Contacts of the helix formed by residues 332 - 355 (chain D) in PDB entry 4E2I
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 ASN 332 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C GLN* 4.0 0.4 - - - +
270D TRP* 5.1 6.7 - - + -
330D SER* 3.2 9.7 + - - +
331D LYS* 1.3 94.5 - - - +
333D GLN* 1.3 63.2 + - - +
334D LYS 3.2 2.7 - - - -
335D THR* 3.6 28.2 + - + +
336D ILE* 3.0 28.4 + - + +
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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
----------------------------------------------------------
274C THR* 5.0 8.4 + - - +
339C GLN* 2.9 40.5 - - + +
343C THR* 3.5 23.8 + - - +
289D LEU* 3.2 26.3 - - + +
293D LEU* 3.8 22.4 - - - +
296D GLN* 4.9 0.2 - - - +
327D PHE* 3.3 39.6 - - + +
328D ALA* 3.0 28.9 - - - +
330D SER* 3.6 6.2 - - - +
332D ASN* 1.3 76.9 - - - +
334D LYS* 1.3 58.8 + - - +
337D CYS* 3.6 9.9 + - - -
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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
----------------------------------------------------------
338C GLN* 5.0 5.3 + - - +
339C GLN* 4.5 6.5 - - + +
342C ASP* 3.8 35.3 + - + +
512C LYS* 4.7 19.6 - - - +
514C LEU* 5.7 4.1 - - - +
516C LYS* 4.8 9.4 - - - +
285D VAL* 4.2 23.8 - - + +
286D LEU* 4.6 7.0 - - + -
289D LEU* 4.3 16.3 - - + +
332D ASN 3.2 0.4 - - - -
333D GLN* 1.3 77.2 - - - +
335D THR* 1.3 60.2 + - - +
337D CYS* 4.0 2.9 - - - +
338D GLN* 3.0 33.8 + - + +
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Residues in contact with THR 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D TRP* 3.6 22.9 - - + -
332D ASN* 3.1 31.7 + - + +
334D LYS* 1.3 77.9 - - - +
336D ILE* 1.3 64.8 + - - +
338D GLN* 3.1 16.8 + - + +
339D GLN* 3.2 10.9 + - - +
331E LYS 5.6 0.9 - - - +
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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
----------------------------------------------------------
268D VAL* 3.9 21.1 - - + -
269D SER 4.6 0.4 - - - +
270D TRP* 3.6 45.3 - - + +
273D VAL* 3.6 33.8 - - + +
274D THR* 5.3 1.6 + - - -
327D PHE* 3.5 26.0 - - + -
330D SER* 3.3 26.5 - - - +
332D ASN* 3.0 14.4 + - + +
335D THR* 1.3 76.3 - - - +
337D CYS* 1.3 61.7 + - - +
338D GLN 3.4 0.2 + - - -
339D GLN* 3.6 4.9 + - - +
340D ALA* 3.5 16.6 + - - +
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Residues in contact with CYS 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D VAL* 4.2 14.6 - - - -
285D VAL* 4.3 9.2 - - + +
288D LEU* 3.4 15.7 - - + +
289D LEU* 3.6 30.1 - - + -
292D TYR* 4.7 1.8 - - - -
327D PHE* 3.5 29.4 - - - -
333D GLN 3.6 9.5 + - - +
334D LYS* 4.3 3.1 - - - +
335D THR 3.3 0.4 - - - -
336D ILE* 1.3 77.0 - - - +
338D GLN* 1.3 65.5 + - - +
339D GLN 3.4 0.2 - - - -
340D ALA* 3.3 9.6 + - - +
341D VAL* 3.0 28.3 + - - +
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Residues in contact with GLN 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C LEU* 4.9 10.7 - - - +
285D VAL* 3.3 37.4 - - + +
334D LYS* 3.0 27.4 + - + +
335D THR* 3.1 12.1 + - + +
337D CYS* 1.3 77.4 - - - +
339D GLN* 1.3 63.4 + - - +
341D VAL* 3.1 20.3 + - - +
342D ASP* 3.0 39.1 + - - +
334E LYS* 5.2 4.2 + - - +
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Residues in contact with GLN 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D TRP* 3.1 29.6 - - + +
274D THR* 4.2 7.3 + - - +
335D THR 3.2 8.4 + - - +
336D ILE 3.9 7.4 - - - +
337D CYS 3.4 0.2 - - - -
338D GLN* 1.3 79.3 - - - +
340D ALA* 1.3 62.5 + - - +
342D ASP* 3.2 13.6 + - + +
343D THR* 2.9 24.4 + - - +
289E LEU* 5.5 1.0 - - + +
330E SER 3.1 12.9 + - - +
331E LYS 3.0 22.6 + - - +
332E ASN* 3.6 0.2 - - - +
333E GLN* 2.8 55.9 - - + +
334E LYS* 4.9 5.4 - - + +
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Residues in contact with ALA 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D VAL* 4.1 4.3 - - + +
274D THR* 3.9 20.6 + - - +
277D ALA* 3.6 15.0 - - + +
288D LEU* 3.4 17.7 - - + -
336D ILE 3.5 10.4 + - - +
337D CYS* 3.3 12.0 + - - +
338D GLN 3.2 0.4 - - - -
339D GLN* 1.3 78.7 - - - +
341D VAL* 1.3 61.6 + - - +
343D THR* 3.0 11.0 + - - -
344D VAL* 2.9 26.4 + - - +
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Residues in contact with VAL 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D CYS 4.3 1.1 - - - +
283D ASP* 3.4 30.5 - - - +
284D ASP 3.1 29.4 - - - +
285D VAL* 3.7 21.3 - - + -
288D LEU* 3.9 5.2 - - + -
337D CYS 3.0 17.5 - - - +
338D GLN* 3.3 9.4 - - - +
340D ALA* 1.3 77.1 - - - +
342D ASP* 1.3 58.1 + - - +
344D VAL* 3.0 11.3 + - - +
345D LEU* 2.9 39.3 + - + +
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Residues in contact with ASP 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D GLN* 3.0 35.9 + - - +
339D GLN* 3.2 12.5 + - + +
341D VAL* 1.3 78.3 - - - +
343D THR* 1.3 57.3 + - - +
345D LEU* 3.5 10.2 + - - +
346D ALA* 2.8 29.7 + - - +
516D LYS* 5.9 0.2 - - - -
286E LEU* 3.8 23.2 - - + +
289E LEU* 4.1 12.3 - - + -
334E LYS* 3.6 37.9 + - + +
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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
----------------------------------------------------------
274D THR* 3.6 24.9 - - + +
278D MET* 3.5 30.1 - - + +
339D GLN 2.9 14.2 + - - -
340D ALA 3.0 8.9 + - - -
342D ASP* 1.3 75.4 - - - +
344D VAL* 1.3 62.3 + - - +
346D ALA* 3.4 6.8 - - - +
347D LYS* 3.1 16.6 + - - +
289E LEU* 4.4 4.6 - - - +
293E LEU* 3.5 23.7 - - + +
333E GLN* 3.2 19.0 + - - +
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Residues in contact with VAL 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D ALA* 3.7 27.6 - - + +
278D MET* 4.3 9.2 - - - +
281D LYS* 3.6 22.4 - - - +
282D CYS 3.2 24.9 - - - +
283D ASP* 3.9 4.9 - - + +
340D ALA 2.9 21.1 + - - +
341D VAL 3.0 6.9 + - - +
343D THR* 1.3 75.7 - - - +
345D LEU* 1.3 65.4 + - - +
347D LYS* 3.1 18.9 + - - +
348D LYS* 3.3 31.7 + - - +
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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
----------------------------------------------------------
283D ASP* 3.9 29.6 - - + +
341D VAL* 2.9 30.5 + - + +
342D ASP* 4.0 10.8 - - - +
344D VAL* 1.3 77.3 - - - +
346D ALA* 1.3 50.8 + - - +
348D LYS* 3.4 14.3 + - + +
349D ARG* 2.8 36.7 + - - +
466D ASP* 4.9 1.6 - - - +
511D LYS* 4.3 24.9 - - + +
286E LEU* 4.1 24.2 - - + -
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D ASP 2.8 20.4 + - - +
343D THR* 3.4 11.4 - - - +
345D LEU* 1.3 75.1 - - - +
347D LYS* 1.3 65.8 + - - +
349D ARG* 3.1 4.9 + - - +
350D VAL* 3.0 29.4 + - - +
286E LEU* 3.4 26.2 - - - +
289E LEU* 4.1 7.4 - - + -
290E GLY* 3.6 17.3 - - - +
293E LEU* 4.8 1.1 - - + -
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Residues in contact with LYS 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D MET* 3.9 27.1 - - + +
343D THR 3.1 11.9 + - - +
344D VAL* 3.1 11.9 + - + +
346D ALA* 1.3 75.9 - - - +
348D LYS* 1.3 57.4 + - + +
350D VAL* 3.0 10.8 + - + +
351D ASP* 2.7 56.1 + - - +
290E GLY* 4.9 1.8 - - - -
294E GLU* 4.3 19.7 + - + +
297E TYR* 5.8 2.8 + - - -
304E LYS* 5.7 4.6 - - - +
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Residues in contact with LYS 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281D LYS* 3.7 23.9 + - - +
283D ASP* 4.4 12.6 - - + +
344D VAL* 3.3 36.1 + - - +
345D LEU* 3.8 17.5 - - + +
347D LYS* 1.3 78.5 - - + +
349D ARG* 1.3 61.7 + - - +
351D ASP* 4.0 8.0 - - - +
352D SER* 3.1 27.5 + - - -
466D ASP* 4.1 17.3 - - + +
467D GLN* 5.5 8.5 - - - +
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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
----------------------------------------------------------
345D LEU 2.8 14.5 + - - +
346D ALA* 3.2 16.6 - - - +
348D LYS* 1.3 77.3 - - - +
350D VAL* 1.3 56.2 + - - +
352D SER* 3.0 13.7 + - - -
353D LEU* 4.0 5.4 - - - +
465D ILE* 3.1 17.0 - - - +
466D ASP* 3.0 29.0 + - - -
511D LYS* 3.5 16.8 - - - +
516D LYS* 2.9 37.3 + - - +
517D ARG* 3.1 26.9 + - - +
284E ASP* 4.3 1.5 + - - -
286E LEU* 3.1 36.4 - - - +
287E LEU* 3.4 39.4 - - + +
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Residues in contact with VAL 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ALA 3.0 15.8 + - - +
347D LYS* 3.0 10.5 + - + +
349D ARG* 1.3 78.4 - - - +
351D ASP* 1.3 61.7 + - - +
352D SER 3.1 2.0 - - - -
353D LEU* 2.9 22.2 + - + +
354D GLN* 3.1 42.4 + - + +
287E LEU* 4.2 9.0 - - + +
290E GLY* 3.7 7.0 - - - -
291E MET* 3.4 43.3 - - + +
294E GLU* 4.3 10.8 - - - +
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Residues in contact with ASP 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LYS* 2.7 54.3 + - - +
348D LYS* 3.4 7.5 + - - +
350D VAL* 1.3 78.2 - - - +
352D SER* 1.3 57.7 + - - +
353D LEU 3.0 5.2 + - - -
354D GLN* 4.5 3.1 - - - +
355D LEU* 3.3 57.2 + - + +
360D MET* 4.0 9.0 - - + +
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Residues in contact with SER 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D LYS 3.1 12.6 + - - -
349D ARG 3.0 19.1 + - - -
351D ASP* 1.3 74.6 - - - +
353D LEU* 1.3 63.7 + - - +
355D LEU 4.9 2.9 - - - +
360D MET* 4.2 20.6 - - - +
466D ASP* 3.1 38.6 + - - -
467D GLN 5.5 1.6 - - - -
517D ARG* 4.1 5.5 + - - -
519D GLN* 5.1 2.7 - - - -
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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
----------------------------------------------------------
349D ARG 4.0 4.0 - - - +
350D VAL 2.9 6.7 + - - +
352D SER* 1.3 89.1 - - - +
354D GLN* 1.3 67.7 + - + +
355D LEU 4.6 2.1 - - - +
517D ARG* 3.2 33.0 - - - +
519D GLN* 5.8 2.9 - - + +
287E LEU* 3.6 33.0 - - + -
291E MET* 6.3 0.9 - - - -
310E GLN* 5.0 6.8 + - - +
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Residues in contact with GLN 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D VAL* 3.1 39.3 + - + +
351D ASP* 5.0 2.0 - - - +
353D LEU* 1.3 81.2 - - + +
355D LEU* 1.3 68.8 + - + +
356D THR* 3.5 5.5 + - - +
359D GLN* 4.6 1.2 - - - +
291E MET* 3.6 13.8 - - + +
294E GLU* 3.4 21.1 + - - -
304E LYS* 4.1 21.1 - - - +
309E GLU* 5.0 4.9 - - - +
310E GLN* 3.2 45.1 + - + +
313E HIS* 5.5 2.6 - - - +
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Residues in contact with LEU 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D ASP* 3.3 48.5 + - + +
352D SER 4.9 0.9 - - - -
353D LEU 4.6 2.4 - - - +
354D GLN* 1.3 83.0 + - + +
356D THR* 1.3 70.3 + - - +
357D ARG 3.8 0.2 + - - -
359D GLN* 3.4 30.3 - - + +
360D MET* 3.8 15.0 - - + +
363D ASN* 3.6 26.7 - - - +
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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