Contacts of the helix formed by residues 410 - 439 (chain A) in PDB entry 5IWS
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 LEU 410 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A TRP* 5.6 0.2 - - - +
278A TRP* 3.6 34.1 - - + -
279A ILE* 4.6 5.4 - - + -
282A LEU* 4.2 0.7 - - + -
294A TYR* 5.1 0.7 - - - +
298A LEU* 4.3 9.2 - - + -
389A ARG* 3.4 36.1 - - - +
405A MSE 2.9 42.2 + - + +
408A ALA* 3.6 24.9 - - + +
409A GLY* 1.3 80.9 - - - +
411A THR* 1.3 63.6 + - - +
412A ARG 3.2 2.9 - - - +
413A ASP* 3.1 20.3 + - - +
414A LEU* 3.3 14.2 + - - +
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Residues in contact with THR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A MSE 4.0 1.0 + - - -
406A VAL* 3.7 38.8 + - + +
409A GLY* 3.4 3.9 - - - -
410A LEU* 1.3 78.3 + - - +
412A ARG* 1.3 65.2 + - - +
414A LEU* 3.2 8.7 + - + +
415A ILE* 2.9 40.9 + - + +
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Residues in contact with ARG 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ASN* 6.0 1.8 - - + +
409A GLY 5.0 11.4 + - - +
411A THR* 1.3 80.4 - - - +
413A ASP* 1.3 59.4 + - - +
415A ILE* 3.2 10.5 + - + +
416A ASN* 2.3 40.7 + - - +
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Residues in contact with ASP 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ASN* 3.0 30.3 + - - +
388A LEU* 4.3 0.7 - - - +
389A ARG* 2.8 54.1 + - - +
390A VAL* 4.3 3.4 - - + +
405A MSE 4.2 14.8 - - + -
409A GLY 5.0 0.3 - - - +
410A LEU* 3.1 22.5 + - - +
412A ARG* 1.3 79.7 - - - +
414A LEU* 1.3 59.3 + - - +
416A ASN* 3.4 10.8 - - - +
417A PHE* 3.1 27.4 + - - +
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Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A VAL* 4.1 14.1 - - + -
398A LEU* 4.7 10.5 - - + +
402A THR* 3.7 37.0 - - + +
405A MSE 3.6 48.5 - - + -
406A VAL* 4.3 9.9 - - + -
410A LEU 3.3 4.9 + - - +
411A THR* 3.2 10.1 + - + +
413A ASP* 1.3 76.2 - - - +
415A ILE* 1.3 66.5 + - + +
417A PHE* 3.3 11.2 + - + +
418A VAL* 3.3 25.6 + - - +
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A THR* 2.9 39.2 + - + +
412A ARG* 3.2 7.8 + - + +
414A LEU* 1.3 77.5 - - + +
416A ASN* 1.3 57.9 + - - +
418A VAL* 3.1 23.2 + - - +
419A ILE* 3.2 25.2 + - + +
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Residues in contact with ASN 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 3.3 24.8 - - + +
387A ASN* 3.0 23.7 + - - +
388A LEU* 3.2 13.2 - - - +
412A ARG* 2.3 43.4 + - - +
413A ASP* 3.4 6.6 - - - +
415A ILE* 1.3 74.7 - - + +
417A PHE* 1.3 60.5 + - - +
419A ILE* 3.7 19.6 - - + +
420A VAL* 2.9 33.8 + - + +
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Residues in contact with PHE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ALA* 4.6 3.1 - - + -
311A VAL* 3.7 34.8 - - + -
312A ILE* 3.8 27.6 - - + -
315A THR* 4.3 12.8 - - + -
388A LEU* 3.8 16.2 - - + -
390A VAL* 4.4 20.2 - - + -
398A LEU* 3.6 28.7 - - + -
413A ASP 3.1 20.2 + - - +
414A LEU* 3.4 15.5 - - + +
415A ILE 3.1 0.4 - - - -
416A ASN* 1.3 78.2 + - - +
418A VAL* 1.3 67.0 + - + +
420A VAL* 3.5 1.8 + - - +
421A SER* 2.8 45.1 + - - -
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Residues in contact with VAL 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU 3.4 15.3 - - - +
415A ILE* 3.1 9.1 + - - +
417A PHE* 1.3 82.8 - - + +
419A ILE* 1.3 56.5 - - + +
421A SER* 3.2 6.5 + - - -
422A LEU* 2.7 55.9 + - + +
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ILE* 3.2 23.7 + - + +
416A ASN* 3.7 22.7 - - + +
417A PHE 3.3 0.2 - - - -
418A VAL* 1.3 77.2 - - + +
420A VAL* 1.3 63.8 + - + +
422A LEU* 3.4 10.0 + - + +
423A VAL* 3.0 38.9 + - + +
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Residues in contact with VAL 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ILE* 3.6 28.9 - - + -
382A LEU* 3.6 26.0 - - + -
386A ILE* 5.1 8.3 - - + -
388A LEU* 4.4 11.9 - - + -
416A ASN* 2.9 24.1 + - + +
417A PHE* 3.9 4.7 - - - +
419A ILE* 1.3 79.0 - - + +
421A SER* 1.3 57.0 + - - +
423A VAL* 3.4 5.1 + - - +
424A PHE* 2.9 48.6 + - + -
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Residues in contact with SER 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ILE* 4.5 12.5 - - - +
315A THR* 4.8 6.7 - - - +
316A ALA* 3.2 29.1 - - - +
417A PHE* 2.8 44.4 + - - -
418A VAL* 3.2 8.9 + - - -
420A VAL* 1.3 74.8 - - - +
422A LEU* 1.3 61.6 + - - +
425A PHE* 2.8 27.2 + - - +
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Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A VAL* 2.7 42.1 + - + +
419A ILE* 3.9 8.7 - - + +
421A SER* 1.3 74.1 - - - +
423A VAL* 1.3 64.6 + - + +
425A PHE* 3.7 9.7 - - + +
426A GLY* 3.5 14.6 + - - -
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ILE* 3.0 30.5 + - + +
420A VAL* 3.8 6.1 - - - +
422A LEU* 1.3 76.6 - - + +
424A PHE* 1.3 61.6 + - + +
426A GLY* 3.2 2.8 + - - -
427A LEU* 2.7 58.7 + - + +
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Residues in contact with PHE 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ILE* 4.1 14.6 - - + -
317A ALA* 4.0 19.4 - - + -
375A THR* 3.5 25.4 - - - -
378A LEU* 4.1 12.1 - - + -
379A ALA* 3.6 30.1 - - + -
382A LEU* 3.8 15.3 - - + -
420A VAL* 2.9 45.8 + - + +
421A SER 4.0 2.2 - - - +
423A VAL* 1.3 82.3 - - + +
425A PHE* 1.3 57.1 + - - +
427A LEU* 3.9 11.2 - - + -
428A ASN* 2.9 42.0 + - - +
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Residues in contact with PHE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ALA* 3.3 21.5 + - + +
319A MSE 3.5 18.4 - - + -
320A GLY* 3.3 38.9 - - - -
323A PHE* 4.5 22.0 - + + -
421A SER 2.8 17.7 + - - +
422A LEU* 3.7 13.2 - - + +
423A VAL 3.2 0.2 - - - -
424A PHE* 1.3 77.9 - - - +
426A GLY* 1.3 62.6 + - - +
429A PHE* 2.9 36.2 + + + +
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Residues in contact with GLY 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A LEU 3.5 6.7 + - - -
423A VAL 3.2 4.7 + - - -
425A PHE* 1.3 82.1 - - - +
427A LEU* 1.3 65.2 + - - +
429A PHE* 4.2 7.2 - - - -
430A THR* 2.8 36.4 + - - +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A VAL* 2.7 47.2 + - + +
424A PHE* 3.8 15.5 - - + +
426A GLY* 1.3 76.5 - - - +
428A ASN* 1.3 63.2 + - - +
430A THR* 3.6 5.4 + - - +
431A LEU* 3.2 26.5 + - - +
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Residues in contact with ASN 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ALA* 2.8 49.4 + - - +
320A GLY 4.5 2.5 - - - -
321A ILE* 3.9 19.5 - - + +
372A TYR* 5.1 2.6 - - - -
375A THR* 3.9 30.6 + - - +
376A THR* 5.6 1.2 - - - +
424A PHE* 2.9 22.8 + - - +
425A PHE 4.2 0.9 - - - +
427A LEU* 1.3 78.3 - - - +
429A PHE* 1.3 60.8 + - - +
431A LEU* 3.8 3.6 - - - +
432A PHE* 2.9 41.8 + - + +
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Residues in contact with PHE 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLY* 3.5 26.4 + - - +
323A PHE* 3.4 38.8 - + + -
324A ALA* 3.5 24.9 - - + +
327A ARG* 4.4 16.6 - - + -
425A PHE* 2.9 24.8 + + + +
426A GLY* 4.0 7.2 - - - +
427A LEU 3.5 0.2 - - - -
428A ASN* 1.3 76.9 - - - +
430A THR* 1.3 68.3 + - + +
433A ASN* 2.7 53.0 + - + +
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Residues in contact with THR 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLY* 2.8 23.5 + - - +
427A LEU* 3.6 8.7 + - - +
429A PHE* 1.3 90.3 - - + +
431A LEU* 1.3 62.9 + - - +
433A ASN* 4.2 5.9 + - - +
434A PHE* 3.2 24.6 + - - +
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Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A VAL* 3.9 15.9 - - + -
375A THR* 3.9 28.5 - - + -
427A LEU* 3.2 19.4 + - + +
428A ASN* 3.9 7.9 - - - +
429A PHE 3.2 0.4 - - - -
430A THR* 1.3 83.1 + - - +
432A PHE* 1.3 63.6 + - + +
434A PHE* 3.4 8.1 + - + +
435A LEU* 3.1 53.9 + - + +
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Residues in contact with PHE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 3.5 51.4 - - + +
324A ALA* 3.9 15.3 - - + -
325A MSE 5.5 0.4 - - + -
361A PHE* 3.9 7.2 - + - -
368A LEU* 3.5 44.0 - - + -
371A VAL* 5.3 2.0 - - + -
372A TYR* 3.6 28.5 - - + -
375A THR* 5.1 0.7 - - - -
428A ASN* 2.9 39.2 + - - +
431A LEU* 1.3 86.0 - - + +
433A ASN* 1.3 61.3 + - - +
434A PHE 3.1 1.8 - - - -
435A LEU* 4.0 4.4 - - + +
436A ILE* 3.0 41.7 + - + +
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Residues in contact with ASN 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ALA* 3.7 8.8 - - + +
327A ARG* 4.8 6.2 - - - +
328A ASN* 3.3 25.4 + - - +
429A PHE* 2.7 42.9 + - + +
430A THR* 4.2 6.6 + - - +
432A PHE* 1.3 72.8 - - - +
434A PHE* 1.3 62.6 + - - +
437A LYS* 3.3 52.8 + - - +
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Residues in contact with PHE 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A THR 3.2 20.7 + - - +
431A LEU* 3.7 9.0 - - + +
432A PHE 3.1 0.8 - - - -
433A ASN* 1.3 79.5 - - - +
435A LEU* 1.3 85.5 + - + +
437A LYS* 3.4 3.4 + - - +
438A LYS* 3.0 71.2 + - + +
439A PHE* 5.1 3.8 - + - -
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Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 5.6 0.9 - - + +
368A LEU* 3.7 31.9 - - + -
371A VAL* 4.4 21.3 - - + -
431A LEU* 3.1 36.3 + - + +
432A PHE* 3.4 1.5 + - - +
434A PHE* 1.3 95.9 - - + +
436A ILE* 1.3 62.0 + - - +
439A PHE* 3.4 45.6 + - + -
441A LEU* 3.6 11.5 - - + +
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Residues in contact with ILE 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A MSE 3.7 39.7 - - + +
328A ASN* 3.8 29.2 - - + +
368A LEU* 4.7 6.1 - - + -
432A PHE* 3.0 30.2 + - + +
433A ASN 4.4 0.4 - - - +
435A LEU* 1.3 76.8 - - - +
437A LYS* 1.3 58.4 + - - +
440A ASN* 3.1 9.5 + - - -
441A LEU* 3.1 50.1 + - + +
443A THR* 3.7 8.7 - - + -
446A ARG* 3.4 24.8 + - - +
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Residues in contact with LYS 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A ARG* 6.0 2.2 - - - +
328A ASN* 3.2 25.6 - - - +
433A ASN* 3.3 38.2 + - - +
434A PHE* 3.4 4.4 + - - +
435A LEU 3.3 0.2 - - - -
436A ILE* 1.3 77.9 - - - +
438A LYS* 1.3 68.2 + - + +
440A ASN* 3.8 6.6 + - - +
446A ARG* 4.9 8.4 + - - +
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Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A PHE* 3.0 56.7 + - + +
436A ILE 3.5 0.2 - - - -
437A LYS* 1.3 83.7 - - + +
439A PHE* 1.3 80.5 + - + +
440A ASN* 3.8 0.5 + - - +
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Residues in contact with PHE 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A VAL* 6.1 4.9 - - + -
434A PHE* 5.1 4.3 - + - -
435A LEU* 3.4 42.8 + - + -
438A LYS* 1.3 89.9 - - + +
440A ASN* 1.3 72.7 + - - +
441A LEU* 3.4 19.3 + - + +
----------------------------------------------------------
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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
------------------------------------------------------------
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