Contacts of the helix formed by residues 378 - 400 (chain A) in PDB entry 2AEX
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 THR 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A PHE* 1.3 82.5 - - - +
379A PRO* 1.3 71.3 - - + +
380A GLN* 3.3 25.5 + - - +
381A GLU* 3.1 37.3 + - - +
382A LYS 3.0 17.7 + - - -
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Residues in contact with PRO 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A PHE* 4.5 2.9 - - + +
378A THR* 1.3 83.3 - - - +
380A GLN* 1.3 70.6 + - + +
382A LYS* 3.3 9.1 + - + +
383A LEU* 2.9 29.7 + - - +
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Residues in contact with GLN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TYR* 4.0 2.4 + - - +
378A THR* 3.3 26.0 + - - +
379A PRO* 1.3 88.2 - - + +
381A GLU* 1.3 62.0 + - + +
383A LEU* 3.4 9.0 + - - +
384A TRP* 2.9 28.2 + - - +
439A GLU* 5.1 4.4 - - - +
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Residues in contact with GLU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A PRO* 3.7 10.0 - - + +
253A HIS* 3.1 33.1 + - - -
287A TYR* 3.4 32.2 - - + +
376A SER 4.1 0.9 - - - +
377A PHE* 3.2 10.0 - - + -
378A THR* 3.1 42.6 + - - +
380A GLN* 1.3 73.2 - - + +
382A LYS* 1.3 60.7 + - - +
384A TRP* 3.4 2.6 + - - +
385A GLN* 2.9 27.2 + - - +
439A GLU* 5.4 0.2 - - - +
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Residues in contact with LYS 382 (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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201A GLU* 4.4 6.7 + - - -
250A LYS* 2.9 27.9 + - - +
252A PRO* 3.7 8.7 - - + +
377A PHE* 4.0 26.5 - - + -
378A THR 3.0 12.0 + - - +
379A PRO* 3.5 12.6 - - + +
380A GLN 3.3 0.2 - - - -
381A GLU* 1.3 73.7 - - - +
383A LEU* 1.3 67.1 + - - +
385A GLN* 2.8 33.8 + - - +
386A GLN* 3.0 41.2 + - + +
424A THR* 5.7 0.9 - - - -
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PRO 2.9 15.2 + - - +
380A GLN* 3.4 13.7 - - - +
382A LYS* 1.3 77.1 - - - +
384A TRP* 1.3 62.4 + - - +
386A GLN* 3.1 10.9 + - + +
387A LEU* 3.0 28.4 + - + +
426A ARG* 3.3 48.7 - - - +
428A GLU* 3.4 12.1 - - - +
430A MET* 4.8 6.1 - - + -
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Residues in contact with TRP 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A THR* 3.0 36.4 + - + -
287A TYR* 3.3 39.7 - + - +
380A GLN 2.9 11.7 + - - +
381A GLU 3.7 1.8 - - - +
382A LYS 3.3 0.2 - - - -
383A LEU* 1.3 72.5 - - - +
385A GLN* 1.3 67.2 + - - +
387A LEU* 3.1 27.8 + - + +
388A ARG* 2.8 39.4 + - + +
391A ARG* 6.0 1.3 - - - -
430A MET* 4.7 19.5 - - + -
433A PRO* 5.4 2.7 - - + -
439A GLU* 3.6 30.1 - - + +
442A ILE* 3.7 23.3 - - + +
443A LEU* 4.0 32.5 - - + -
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PRO 3.3 14.6 - - - +
250A LYS 2.9 16.5 - - - +
251A ASN 3.5 2.8 - - - +
252A PRO* 3.5 16.5 - - + -
286A THR* 3.5 29.2 + - + +
381A GLU 2.9 14.0 + - - +
382A LYS* 2.8 42.9 + - - +
384A TRP* 1.3 77.0 - - - +
386A GLN* 1.3 70.8 + - - +
388A ARG* 3.2 2.9 + - - +
389A ARG* 2.8 55.4 + - + +
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Residues in contact with GLN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 4.7 3.6 + - - -
382A LYS* 3.0 27.6 + - + +
383A LEU* 3.1 12.7 + - + +
385A GLN* 1.3 106.9 + - - +
387A LEU* 1.3 57.7 + - - +
389A ARG* 3.3 6.2 + - - +
390A GLY 3.0 22.7 + - - -
424A THR* 2.6 47.3 + - - -
425A ALA* 3.4 3.6 + - - -
426A ARG* 3.0 32.9 + - + -
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Residues in contact with LEU 387 (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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383A LEU* 3.0 22.3 + - + +
384A TRP* 3.1 30.5 + - + +
386A GLN* 1.3 75.3 - - - +
388A ARG* 1.3 62.8 + - + +
390A GLY* 3.2 3.1 + - - -
391A ARG* 3.0 30.3 + - - +
426A ARG* 3.6 30.1 - - + +
427A TRP* 4.3 0.7 - - - -
428A GLU* 3.8 34.3 - - + +
430A MET* 3.6 37.0 - - + -
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Residues in contact with ARG 388 (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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284A THR* 3.6 17.5 - - + +
285A PRO* 2.9 27.0 + - - +
286A THR* 3.5 29.2 + - - +
330A GLU* 4.4 1.2 + - - -
331A ARG 4.9 0.6 + - - -
332A ARG 3.0 26.8 + - - -
333A GLY* 4.1 2.8 - - - -
384A TRP* 2.8 43.0 + - + +
385A GLN* 3.2 8.7 + - - +
387A LEU* 1.3 75.7 - - - +
389A ARG* 1.3 58.2 + - + +
391A ARG* 3.3 30.9 + - - +
392A TYR* 3.1 23.9 + - - +
442A ILE* 4.3 2.2 - - - +
443A LEU* 5.7 1.3 - - - -
446A LEU* 3.4 36.7 - - - +
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Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU* 3.1 32.5 + - - -
248A HIS* 3.4 19.5 + - - -
249A PRO* 2.8 34.2 + - - +
254A ALA 4.4 5.9 + - - -
256A THR* 2.9 29.6 + - - +
286A THR* 5.3 3.8 + - - -
385A GLN* 2.8 42.3 + - + +
386A GLN* 3.6 8.5 - - - +
387A LEU 3.3 0.2 - - - -
388A ARG* 1.3 74.9 - - + +
390A GLY* 1.3 65.1 + - - +
392A TYR* 3.2 8.6 + - - +
393A VAL* 3.1 25.8 + - - +
422A PRO* 3.9 13.4 - - + +
424A THR 3.7 19.5 - - - +
425A ALA* 4.0 2.9 - - + -
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Residues in contact with GLY 390 (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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386A GLN 3.0 11.1 + - - -
387A LEU 3.2 4.6 + - - -
389A ARG* 1.3 77.6 - - - +
391A ARG* 1.3 55.1 + - - +
393A VAL* 3.3 1.9 + - - +
394A GLU* 2.9 25.2 + - - +
425A ALA* 3.7 6.0 - - - +
426A ARG 3.6 11.0 - - - -
427A TRP* 3.1 36.2 + - - -
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Residues in contact with ARG 391 (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 ILE* 3.6 24.7 - - + +
328A ARG* 3.2 53.5 - - - +
330A GLU* 2.7 38.4 + - - +
332A ARG* 5.2 1.3 - - - +
384A TRP* 6.0 1.8 - - - -
387A LEU* 3.0 21.3 + - - +
388A ARG* 3.3 26.7 + - - +
390A GLY* 1.3 72.7 - - - +
392A TYR* 1.3 65.5 + - - +
394A GLU* 3.1 12.1 + - - +
395A PHE* 3.1 18.7 + - - +
427A TRP* 6.3 1.0 - - - -
428A GLU 5.8 2.2 + - - -
443A LEU* 4.6 9.9 - - - +
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Residues in contact with TYR 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A VAL* 3.4 26.7 - - + +
248A HIS* 4.1 13.2 - + + -
256A THR* 3.9 15.5 - - + -
258A HIS* 3.5 20.9 - - + +
284A THR* 3.8 26.4 - - + +
332A ARG* 3.5 52.1 + - + -
388A ARG 3.1 12.4 + - - +
389A ARG* 3.2 14.3 + - - +
391A ARG* 1.3 78.1 - - - +
393A VAL* 1.3 68.3 + - + +
395A PHE* 3.3 15.2 + - - +
396A ASN* 3.9 9.0 + - - -
420A SER* 3.9 28.8 - - - -
422A PRO* 5.4 0.9 - - + -
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Residues in contact with VAL 393 (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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389A ARG 3.1 14.7 + - - +
390A GLY 3.6 7.6 - - - +
391A ARG 3.2 0.2 - - - -
392A TYR* 1.3 77.6 - - + +
394A GLU* 1.3 57.9 + - - +
396A ASN* 3.0 25.8 + - + +
397A LEU* 3.1 29.6 + - + +
421A LEU* 4.0 23.1 - - + -
422A PRO* 3.5 30.7 - - + -
425A ALA* 4.6 6.5 - - + -
427A TRP* 4.0 14.6 - - + -
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Residues in contact with GLU 394 (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 ILE* 3.9 8.2 - - + +
327A HIS* 2.9 17.7 - - - -
328A ARG* 2.9 42.8 + - - -
390A GLY 2.9 15.3 + - - +
391A ARG* 3.1 14.9 + - - +
393A VAL* 1.3 73.8 - - - +
395A PHE* 1.3 65.6 + - - +
397A LEU* 3.9 15.2 - - + +
398A LEU* 3.0 46.3 + - + +
427A TRP* 4.0 20.0 - - - +
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Residues in contact with PHE 395 (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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322A TYR* 3.6 35.0 - + - -
323A PHE* 3.6 33.7 - + - -
324A PHE 3.8 12.1 - - - -
325A ILE* 3.9 29.3 - - + +
332A ARG* 3.8 28.3 - - - -
391A ARG 3.1 7.9 + - - +
392A TYR 3.6 10.3 - - - +
393A VAL 3.2 0.8 - - - -
394A GLU* 1.3 75.9 - - - +
396A ASN* 1.3 59.9 + - - +
399A TYR* 2.9 41.0 + - + +
400A ASP* 3.2 34.3 + - + -
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Residues in contact with ASN 396 (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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332A ARG* 4.9 6.7 - - - +
392A TYR* 3.9 20.4 + - - -
393A VAL* 3.0 12.1 + - + +
395A PHE* 1.3 76.0 - - - +
397A LEU* 1.3 66.9 + - + +
398A LEU 3.9 0.2 - - - -
400A ASP* 2.9 62.9 + - - +
401A ARG* 3.2 7.2 + - - -
412A SER* 4.2 1.6 + - - -
417A ILE* 3.6 30.4 - - + +
420A SER* 3.8 19.6 + - - -
421A LEU* 5.9 1.9 - - + +
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Residues in contact with LEU 397 (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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393A VAL* 3.1 33.7 + - + +
394A GLU* 3.6 20.2 - - + +
396A ASN* 1.3 78.8 - - + +
398A LEU* 1.3 68.8 + - + +
401A ARG* 4.8 8.2 - - - +
427A TRP* 4.9 12.1 - - + +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 4.3 0.9 - - + -
327A HIS* 3.2 41.1 - - + +
394A GLU* 3.0 27.4 + - + +
396A ASN 3.9 0.4 - - - -
397A LEU* 1.3 88.1 - - + +
399A TYR* 1.3 90.0 + - + +
400A ASP 3.8 0.4 - - - -
401A ARG* 5.5 1.9 + - - +
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Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PHE 4.0 5.8 - - - +
325A ILE* 3.5 19.5 - - + -
326A ALA* 3.3 31.4 - - + +
327A HIS* 2.8 37.6 + - - +
395A PHE* 2.9 33.1 + + + +
398A LEU* 1.3 107.7 - - + +
400A ASP* 1.3 62.5 + - - +
401A ARG 4.0 1.1 - - - -
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Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A TYR* 4.8 7.3 + - - +
323A PHE* 5.9 0.3 - - - -
332A ARG* 5.8 0.3 + - - -
395A PHE* 3.2 28.0 + - + +
396A ASN* 2.9 36.8 + - - +
399A TYR* 1.3 80.6 - - - +
401A ARG* 1.3 60.0 + - - +
402A GLY 4.5 0.9 + - - -
403A THR* 5.4 0.3 - - - +
411A GLY* 3.4 10.9 - - - -
412A SER* 2.8 48.1 + - - +
417A ILE* 3.3 7.6 - - - +
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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