Contacts of the helix formed by residues 365 - 388 (chain B) in PDB entry 3PU3
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 365 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B EDO 2.8 45.1 + - - -
29B EDO 5.0 0.8 + - - -
222B TRP* 3.8 20.6 - - + -
228B LEU* 4.1 11.4 - - - +
229B ALA 4.3 3.0 + - - +
231B PRO* 4.4 1.5 - - + +
363B PHE* 3.5 2.1 + - - -
364B PRO* 1.3 80.7 - - - +
366B PHE* 1.3 65.2 + - - +
367B GLU 3.2 2.0 - - - -
368B THR* 3.0 28.2 + - - +
369B ALA* 3.0 12.6 + - - +
420B ASP 5.0 0.9 - - - +
421B GLU* 3.3 26.6 + - - +
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Residues in contact with PHE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B GLY* 3.4 34.5 - - - -
337B LEU* 3.6 26.9 - - + -
345B GLN* 3.8 23.8 - - + -
346B MET* 3.9 15.0 - - + -
349B TYR* 3.3 50.5 - + + -
363B PHE* 3.6 28.0 + + + +
364B PRO 3.2 4.2 + - - -
365B ASN* 1.3 75.0 - - - +
367B GLU* 1.3 66.0 + - - +
369B ALA* 3.1 5.7 + - - +
370B CYS* 3.0 43.3 + - - -
409B TRP* 4.6 1.3 - + - -
421B GLU* 3.7 1.0 + - - -
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B TYR* 2.5 32.0 + - + +
353B ARG* 2.9 14.9 + - - -
366B PHE* 1.3 76.4 - - + +
368B THR* 1.3 55.7 - - - +
370B CYS* 3.1 4.9 + - - +
371B TRP* 2.8 36.0 + - + -
409B TRP* 3.4 44.7 - - + -
418B HIS* 2.8 41.7 + - - +
421B GLU* 3.0 27.2 + - + +
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Residues in contact with THR 368 (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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222B TRP* 3.4 25.8 - - + -
228B LEU* 3.7 16.3 - - + +
365B ASN* 3.0 27.6 + - - +
367B GLU* 1.3 73.1 - - - +
369B ALA* 1.3 66.6 + - - +
371B TRP* 3.0 5.7 + - - +
372B TYR* 3.0 39.0 + - + -
421B GLU* 2.5 33.3 + - - +
423B PRO* 3.9 5.8 - - + -
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Residues in contact with ALA 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 4.3 12.7 - - + +
218B VAL* 4.7 11.9 - - + +
221B TYR* 5.9 0.2 - - - +
222B TRP* 3.7 20.3 - - + -
337B LEU* 4.0 21.8 - - + -
363B PHE* 5.1 2.2 - - + -
365B ASN 3.0 11.2 + - - +
366B PHE* 3.5 9.0 - - - +
368B THR* 1.3 77.3 - - - +
370B CYS* 1.3 57.9 + - - +
372B TYR* 3.2 4.5 + - - +
373B MET* 2.9 28.2 + - - +
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Residues in contact with CYS 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B TRP* 4.0 13.0 - - - -
337B LEU* 5.4 0.2 - - - -
346B MET* 4.2 3.8 - - - -
366B PHE* 3.0 47.0 + - - -
367B GLU 3.3 8.5 - - - +
369B ALA* 1.3 78.8 - - - +
371B TRP* 1.3 57.9 + - - +
373B MET* 3.2 8.4 + - - +
374B GLY 2.8 23.7 + - - -
402B LEU* 4.0 23.9 - - + +
406B PHE* 3.2 11.3 - - + -
409B TRP* 3.8 19.1 - - + -
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Residues in contact with TRP 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B GLU* 2.8 37.7 + - - +
368B THR 3.0 6.7 + - - +
370B CYS* 1.3 72.7 - - - +
372B TYR* 1.3 62.8 + - - +
374B GLY* 3.0 10.4 + - - -
375B LYS 3.0 11.4 + - - -
406B PHE* 3.5 47.1 - + + -
409B TRP* 3.8 24.6 - + + +
410B THR* 3.5 33.2 - - + -
418B HIS* 5.1 4.2 + - + +
421B GLU 3.8 16.2 + - - -
422B LEU* 3.4 26.4 - - + +
423B PRO* 3.7 18.4 - - + -
426B PHE* 3.3 17.2 - + + -
428B PRO* 3.8 18.8 - - + -
431B LEU* 3.9 20.3 - - + +
432B ILE* 4.7 0.4 - - + -
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Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B EDO 3.2 22.9 + - - -
47B EDO 5.2 3.0 + - - -
221B TYR* 3.7 20.8 - - + +
222B TRP* 3.7 34.3 - + + +
223B PRO* 3.3 31.1 - - + +
226B ALA* 3.3 22.5 - - - +
228B LEU* 5.4 2.3 + - - +
368B THR* 3.0 35.5 + - + +
369B ALA* 3.7 5.8 - - - +
371B TRP* 1.3 73.6 - - - +
373B MET* 1.3 66.9 + - - +
375B LYS* 3.4 2.9 + - + -
376B HIS* 3.0 19.8 + - - +
423B PRO* 3.5 25.3 - - + +
424B GLU* 4.2 6.6 + - - -
426B PHE* 4.2 16.4 - + - -
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Residues in contact with MET 373 (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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217B TRP* 3.4 42.4 - - + -
221B TYR* 3.5 30.7 - - + +
339B SER* 3.5 22.9 - - - +
342B VAL* 5.4 2.7 - - + -
369B ALA 2.9 14.0 + - - +
370B CYS 3.2 8.7 + - - +
372B TYR* 1.3 77.1 - - - +
374B GLY* 1.3 56.9 + - - +
376B HIS* 3.3 12.1 + - + +
377B LEU* 2.9 62.5 + - + +
395B LEU* 4.5 6.3 - - + -
402B LEU* 3.8 11.2 - - + -
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Residues in contact with GLY 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B CYS 2.8 14.9 + - - -
371B TRP 3.0 4.9 + - - -
373B MET* 1.3 74.0 - - - +
375B LYS* 1.3 65.7 + - - +
377B LEU* 3.2 10.7 + - - +
378B LEU* 3.0 22.2 + - - +
402B LEU* 4.7 0.6 - - - +
406B PHE* 3.8 21.5 - - - -
431B LEU* 4.0 8.5 - - - +
435B LEU* 4.1 5.9 - - - +
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Residues in contact with LYS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B EDO 4.1 22.8 + - - +
47B EDO 4.6 22.6 - - - -
371B TRP 3.0 6.5 + - - -
372B TYR* 3.7 8.8 - - + +
374B GLY* 1.3 74.0 - - - +
376B HIS* 1.3 66.3 + - - +
378B LEU* 3.2 5.4 + - - +
379B GLU* 3.0 48.5 + - + +
426B PHE* 3.8 34.7 - - + -
431B LEU* 4.2 12.9 - - + +
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Residues in contact with HIS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B EDO 3.9 8.0 + - - +
221B TYR* 3.1 56.2 + + + -
372B TYR 3.0 17.8 + - - +
373B MET* 3.5 15.3 - - + +
375B LYS* 1.3 77.1 - - - +
377B LEU* 1.3 64.4 + - + +
379B GLU* 3.2 18.6 + - - +
380B ALA* 2.9 34.2 + - + +
395B LEU* 5.9 4.4 - - - +
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Residues in contact with LEU 377 (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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373B MET* 2.9 41.6 + - + +
374B GLY* 3.6 6.7 - - - +
375B LYS 3.2 0.2 - - - -
376B HIS* 1.3 79.3 - - + +
378B LEU* 1.3 67.0 + - - +
380B ALA* 2.8 8.2 + - + +
381B PHE* 2.8 33.2 + - + -
391B LEU* 5.0 6.5 - - + -
395B LEU* 4.3 32.3 - - + +
398B GLY* 4.6 0.9 - - - -
399B ALA* 3.9 22.2 - - + +
402B LEU* 3.4 33.0 - - + -
435B LEU* 4.6 8.1 - - + -
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Residues in contact with LEU 378 (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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374B GLY 3.0 12.4 + - - +
375B LYS* 3.5 9.2 - - - +
377B LEU* 1.3 75.3 - - - +
379B GLU* 1.3 64.6 + - + +
381B PHE* 3.0 4.2 + - - +
382B LYS* 2.9 43.1 + - + +
431B LEU* 4.0 17.3 - - + -
434B ASP* 3.9 38.1 - - + +
435B LEU* 3.8 14.0 - - + +
438B GLU* 3.6 28.0 - - + -
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Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B EDO 4.4 9.2 + - - -
375B LYS* 3.0 34.5 + - + +
376B HIS* 3.4 29.4 + - - +
378B LEU* 1.3 78.3 - - + +
380B ALA* 1.3 60.3 + - - +
382B LYS* 3.2 22.4 + - + +
383B GLY* 3.2 17.8 + - - -
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Residues in contact with ALA 380 (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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376B HIS* 2.9 25.2 + - + +
377B LEU* 2.8 14.4 + - + +
379B GLU* 1.3 76.1 - - - +
381B PHE* 1.3 58.5 + - - +
383B GLY* 3.5 2.8 + - - +
384B SER 3.2 18.7 + - - -
391B LEU* 3.6 33.3 - - + +
395B LEU* 5.9 3.1 - - + -
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Residues in contact with PHE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 2.8 30.5 + - + -
378B LEU* 3.4 8.7 - - - +
380B ALA* 1.3 74.0 - - - +
382B LYS* 1.3 64.7 + - - +
383B GLY 3.1 1.8 - - - -
384B SER* 2.5 32.1 + - - -
385B HIS* 3.2 8.6 - + - -
391B LEU* 4.0 29.6 - - + -
395B LEU 5.0 0.7 - - - -
396B VAL* 4.4 13.9 - - + -
399B ALA* 3.8 30.1 - - + -
435B LEU* 4.5 4.7 - - + -
438B GLU* 3.3 51.6 - - + +
439B ILE* 4.4 12.8 - - + -
442B SER* 4.0 18.2 - - - -
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 2.9 37.7 + - + +
379B GLU* 3.2 21.9 + - + +
381B PHE* 1.3 76.0 - - - +
383B GLY* 1.3 60.2 + - - +
385B HIS* 3.6 17.6 + - - +
386B LYS* 3.7 9.7 + - - +
438B GLU* 4.1 3.8 + - - +
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Residues in contact with GLY 383 (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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379B GLU 3.2 9.2 + - - -
380B ALA* 3.5 4.9 + - - -
381B PHE 3.1 1.0 - - - -
382B LYS* 1.3 77.8 - - - +
384B SER* 1.3 58.3 + - - +
385B HIS 3.0 2.5 - - - -
386B LYS* 2.8 24.1 + - - +
387B SER* 2.8 21.0 + - - -
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Residues in contact with SER 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA 3.2 13.0 + - - -
381B PHE* 2.5 28.8 + - - -
383B GLY* 1.3 76.6 - - - +
385B HIS* 1.3 73.8 + - - +
388B GLY* 2.9 30.8 + - - -
389B LYS 3.4 23.2 - - - +
390B GLN* 4.7 4.7 - - - -
391B LEU* 4.5 11.7 - - - -
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Residues in contact with HIS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B PHE* 3.2 23.1 + + - +
382B LYS* 4.0 9.2 - - - +
383B GLY 3.0 0.8 - - - -
384B SER* 1.3 86.3 + - - +
386B LYS* 1.3 62.4 + - - +
388B GLY* 4.1 4.1 + - - -
438B GLU* 2.8 27.3 + - - -
441B LEU* 3.9 30.6 - - + +
442B SER* 5.6 1.8 - - - -
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Residues in contact with LYS 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LYS 3.7 4.8 + - - +
383B GLY* 2.8 19.3 + - - +
385B HIS* 1.3 79.5 - - - +
387B SER* 1.3 63.2 + - - +
388B GLY 3.3 0.2 - - - -
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Residues in contact with SER 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLY 2.8 15.2 + - - -
386B LYS* 1.3 75.4 - - - +
388B GLY* 1.3 59.5 + - - +
389B LYS* 3.1 20.2 + - - +
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Residues in contact with GLY 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B SER 2.9 16.9 + - - -
385B HIS* 4.7 3.8 - - - -
386B LYS 3.3 3.2 - - - +
387B SER* 1.3 78.6 - - - +
389B LYS* 1.3 60.1 + - - +
390B GLN* 3.7 5.0 + - - +
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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
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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