Contacts of the helix formed by residues 327 - 352 (chain D) in PDB entry 4EC4
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 CYS 327 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D ASN 4.5 1.7 + - - -
300D CYS* 3.9 3.1 - - - -
302D HIS* 4.0 5.2 - - - -
303D CYS* 3.3 28.0 - - + +
320D HIS* 4.0 0.4 - - - -
324D TYR 3.4 15.1 + - - +
325D PRO 3.3 4.2 - - - +
326D GLY* 1.3 74.9 - - - +
328D LYS* 1.3 61.1 + - - +
329D TYR* 3.2 10.7 + - - -
330D LEU* 3.2 14.2 + - + +
331D LEU* 2.9 26.9 + - - +
339D ILE* 5.8 0.2 - - - +
401D ZN 2.3 36.3 - - - -
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Residues in contact with LYS 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D SER* 4.3 7.8 - - - +
254D THR* 3.2 36.4 + - - +
255D ASN* 2.9 42.8 + - - +
302D HIS* 3.8 9.9 + - + -
326D GLY 3.3 6.3 + - - +
327D CYS* 1.3 74.9 - - - +
329D TYR* 1.3 56.7 + - - +
331D LEU* 3.5 27.5 - - + +
332D GLU* 3.1 29.1 + - + +
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Residues in contact with TYR 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ALA 5.9 0.9 - - - -
268D ARG* 3.6 14.6 + - - -
286D ARG* 3.3 15.9 + - - +
287D ALA 3.9 5.8 - - - -
288D GLY* 3.6 27.8 - - - -
300D CYS* 5.2 0.7 - - - -
301D PHE* 3.5 31.9 - + - -
302D HIS* 3.7 30.9 + + + -
317D TRP* 4.5 2.0 - + - -
320D HIS* 4.8 3.6 - + - -
327D CYS* 3.2 3.8 - - - -
328D LYS* 1.3 75.1 - - - +
330D LEU* 1.3 70.2 + - - +
331D LEU 3.1 1.3 - - - -
332D GLU* 3.0 15.0 + - + +
333D GLN* 2.8 66.1 + - + +
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Residues in contact with LEU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D TRP* 3.7 39.0 - - + +
320D HIS* 3.9 18.8 - - + +
321D ALA* 3.6 37.0 - - + +
324D TYR 3.9 12.1 - - - +
325D PRO* 4.7 1.8 - - + -
327D CYS* 3.2 16.9 + - + +
329D TYR* 1.3 82.7 - - - +
331D LEU* 1.3 58.1 + - - +
333D GLN* 3.2 2.8 + - - -
334D LYS* 2.8 46.8 + - + +
338D TYR* 4.6 4.7 - - + -
339D ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D PRO 5.7 2.2 - - - +
326D GLY 5.5 3.6 - - - +
327D CYS 2.9 17.0 + - - +
328D LYS* 3.5 37.2 - - + +
329D TYR 3.1 0.2 - - - -
330D LEU* 1.3 76.2 - - - +
332D GLU* 1.3 56.4 + - - +
335D GLY* 2.7 32.6 + - - -
336D GLN* 3.8 50.9 - - + +
339D ILE* 4.1 10.8 - - + -
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Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D ASN* 6.0 4.5 - - - +
328D LYS* 3.1 15.9 + - + +
329D TYR* 3.0 19.2 + - + +
331D LEU* 1.3 80.9 - - + +
333D GLN* 1.3 67.3 + - + +
334D LYS 3.3 0.5 + - - -
335D GLY* 4.1 2.4 + - - -
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Residues in contact with GLN 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ARG* 4.8 2.9 - - - +
317D TRP* 3.5 29.9 - - + -
329D TYR* 2.8 65.2 + - + +
330D LEU 3.9 0.9 - - - +
332D GLU* 1.3 79.2 - - + +
334D LYS* 1.3 70.7 + - - +
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Residues in contact with LYS 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 5.3 3.6 - - - +
317D TRP* 3.7 55.6 - - + +
330D LEU* 2.8 18.4 + - + +
333D GLN* 1.3 89.7 + - - +
335D GLY* 1.3 66.4 + - - +
337D GLU* 5.2 1.2 - - - +
338D TYR* 3.3 55.6 + - + +
339D ILE* 5.1 0.4 - - + -
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Residues in contact with GLY 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D LEU* 2.7 24.1 + - - -
332D GLU 4.1 2.7 + - - -
333D GLN 3.9 0.4 - - - -
334D LYS* 1.3 76.9 - - - +
336D GLN* 1.3 64.5 + - - -
337D GLU* 3.2 4.8 + - - -
338D TYR 3.7 2.3 + - - -
339D ILE* 2.9 21.6 - - - +
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Residues in contact with GLN 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325D PRO 4.9 8.1 + - - -
331D LEU* 3.8 33.6 - - + +
335D GLY* 1.3 71.5 - - - -
337D GLU* 1.3 71.3 + - - +
339D ILE* 3.6 12.0 - - - +
340D ASN* 2.4 67.3 + - - +
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Residues in contact with GLU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LYS* 5.7 2.5 + - - +
337B GLU* 3.6 24.7 - - + +
338B TYR* 4.0 29.9 - - + +
341B ASN* 3.2 33.3 + - + +
334D LYS 5.2 0.9 - - - +
335D GLY* 3.2 3.3 - - - -
336D GLN* 1.3 82.6 + - - +
338D TYR* 1.3 67.8 + - - +
340D ASN* 3.0 5.5 + - - +
341D ASN* 2.9 30.3 + - - +
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Residues in contact with TYR 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 4.1 32.2 - - + +
315D ASP* 3.4 10.4 + - - -
317D TRP* 3.4 29.6 - - + +
318D GLU* 3.1 27.5 + - - +
321D ALA* 4.3 6.3 - - + -
330D LEU* 4.6 3.8 - - + -
334D LYS* 3.3 52.7 + - + +
335D GLY 3.7 1.0 + - - -
336D GLN 3.6 0.2 - - - -
337D GLU* 1.3 78.3 - - - +
339D ILE* 1.3 72.5 + - + +
341D ASN* 3.2 2.9 + - - +
342D ILE* 3.2 43.1 + - + +
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Residues in contact with ILE 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ALA* 4.2 10.8 - - + -
325D PRO* 3.7 38.6 - - + +
327D CYS 5.8 0.2 - - - +
330D LEU* 4.1 27.8 - - + +
331D LEU* 4.1 23.6 - - + +
334D LYS* 5.0 0.4 - - + -
335D GLY 2.9 32.8 - - - +
336D GLN* 3.6 15.5 - - - +
337D GLU 3.4 0.4 - - - -
338D TYR* 1.3 83.2 - - + +
340D ASN* 1.3 71.4 + - - +
342D ILE* 3.1 10.6 + - - +
343D HIS* 3.3 22.8 + - + -
403D P33 5.5 3.8 - - - +
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Residues in contact with ASN 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 3.9 17.0 - - - +
336D GLN* 2.4 47.2 + - - +
337D GLU* 3.0 5.3 + - - +
339D ILE* 1.3 80.4 - - - +
341D ASN* 1.3 60.7 + - - +
343D HIS* 3.3 6.6 + - - +
344D LEU* 2.9 39.4 + - + +
403D P33 3.4 27.1 + - - +
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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
----------------------------------------------------------
337B GLU* 2.7 49.7 + - - +
340B ASN* 4.0 5.5 - - - +
341B ASN* 2.9 37.9 - - - +
344B LEU* 3.7 16.1 - - + +
337D GLU 2.9 15.8 + - - +
338D TYR 3.8 3.6 - - - +
340D ASN* 1.3 76.1 - - - +
342D ILE* 1.3 61.1 + - + +
344D LEU* 3.8 3.7 - - - +
345D THR* 2.6 36.2 + - - +
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Residues in contact with ILE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D GLU* 3.8 39.7 - - + +
321D ALA* 4.2 4.9 - - + -
322D LYS* 4.1 27.4 - - + +
338D TYR* 3.2 40.9 + - + +
339D ILE 3.1 9.7 + - - +
341D ASN* 1.3 77.8 - - + +
343D HIS* 1.3 60.0 + - + +
345D THR* 4.4 4.1 - - - +
346D HIS* 3.0 32.7 + - + -
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Residues in contact with HIS 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321D ALA 2.7 28.6 + - - -
322D LYS* 3.4 20.6 - - - -
325D PRO* 3.4 17.3 - - + +
339D ILE* 3.3 27.7 + - + +
340D ASN* 3.3 7.0 + - - +
341D ASN 3.1 0.4 - - - -
342D ILE* 1.3 78.8 - - + +
344D LEU* 1.3 60.5 + - - +
345D THR 3.2 1.3 - - - -
346D HIS* 3.1 7.9 + - - +
347D SER* 2.6 34.7 + - - +
403D P33 4.0 41.1 + - - +
250K PHE* 3.8 22.3 - + - -
253K SER* 5.8 3.3 + - - +
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Residues in contact with LEU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B ASN* 3.8 26.7 - - - +
344B LEU* 4.2 19.5 - - + +
345B THR* 4.1 24.5 - - - +
348B LEU* 4.1 27.8 - - + +
340D ASN* 2.9 28.8 + - + +
341D ASN* 3.8 11.4 - - - +
343D HIS* 1.3 75.4 - - - +
345D THR* 1.3 57.8 + - - +
347D SER* 3.3 6.4 + - - -
348D LEU* 2.9 30.0 + - - +
403D P33 4.9 10.0 + - - +
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Residues in contact with THR 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.8 26.3 - - + +
341D ASN 2.6 25.3 + - - -
342D ILE* 4.4 5.6 - - - +
344D LEU* 1.3 77.2 - - - +
346D HIS* 1.3 62.3 + - - +
348D LEU* 3.4 9.4 + - + +
349D GLU* 3.1 22.4 + - - +
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Residues in contact with HIS 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D GLU* 4.5 13.1 + - - -
322D LYS* 3.5 44.2 + - + +
342D ILE* 3.0 25.5 + - + +
343D HIS* 3.1 9.8 + - - +
345D THR* 1.3 80.1 - - - +
347D SER* 1.3 54.4 + - - +
349D GLU* 2.9 41.8 + - - +
350D GLU* 2.8 23.5 + - - +
248K ARG* 3.9 10.5 + - - -
250K PHE* 3.6 23.8 - + + -
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Residues in contact with SER 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.0 13.8 - - - +
343D HIS* 2.6 25.6 + - - +
344D LEU* 3.7 6.9 - - - -
346D HIS* 1.3 75.0 - - - +
348D LEU* 1.3 65.6 + - - +
350D GLU* 3.4 7.3 + - - -
351D CYS* 3.3 12.1 + - - +
250K PHE* 5.6 3.0 - - - -
253K SER* 3.2 26.4 + - - +
254K THR* 3.2 32.1 - - - +
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Residues in contact with LEU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 4.5 18.4 - - + +
347B SER* 3.6 32.5 - - - +
348B LEU* 3.7 19.4 - - + +
351B CYS* 4.7 3.6 - - + -
344D LEU 2.9 15.3 + - - +
345D THR* 3.5 9.9 - - + +
347D SER* 1.3 76.5 - - - +
349D GLU* 1.3 63.6 + - - +
351D CYS* 3.0 20.9 + - - +
352D LEU* 3.4 28.3 - - + +
253G SER 5.9 1.6 - - - +
254G THR* 4.6 13.5 - - - +
255G ASN 6.0 0.4 - - - +
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Residues in contact with GLU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345D THR 3.1 7.8 + - - +
346D HIS* 2.9 50.6 + - - +
348D LEU* 1.3 80.1 - - - +
350D GLU* 1.3 61.9 + - - +
352D LEU* 3.1 28.4 + - - +
248K ARG* 3.8 18.8 + - - +
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Residues in contact with GLU 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D HIS 2.8 23.0 + - - +
347D SER* 3.6 12.3 - - - +
348D LEU 3.2 0.4 - - - -
349D GLU* 1.3 78.8 - - - +
351D CYS* 1.3 62.1 + - - +
352D LEU 3.2 5.2 + - - +
353D VAL 4.4 0.3 - - - +
246K SER* 5.9 1.1 - - - +
248K ARG* 2.6 28.4 + - - +
250K PHE* 4.5 2.9 - - - -
251K PRO 3.1 12.4 - - - +
252K ASN* 2.9 26.8 - - - +
253K SER 5.3 1.1 + - - -
254K THR* 4.3 6.3 - - + +
256K LEU* 4.1 19.7 - - + +
258K ARG* 2.5 41.1 + - - +
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Residues in contact with CYS 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 5.2 3.4 - - - -
351B CYS* 3.3 44.6 - - + -
352B LEU* 4.7 15.5 - - - -
347D SER 3.3 10.0 + - - +
348D LEU* 3.0 15.8 + - - +
350D GLU* 1.3 79.8 - - - +
352D LEU* 1.3 57.2 + - - +
353D VAL* 3.1 19.4 - - - +
254K THR* 4.7 13.0 - - - +
255K ASN 6.0 0.4 - - - -
256K LEU* 5.8 7.7 - - - +
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Residues in contact with LEU 352 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B CYS* 3.0 35.7 - - - -
348D LEU* 3.4 28.0 - - + +
349D GLU* 3.1 18.2 + - - +
350D GLU 3.1 4.3 - - - +
351D CYS* 1.3 78.1 - - - +
353D VAL* 1.3 56.9 + - + +
254G THR* 5.4 0.2 - - - +
255G ASN* 3.6 37.5 - - + +
256G LEU* 4.0 11.7 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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