Contacts of the helix formed by residues 373 - 395 (chain A) in PDB entry 1U2X
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 SER 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A PRO 3.5 2.2 + - - -
372A LEU* 1.3 76.6 - - - +
374A GLU* 1.3 57.9 + - - +
375A GLU* 3.4 10.3 + - - +
376A GLU* 2.9 38.3 + - - +
377A LEU* 2.9 31.8 + - - +
435A LYS* 4.7 3.1 - - - +
472A HIS* 4.7 0.8 + - - -
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Residues in contact with GLU 374 (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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373A SER* 1.3 72.5 - - - +
375A GLU* 1.3 56.9 + - - +
377A LEU* 3.4 3.9 + - - +
378A ALA* 2.9 29.5 + - - +
435A LYS* 4.6 25.6 - - + +
436A VAL 4.4 10.8 + - - +
437A VAL* 3.9 28.3 - - + +
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Residues in contact with GLU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A SER* 3.2 8.5 + - - +
374A GLU* 1.3 79.1 - - - +
376A GLU* 1.3 58.8 + - + +
378A ALA* 3.5 12.1 + - - +
379A LYS* 2.9 51.3 + - - +
382A GLU* 4.7 4.0 - - - +
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Residues in contact with GLU 376 (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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372A LEU* 3.2 16.7 - - + +
373A SER* 2.9 40.3 + - - +
375A GLU* 1.3 74.7 - - + +
377A LEU* 1.3 65.7 + - - +
379A LYS* 3.3 14.1 + - - +
380A SER* 3.0 21.1 + - - -
468A PHE* 3.5 42.6 - - + +
471A ARG* 5.7 2.3 + - - +
472A HIS* 2.9 32.2 + - - -
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Residues in contact with LEU 377 (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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353A ILE* 3.8 28.9 - - + -
364A TYR* 3.5 26.8 - - + -
366A THR* 3.9 21.3 - - + -
370A ASN* 4.7 0.9 - - - +
372A LEU* 3.8 27.6 - - + +
373A SER 2.9 21.7 + - - +
374A GLU* 3.6 4.3 - - - +
376A GLU* 1.3 76.8 - - - +
378A ALA* 1.3 61.2 + - - +
380A SER* 3.2 4.9 + - - -
381A LEU* 3.1 19.1 + - - +
435A LYS* 4.3 20.4 - - + +
437A VAL* 4.1 23.8 - - + -
465A TYR* 4.5 1.3 - - + -
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Residues in contact with ALA 378 (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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374A GLU 2.9 17.6 + - - +
375A GLU* 3.6 15.3 - - - +
377A LEU* 1.3 76.4 - - - +
379A LYS* 1.3 63.2 + - - +
381A LEU* 3.4 4.3 + - - +
382A GLU* 2.9 32.5 + - - +
437A VAL* 3.8 14.4 - - + +
439A ILE* 4.0 20.2 - - + +
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Residues in contact with LYS 379 (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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375A GLU* 2.9 49.2 + - - +
376A GLU* 3.3 15.0 + - - +
378A ALA* 1.3 76.5 - - - +
380A SER* 1.3 56.4 + - - +
382A GLU* 3.5 14.6 - - - +
383A PHE* 2.9 27.4 + - - +
464A THR* 5.3 0.4 - - - +
468A PHE* 3.9 34.0 - - + -
471A ARG* 5.0 3.6 - - - +
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Residues in contact with SER 380 (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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364A TYR* 2.8 19.6 + - - -
372A LEU* 5.3 1.8 - - - -
376A GLU 3.0 13.1 + - - -
377A LEU* 3.2 9.8 + - - -
379A LYS* 1.3 73.0 - - - +
381A LEU* 1.3 66.7 + - - +
383A PHE* 3.2 4.9 + - - +
384A GLY 3.1 16.6 + - - -
461A ALA* 2.6 33.4 + - - -
464A THR* 3.1 21.4 + - - -
465A TYR* 3.7 8.2 + - - -
468A PHE* 4.3 4.7 - - - -
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Residues in contact with LEU 381 (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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355A GLN* 3.8 22.4 - - + -
362A LEU* 3.4 30.7 - - + +
363A MSE 3.9 8.5 - - - +
364A TYR* 3.4 56.3 - - + +
377A LEU 3.1 9.6 + - - +
378A ALA 3.7 4.7 - - - +
380A SER* 1.3 72.8 + - - +
382A GLU* 1.4 60.2 + - - +
384A GLY* 3.0 3.6 + - - +
385A THR* 2.9 26.3 + - - +
437A VAL* 4.0 18.6 - - + +
439A ILE* 3.7 20.4 - - + -
461A ALA* 4.6 5.8 - - + -
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Residues in contact with GLU 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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375A GLU* 4.7 5.2 - - - +
378A ALA* 2.9 31.4 + - - +
379A LYS* 3.5 14.4 + - - +
381A LEU* 1.4 76.7 - - - +
383A PHE* 1.3 60.3 + - - +
385A THR* 3.5 4.0 - - + +
386A THR* 2.7 36.0 + - - +
403A TYR* 4.6 0.7 - - - -
411A PHE* 4.1 23.1 - - + -
439A ILE* 3.6 21.5 - - + +
442A ARG* 4.8 4.9 + - - -
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Residues in contact with PHE 383 (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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23A MSE 4.2 25.1 - - + -
24A ILE* 4.2 21.5 - - + -
25A PRO* 4.5 8.3 - - + -
130A LEU* 4.5 9.2 - - + -
379A LYS 2.9 13.9 + - - +
380A SER 3.2 7.8 + - - +
382A GLU* 1.3 76.7 - - - +
384A GLY* 1.3 56.4 + - - +
386A THR* 3.3 1.4 + - - -
387A LEU* 2.9 38.1 + - + +
403A TYR* 3.5 45.9 - + - +
460A GLY* 3.5 33.4 - - - -
463A LEU* 4.6 6.5 - - + -
464A THR* 3.4 23.1 - - + -
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Residues in contact with GLY 384 (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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380A SER 3.1 8.2 + - - -
381A LEU 3.0 7.4 + - - -
383A PHE* 1.3 78.3 - - - +
385A THR* 1.3 56.7 + - - +
387A LEU* 3.7 1.7 - - - +
388A ALA* 3.0 29.3 + - - +
457A ILE* 3.5 35.3 - - - -
460A GLY* 4.2 4.5 - - - -
461A ALA* 3.9 7.9 - - - -
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Residues in contact with THR 385 (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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362A LEU* 3.7 19.8 - - - +
381A LEU 2.9 14.7 + - - +
382A GLU* 3.5 15.5 - - - +
384A GLY* 1.3 73.2 - - - +
386A THR* 1.3 62.2 + - - +
388A ALA* 3.8 5.9 - - - +
389A ALA* 3.0 28.6 + - - +
411A PHE* 4.3 3.4 - - + -
439A ILE* 4.3 10.5 - - + -
440A PRO 4.3 3.4 - - - +
441A THR* 3.3 12.8 - - - +
442A ARG* 2.9 43.2 + - + +
457A ILE* 4.6 4.3 - - - +
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Residues in contact with THR 386 (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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382A GLU* 2.7 24.7 + - - +
383A PHE 3.7 0.4 - - - -
385A THR* 1.3 75.2 - - - +
387A LEU* 1.3 59.8 + - - +
389A ALA* 3.2 1.2 + - - +
390A ALA* 2.8 29.8 + - - +
403A TYR* 3.4 33.2 + - + +
406A GLY* 3.5 5.4 - - - -
407A LEU* 3.7 35.3 - - + +
442A ARG* 2.9 27.3 + - - +
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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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126A THR* 3.9 17.3 - - + -
127A LEU* 5.9 0.7 - - + -
130A LEU* 4.0 37.7 - - + -
383A PHE* 2.9 20.2 + - + +
384A GLY 3.7 3.8 - - - +
386A THR* 1.3 75.8 - - - +
388A ALA* 1.3 63.0 + - - +
390A ALA* 3.3 5.4 + - - +
391A ARG* 3.1 21.5 + - - +
397A ILE* 4.1 20.2 - - + -
403A TYR* 3.8 21.0 - - + -
456A THR* 3.7 24.7 - - + +
459A ALA* 4.8 1.8 - - + -
460A GLY* 3.8 18.8 - - - +
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Residues in contact with ALA 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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384A GLY 3.0 17.7 + - - +
385A THR* 3.8 4.5 - - - +
387A LEU* 1.3 80.2 - - - +
389A ALA* 1.3 56.2 + - - +
391A ARG* 3.3 2.4 + - - +
392A ALA* 2.9 29.2 + - - +
444A VAL* 5.8 0.2 - - - -
453A LEU* 4.0 20.0 - - + +
456A THR* 3.7 11.1 - - - +
457A ILE* 3.5 27.6 - - + +
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Residues in contact with ALA 389 (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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385A THR 3.0 19.3 + - - +
386A THR 3.5 4.7 - - - +
388A ALA* 1.3 72.9 - - - +
390A ALA* 1.3 65.8 + - - +
392A ALA* 3.5 2.7 + - - +
393A SER* 2.9 29.8 + - - -
406A GLY* 4.2 5.8 - - - +
409A VAL* 3.9 24.0 - - + -
442A ARG* 3.8 22.6 + - + +
444A VAL* 4.0 10.8 - - - +
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Residues in contact with ALA 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 THR 2.8 13.1 + - - +
387A LEU 3.4 10.1 - - - +
388A ALA 3.2 0.2 - - - -
389A ALA* 1.3 75.4 - - - +
391A ARG* 1.3 55.9 + - - +
393A SER* 3.0 6.5 + - - -
394A LEU* 2.9 33.9 + - + +
397A ILE* 4.1 10.3 - - + -
402A ASP 3.4 25.8 - - - +
403A TYR* 3.9 6.7 - - - +
405A VAL* 4.4 3.4 - - + -
406A GLY* 3.5 17.6 - - - +
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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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116A LEU 5.9 0.2 + - - -
122A ILE* 3.9 23.3 - - - +
126A THR* 3.8 18.6 + - - -
387A LEU 3.1 15.9 + - - +
388A ALA 3.9 3.4 - - - +
390A ALA* 1.3 74.9 - - - +
392A ALA* 1.3 56.7 + - - +
395A GLY* 2.7 35.2 + - - +
396A ASP* 4.3 12.2 - - - +
397A ILE* 4.1 19.7 - - + +
449A LEU* 3.3 30.5 - - + +
451A VAL* 3.0 30.5 + - - +
452A GLY 3.3 9.3 + - - -
453A LEU* 3.6 10.1 - - + +
456A THR* 3.3 33.0 + - + +
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Residues in contact with ALA 392 (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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388A ALA 2.9 16.5 + - - +
389A ALA 3.8 3.1 - - - +
390A ALA 3.3 0.2 - - - -
391A ARG* 1.3 77.9 - - - +
393A SER* 1.3 56.8 + - - +
444A VAL* 3.4 34.3 - - + -
447A PRO* 3.2 14.0 - - + +
448A VAL* 3.1 30.1 + - - +
449A LEU* 4.2 8.5 - - - -
453A LEU* 4.0 13.4 - - + +
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Residues in contact with SER 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 ALA 2.9 15.5 + - - -
390A ALA 3.0 8.8 + - - -
392A ALA* 1.3 77.7 - - - +
394A LEU* 1.3 61.9 + - - +
405A VAL* 4.4 4.7 - - - -
409A VAL* 3.8 7.3 - - - +
444A VAL* 4.0 7.2 - - - +
448A VAL* 3.0 14.3 - - - +
393B SER* 3.7 33.7 + - - -
444B VAL* 5.3 2.1 - - - +
447B PRO* 6.5 0.4 - - - -
448B VAL* 3.6 23.8 - - - +
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Residues in contact with LEU 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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390A ALA 2.9 18.3 + - - +
393A SER* 1.3 78.8 - - - +
395A GLY* 1.3 60.3 + - - +
396A ASP* 3.6 19.1 + - - +
397A ILE* 5.1 0.2 - - + -
398A ARG* 4.3 3.4 - - - +
402A ASP* 3.7 44.4 - - + +
405A VAL* 4.2 8.5 - - + -
448A VAL* 3.7 5.4 - - - +
393B SER* 3.5 25.4 - - - +
394B LEU* 3.0 36.6 - - + -
405B VAL* 4.2 18.5 - - + +
408B LYS* 5.6 4.7 - - - +
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Residues in contact with GLY 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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391A ARG 2.7 21.5 + - - -
394A LEU* 1.3 72.5 - - - +
396A ASP* 1.3 64.3 + - - +
448A VAL* 3.4 17.2 - - - +
449A LEU* 3.2 30.3 - - - +
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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
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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