3.3 16.4 - - - +
333B PRO* 3.7 11.4 - - + +
334B TYR 3.1 1.0 - - - -
335B GLU* 1.3 76.5 - - - +
337B ILE* 1.3 63.2 + - - +
339B SER* 3.6 5.5 + - - -
340B PHE* 3.4 19.6 + - - +
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Residues in contact with ILE 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B ARG* 4.8 12.7 - - - +
321B GLU* 3.1 33.2 - - - +
333B PRO 3.6 11.9 + - - +
334B TYR* 3.0 20.4 + - + +
336B ILE* 1.3 74.5 - - - +
338B GLU* 1.3 66.2 + - - +
340B PHE* 3.2 7.3 + - - +
341B ASN* 3.0 36.0 + - - +
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 6.0 0.9 - - - -
277B PHE 5.4 3.4 - - - +
279B PRO* 3.6 29.5 - - + +
334B TYR* 3.1 41.8 + - + +
335B GLU* 4.4 3.8 - - - +
337B ILE* 1.3 74.9 - - - +
339B SER* 1.3 55.9 + - - +
341B ASN* 2.9 22.4 + - - +
342B VAL* 2.6 48.7 + - + +
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PRO* 3.3 22.9 - - - +
283B ILE* 3.2 25.9 - - - +
284B VAL* 3.9 5.7 - - - +
287B THR* 3.7 20.2 - - - -
324B LEU* 5.0 0.7 - - - -
335B GLU* 3.1 22.0 + - - +
336B ILE 3.7 6.1 - - - -
337B ILE 3.2 0.4 - - - -
338B GLU* 1.3 76.7 - - - +
340B PHE* 1.3 61.1 + - - +
342B VAL* 3.4 3.4 + - - +
343B VAL* 3.1 28.4 + - - +
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Residues in contact with PHE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B THR* 3.8 19.4 - - + +
291B ALA* 4.0 18.8 - - + -
295B LEU* 3.9 22.4 - - + -
313B VAL* 3.4 24.9 - - + -
316B ILE* 4.0 5.6 - - + -
317B ARG* 3.5 52.5 - - + -
320B THR* 3.7 18.8 - - - -
321B GLU* 4.6 10.5 - - + +
336B ILE 3.4 8.5 + - - +
337B ILE 3.2 9.2 + - - +
339B SER* 1.3 75.6 - - - +
341B ASN* 1.3 64.1 + - - +
343B VAL* 3.3 0.6 + - + -
344B ALA* 2.8 38.5 + - + +
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Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317B ARG* 3.2 26.1 + - - +
334B TYR* 5.9 1.6 - - - -
337B ILE* 3.0 33.3 + - - +
338B GLU* 2.9 27.2 + - - +
340B PHE* 1.3 79.2 - - - +
342B VAL* 1.3 56.6 + - - +
344B ALA* 3.8 4.8 - - - +
345B LYS* 2.9 32.2 + - - +
539B TYR* 4.9 16.6 + - + +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B PRO* 3.6 26.7 - - + -
284B VAL* 4.2 22.7 - - + -
338B GLU* 2.6 37.7 + - + +
339B SER* 3.7 5.8 - - - +
341B ASN* 1.3 71.3 - - - +
343B VAL* 1.3 58.0 + - - +
345B LYS* 3.2 8.0 + - - +
346B GLU* 2.9 31.0 + - + +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B VAL* 3.5 34.1 - - + +
287B THR* 3.7 14.1 - - + +
288B HIS* 3.6 39.5 - - + +
291B ALA* 4.6 2.0 - - + -
292B MET 4.9 0.7 - - - +
295B LEU* 4.0 16.6 - - + -
339B SER 3.1 17.7 + - - +
340B PHE* 3.9 3.4 - - + +
342B VAL* 1.3 76.7 - - - +
344B ALA* 1.3 63.1 + - - +
346B GLU* 3.3 5.3 + - - +
347B VAL* 3.0 28.1 + - + +
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.7 26.4 - - + +
299B PHE* 3.9 9.7 - - + -
313B VAL* 5.8 2.9 - - + -
340B PHE* 2.8 36.7 + - + +
341B ASN* 3.9 4.7 - - - +
343B VAL* 1.3 72.9 - - - +
345B LYS* 1.3 61.0 + - - +
348B PHE* 3.2 24.6 + - - +
540B ASN* 4.4 3.8 + - - +
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Residues in contact with LYS 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASN 2.9 19.7 + - - +
342B VAL* 3.6 6.7 - - - +
344B ALA* 1.3 74.4 - - - +
346B GLU* 1.3 64.2 + - - +
348B PHE* 3.4 1.6 + - - +
349B ARG* 3.0 65.5 + - - +
539B TYR 4.9 3.6 - - - +
540B ASN* 3.9 36.5 + - - +
541B GLY 4.7 3.8 + - - -
542B ASP* 4.8 2.6 + - - -
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Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B HIS* 3.8 25.6 + - - +
342B VAL* 2.9 19.0 + - + +
343B VAL* 3.3 5.4 + - - +
345B LYS* 1.3 74.9 - - - +
347B VAL* 1.3 61.8 + - - +
349B ARG* 3.3 6.0 + - + +
350B SER* 2.8 43.6 + - - -
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B HIS* 4.5 8.3 - - + -
292B MET* 4.0 33.7 - - + -
295B LEU* 3.9 12.3 - - + -
296B TYR* 3.7 39.9 - - + +
299B PHE* 4.1 5.4 - - + -
343B VAL* 3.0 25.5 + - + +
344B ALA 4.2 3.1 - - - +
346B GLU* 1.3 77.2 - - - +
348B PHE* 1.3 64.9 + - - +
350B SER* 3.2 20.8 + - - +
351B ILE* 3.4 12.7 - - + +
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Residues in contact with PHE 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B PHE* 3.5 34.3 - + + -
344B ALA 3.2 17.7 + - - +
345B LYS 3.6 4.0 - - - +
346B GLU 3.3 0.2 - - - -
347B VAL* 1.3 80.4 - - - +
349B ARG* 1.3 66.1 + - + +
351B ILE* 3.6 11.3 + - - +
352B VAL* 3.8 21.7 + - + +
359B CYS* 3.7 28.0 - - + -
514B VAL* 5.7 5.2 - - + -
536B ILE* 3.5 33.4 - - + -
537B GLU* 3.7 33.0 - - + -
540B ASN* 3.5 32.3 - - + +
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Residues in contact with ARG 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B LYS* 3.0 45.5 + - + +
346B GLU* 4.1 4.9 - - - +
348B PHE* 1.3 80.7 - - + +
350B SER* 1.3 64.6 + - - +
352B VAL* 3.5 2.5 + - - -
353B LEU* 3.1 32.1 + - + +
514B VAL* 3.6 22.8 - - + +
515B THR* 3.1 31.4 + - - +
517B THR* 6.0 0.4 - - - +
540B ASN 3.0 31.8 + - - +
541B GLY* 3.7 4.9 + - - -
542B ASP* 2.5 46.4 + - - -
563B LEU* 5.4 1.2 - - - +
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Residues in contact with SER 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B MET* 5.6 5.7 - - - +
296B TYR* 5.6 1.6 - - - -
346B GLU* 2.8 28.5 + - - -
347B VAL* 3.2 14.1 + - - +
348B PHE 3.4 0.2 - - - -
349B ARG* 1.3 77.9 - - - +
351B ILE* 1.3 63.7 + - - +
353B LEU* 4.4 9.0 - - - -
354B ASN* 2.9 46.5 + - - +
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Residues in contact with ILE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B TYR* 3.7 36.6 - - + -
299B PHE* 3.6 38.8 - - + +
300B THR* 4.3 3.6 - - + -
347B VAL* 3.4 21.9 + - + +
348B PHE 3.9 6.3 - - - +
349B ARG 3.2 1.0 - - - -
350B SER* 1.3 78.1 - - - +
352B VAL* 1.3 61.0 + - + +
355B GLU* 2.9 38.4 + - - +
356B TYR 3.5 1.0 + - - -
357B LYS* 3.8 38.0 - - + +
358B ARG 5.2 2.5 - - - +
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PHE* 3.8 21.1 + - + +
349B ARG 3.5 6.3 + - - +
351B ILE* 1.3 76.9 - - + +
353B LEU* 1.3 61.6 + - - +
356B TYR* 3.2 14.2 + - - -
357B LYS 3.3 19.5 - - - +
358B ARG* 4.1 16.4 - - + -
359B CYS 5.2 1.1 - - - +
364B LEU* 3.9 9.0 - - + -
514B VAL* 4.6 15.7 - - + -
528B ARG* 3.2 27.8 + - + -
530B LEU* 3.7 28.3 - - + -
537B GLU* 5.2 3.4 - - - +
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Residues in contact with LEU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ARG* 3.1 28.5 + - + +
350B SER* 3.9 6.7 - - - +
352B VAL* 1.3 78.1 - - - +
354B ASN* 1.3 70.0 + - - +
356B TYR* 4.1 2.8 - - - -
514B VAL* 3.7 28.7 - - + +
515B THR 3.8 17.7 - - - +
516B LYS* 3.9 28.5 - - + +
526B ASP* 4.4 11.0 - - + +
527B TYR* 4.5 1.3 - - - -
528B ARG* 2.7 44.9 + - + +
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Residues in contact with ASN 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B SER* 2.9 35.5 + - - +
351B ILE* 5.1 0.2 - - - -
353B LEU* 1.3 82.5 - - - +
355B GLU* 1.3 69.8 + - + +
356B TYR* 3.8 12.5 - - - -
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Residues in contact with GLU 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B TYR* 2.6 36.7 + - - -
351B ILE* 2.9 19.4 + - - +
354B ASN* 1.3 86.0 - - + +
356B TYR* 1.3 70.5 + - - +
357B LYS* 2.4 52.8 + - + +
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Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ILE 3.5 0.4 + - - -
352B VAL 3.2 17.1 + - - -
353B LEU 4.1 1.1 - - - -
354B ASN 3.8 13.2 - - - -
355B GLU* 1.3 78.9 - - - +
357B LYS* 1.3 57.0 + - - +
363B ASP* 4.3 12.6 - - - +
364B LEU* 3.9 28.8 - - + +
526B ASP* 4.6 0.9 + - - -
528B ARG* 3.1 50.7 + - - -
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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) + - + + + + + -
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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