Contacts of the helix formed by residues 406 - 430 (chain A) in PDB entry 1O86
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 406 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A MET 4.4 7.4 - - - +
224A TYR* 3.5 23.7 - - + -
404A GLY* 3.7 9.3 - - - -
405A ALA* 1.3 77.6 - - - +
407A PRO* 1.3 74.7 - - + +
408A GLY* 2.6 35.9 + - - -
409A PHE* 3.0 33.1 + - - +
410A HIS 3.6 3.1 + - - -
525A VAL* 4.2 6.7 - - - +
570A PHE* 5.0 1.6 - - - -
574A TRP* 3.4 35.0 - - + +
587A MET* 5.7 2.6 - - - +
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Residues in contact with PRO 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A MET* 4.1 31.4 - - + +
224A TYR* 3.5 21.3 - - + +
404A GLY* 5.8 0.7 - - - +
406A ASN* 1.3 87.6 - - + +
408A GLY* 1.3 59.8 + - - +
410A HIS* 3.3 17.7 + - + +
411A GLU* 3.3 18.2 + - - +
522A ARG* 3.7 24.7 - - - +
570A PHE* 6.0 0.4 - - + -
704A CL 3.6 20.4 - - + -
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Residues in contact with GLY 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TYR* 3.8 3.8 + - - -
406A ASN* 2.6 16.8 + - - -
407A PRO* 1.3 74.9 - - - +
409A PHE* 1.3 58.7 + - - -
411A GLU* 3.2 3.6 + - - +
412A ALA* 3.0 23.9 + - - +
522A ARG* 3.5 21.1 - - - -
525A VAL* 3.9 14.4 - - - -
526A SER* 3.7 3.9 - - - -
529A ILE* 3.8 6.5 - - - -
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A TYR* 3.7 22.0 - + + +
405A ALA* 3.6 14.1 - - + +
406A ASN* 3.0 42.3 + - - +
408A GLY* 1.3 76.0 - - - +
410A HIS* 1.3 63.6 + - - +
412A ALA* 3.1 12.0 + - - +
413A ILE* 3.3 21.2 + - + +
525A VAL* 5.9 0.2 - - + -
529A ILE* 3.8 21.3 - - + -
533A PHE* 3.7 26.5 - + - -
565A ALA* 5.7 1.3 - - + -
574A TRP* 3.9 18.4 - + + -
577A ALA* 3.5 24.7 - - + -
578A MET* 3.8 31.9 - - + -
581A ILE* 4.4 6.3 - - + -
587A MET* 6.3 0.2 - - + -
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Residues in contact with HIS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A HIS 5.4 0.7 - - - +
386A GLY 4.9 0.3 - - - -
387A HIS* 2.9 53.2 + + + +
390A TYR* 3.4 35.3 - + + +
391A PHE* 3.5 23.2 - + - -
394A TYR* 3.0 22.3 + - - -
403A GLU* 4.6 6.7 + - - -
404A GLY* 3.5 27.8 - - - -
406A ASN 3.6 4.4 + - - +
407A PRO* 3.3 14.0 + - + +
408A GLY 3.3 0.4 - - - -
409A PHE* 1.3 80.2 - - - +
411A GLU* 1.3 62.6 + - - +
413A ILE* 4.1 10.0 + - - +
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Residues in contact with GLU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A HIS* 2.9 29.2 + - + +
387A HIS* 3.3 11.6 - - - -
407A PRO 3.4 13.8 - - - +
408A GLY 3.2 7.8 + - - +
409A PHE 3.1 0.4 - - - -
410A HIS* 1.3 79.9 - - - +
412A ALA* 1.3 59.7 + - - +
413A ILE 3.6 0.4 + - - -
414A GLY 4.5 1.6 + - - -
415A ASP* 3.8 5.9 + - - +
522A ARG* 3.8 35.6 + - + +
523A TYR* 3.2 17.8 + - + -
526A SER* 3.4 19.7 + - - +
701A ZN 2.0 38.2 - - - -
702A LPR 3.1 5.4 - - - +
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Residues in contact with ALA 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLY 3.0 15.0 + - - +
409A PHE 3.1 4.4 + - - +
411A GLU* 1.3 77.4 - - - +
413A ILE* 1.3 65.8 + - - +
414A GLY 3.5 0.2 - - - -
415A ASP* 3.1 5.4 + - - +
416A VAL* 3.0 26.7 + - - +
526A SER* 3.3 12.3 + - - +
529A ILE* 3.9 24.2 - - + -
530A GLN* 4.1 11.8 - - + +
533A PHE* 4.1 12.3 - - + -
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Residues in contact with ILE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PHE* 4.1 14.4 - - + -
386A GLY* 3.9 23.8 - - - +
389A GLN* 4.9 0.2 - - + -
390A TYR* 3.6 22.7 - - + -
409A PHE* 3.3 19.1 - - + +
410A HIS 4.3 2.2 - - - +
411A GLU 3.6 1.0 - - - -
412A ALA* 1.3 75.7 - - - +
414A GLY* 1.3 65.0 + - - +
416A VAL* 3.2 17.4 + - - +
417A LEU* 3.6 9.4 + - - +
533A PHE* 4.9 11.9 - - + -
562A LEU* 4.2 26.7 - - + -
566A MET* 4.0 32.3 - - + -
581A ILE* 5.7 1.8 - - + -
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Residues in contact with GLY 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A PHE* 4.4 5.8 - - - -
382A HIS* 3.2 29.7 - - - +
383A HIS* 3.9 8.5 + - - -
386A GLY* 3.6 12.6 - - - -
410A HIS 5.2 0.6 + - - -
411A GLU 4.5 2.2 + - - -
412A ALA 3.5 0.6 - - - -
413A ILE* 1.3 79.6 - - - +
415A ASP* 1.3 63.8 + - - +
417A LEU* 3.3 5.9 + - - +
418A ALA* 3.0 21.7 + - - +
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Residues in contact with ASP 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 5.3 1.7 - - - +
383A HIS* 2.7 36.8 + - - +
411A GLU 3.9 5.4 + - - -
412A ALA 3.1 7.3 + - - +
414A GLY* 1.3 72.5 - - - +
416A VAL* 1.3 66.6 + - - +
418A ALA* 3.2 8.4 + - - +
419A LEU* 2.9 27.7 + - - +
454A LYS* 3.5 11.0 + - - +
526A SER* 4.3 1.0 + - - -
527A PHE* 3.7 8.3 - - - -
530A GLN* 3.0 36.2 + - - +
2000A GLY* 3.5 22.7 - - - -
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Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ALA 3.0 24.1 + - - +
413A ILE* 3.2 9.2 + - - +
415A ASP* 1.3 75.8 - - - +
417A LEU* 1.3 69.6 + - + +
419A LEU* 3.2 25.5 + - - +
420A SER* 3.7 4.3 + - - -
530A GLN* 3.8 12.8 - - + +
533A PHE* 3.8 28.5 - - + -
534A HIS* 4.4 20.4 + - - +
537A LEU* 3.7 29.2 - - + -
552A ILE* 4.6 6.5 - - + +
562A LEU* 5.0 4.0 - - + -
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Residues in contact with LEU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 3.5 43.7 - - + -
323A PHE* 3.6 51.1 - - + +
326A LEU* 3.9 18.6 - - + -
382A HIS* 4.6 7.0 - - + -
413A ILE 3.7 12.6 - - - +
414A GLY 3.3 7.5 + - - +
415A ASP 3.3 0.4 - - - -
416A VAL* 1.3 83.3 - - + +
418A ALA* 1.3 63.3 + - - +
420A SER* 3.0 17.4 + - - -
421A VAL* 3.1 15.0 + - - +
552A ILE* 4.6 3.6 - - + -
562A LEU* 4.2 16.6 - - + -
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Residues in contact with ALA 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 3.9 31.2 - - + +
382A HIS* 4.0 15.6 - - + +
414A GLY 3.0 14.1 + - - +
415A ASP* 3.2 11.4 + - - +
417A LEU* 1.3 76.9 - - - +
419A LEU* 1.3 62.0 + - - +
421A VAL* 3.5 12.5 - - + +
422A SER* 2.9 30.1 + - - +
454A LYS* 6.1 0.9 - - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASP 2.9 18.4 + - - +
416A VAL* 3.2 12.1 - - - +
417A LEU 3.1 0.4 - - - -
418A ALA* 1.3 78.9 - - - +
420A SER* 1.3 61.1 + - - +
422A SER* 3.4 14.8 + - - -
423A THR* 3.7 11.0 + - - +
446A PHE* 5.1 1.4 - - - -
450A MET* 3.7 27.9 - - + +
454A LYS* 4.0 12.1 - - - -
530A GLN* 4.0 20.0 - - - +
531A PHE* 4.0 31.0 - - + -
534A HIS* 3.7 42.3 - - + +
595A TYR* 4.7 6.0 + - + +
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 3.6 12.3 - - - -
416A VAL 3.7 1.5 + - - -
417A LEU 3.0 9.9 + - - -
419A LEU* 1.3 78.4 - - - +
421A VAL* 1.3 61.5 + - - +
423A THR* 2.6 27.7 + - - -
426A HIS* 3.3 7.2 + - - +
534A HIS* 3.9 10.3 + - - -
550A CYS 3.9 11.7 + - - -
551A ASP* 3.5 22.8 - - - -
552A ILE* 3.0 28.7 + - - +
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Residues in contact with VAL 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 3.5 25.4 - - + -
375A LEU* 6.0 2.0 - - + -
378A LEU* 4.5 17.0 - - + -
379A VAL* 6.3 2.9 - - + -
382A HIS* 3.5 33.4 - - + +
417A LEU 3.1 14.2 + - - +
418A ALA* 3.2 9.6 + - - +
420A SER* 1.3 75.7 - - - +
422A SER* 1.3 61.9 + - - +
423A THR 3.3 1.0 + - - -
426A HIS* 3.4 33.9 - - + +
427A LEU* 3.5 13.8 - - + +
430A LEU* 4.5 7.2 - - + -
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Residues in contact with SER 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LEU* 4.9 6.8 - - - +
379A VAL* 4.3 17.2 - - - +
418A ALA* 2.9 18.6 + - - +
419A LEU* 3.7 6.9 - - - -
420A SER 3.2 0.4 - - - -
421A VAL* 1.3 76.6 - - - +
423A THR* 1.3 65.9 + - - +
424A PRO 3.4 0.7 - - - -
427A LEU* 3.5 20.6 - - - +
446A PHE* 3.4 12.8 - - - -
449A LYS* 5.4 2.7 - - - -
450A MET* 3.9 28.2 - - - +
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Residues in contact with THR 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU 3.8 9.2 - - - +
420A SER 2.6 21.5 + - - +
422A SER* 1.3 78.1 - - - +
424A PRO* 1.3 75.1 - - - +
425A LYS* 4.3 4.6 - - - +
426A HIS* 2.9 17.1 + - - +
427A LEU* 2.9 19.9 + - - +
446A PHE* 3.8 6.7 - - + -
548A HIS 3.7 18.8 - - - +
549A LYS* 4.7 5.4 - - - -
550A CYS 3.5 25.8 - - - +
551A ASP* 4.1 7.2 + - - +
595A TYR* 5.8 0.4 - - - +
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Residues in contact with PRO 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A SER 3.4 0.6 - - - +
423A THR* 1.3 85.4 - - - +
425A LYS* 1.3 58.1 + - - +
427A LEU* 3.3 2.8 + - - +
428A HIS* 2.9 29.3 + - - +
433A LEU* 3.6 24.5 - - + +
442A HIS* 5.5 2.2 - - + +
446A PHE* 3.5 44.6 - - + -
548A HIS 5.7 0.2 - - - +
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Residues in contact with LYS 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A THR* 3.2 5.3 - - - +
424A PRO* 1.3 80.2 - - - +
426A HIS* 1.3 62.3 + - - +
428A HIS* 3.3 10.3 + - + +
429A SER* 3.1 21.4 + - - -
551A ASP* 5.9 2.0 - - + +
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Residues in contact with HIS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PHE* 3.7 26.5 - + - -
420A SER 3.3 8.7 + - - +
421A VAL* 3.4 34.1 - - + +
423A THR* 2.9 22.2 + - - +
425A LYS* 1.3 76.0 - - - +
427A LEU* 1.3 67.9 + - - +
429A SER* 2.5 32.6 + - - -
430A LEU* 3.2 21.7 + - + +
551A ASP* 2.9 25.8 + - - +
553A TYR* 4.1 17.3 - + - -
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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
----------------------------------------------------------
301A THR* 4.9 3.8 - - + +
375A LEU* 4.3 31.6 - - + -
378A LEU* 5.2 1.8 - - + -
421A VAL* 3.5 25.8 - - + +
422A SER* 3.5 19.7 - - - +
423A THR 2.9 8.7 + - - +
424A PRO 3.6 7.2 - - - +
426A HIS* 1.3 75.8 - - - +
428A HIS* 1.3 61.0 + - - +
430A LEU* 3.0 19.3 + - + +
432A LEU* 2.9 46.3 + - + +
433A LEU* 3.6 31.0 - - + -
449A LYS* 4.5 8.5 - - - +
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Residues in contact with HIS 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A PRO 2.9 14.1 + - - +
425A LYS* 3.5 13.7 + - + +
426A HIS 3.1 0.2 - - - -
427A LEU* 1.3 76.9 - - - +
429A SER* 1.3 60.5 + - - +
431A ASN* 2.8 22.0 + - - +
433A LEU* 2.8 34.9 - - + +
434A SER* 3.1 27.1 + - - +
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Residues in contact with SER 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LYS* 3.1 12.2 + - - -
426A HIS* 2.5 34.8 + - - -
428A HIS* 1.3 79.5 + - - +
430A LEU* 1.3 63.4 + - - +
431A ASN* 3.2 1.8 + - - +
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Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLN* 4.4 0.7 - - - +
310A TRP* 3.9 35.0 + - + -
314A ARG* 4.9 3.6 + - - +
318A GLU* 3.8 28.0 - - + +
378A LEU* 4.6 5.8 - - + -
421A VAL* 4.5 13.5 - - + -
426A HIS* 3.7 32.3 - - + +
427A LEU* 3.0 14.2 + - + +
429A SER* 1.3 84.3 + - - +
431A ASN* 1.3 70.5 + - - +
432A LEU* 3.8 24.3 - - + +
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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