Contacts of the helix formed by residues 427 - 454 (chain A) in PDB entry 1OY6
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 PRO 427 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 3.2 24.7 - - + +
426A PRO* 1.3 110.4 - - + +
428A LYS* 1.3 63.5 + - - +
429A GLU* 3.2 20.6 - - + +
430A ALA* 3.2 15.3 + - + +
431A THR* 3.3 7.2 + - - -
494A ALA 5.7 1.8 - - - -
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Residues in contact with LYS 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP* 3.2 31.6 + - - +
8A ARG 4.4 0.2 - - - +
9A PRO* 4.3 10.6 - - - +
427A PRO* 1.3 74.0 - - - +
429A GLU* 1.3 63.6 + - - +
431A THR* 3.3 10.9 + - - -
432A ARG* 2.8 51.3 + - - +
491A ALA 4.5 0.4 + - - -
494A ALA* 3.2 24.8 + - + +
495A THR* 3.1 37.1 + - - +
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Residues in contact with GLU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PRO* 3.2 12.4 - - + +
428A LYS* 1.3 85.7 + - - +
430A ALA* 1.3 64.1 + - - +
432A ARG* 3.8 21.8 + - - +
433A LYS* 3.0 55.8 + - + +
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Residues in contact with ALA 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A VAL* 4.0 7.2 - - + -
419A VAL* 3.7 20.3 - - + +
425A LEU* 2.9 34.5 - - + +
426A PRO 3.7 4.7 - - - +
427A PRO* 3.2 16.1 + - + +
429A GLU* 1.3 77.7 - - - +
431A THR* 1.3 57.9 + - - +
433A LYS 3.8 0.2 - - - -
434A SER* 2.9 32.2 + - - -
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Residues in contact with THR 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A VAL* 3.5 18.8 - - + +
420A MET* 5.6 0.2 - - - -
426A PRO 4.1 2.8 + - - -
427A PRO 3.3 10.9 + - - -
428A LYS 3.5 7.6 - - - -
430A ALA* 1.3 76.5 - - - +
432A ARG* 1.3 57.7 + - - +
434A SER* 2.6 18.3 + - - -
435A MET* 3.0 34.1 + - + +
490A PRO 4.0 0.2 - - - +
493A CYS* 3.6 32.0 + - + -
494A ALA* 3.6 33.8 + - + +
497A LEU* 5.8 0.3 - - - +
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Residues in contact with ARG 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP* 4.1 32.3 + - - +
428A LYS* 2.8 48.3 + - - +
429A GLU* 3.8 22.3 + - - +
430A ALA 3.1 0.6 - - - -
431A THR* 1.3 72.0 - - - +
433A LYS* 1.3 86.3 + - + +
434A SER 3.2 4.0 - - - -
435A MET* 3.2 29.7 + - - +
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Residues in contact with LYS 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A VAL* 6.1 0.4 - - - -
429A GLU* 3.0 53.5 + - + +
430A ALA 3.8 0.7 - - - -
432A ARG* 1.3 102.4 - - + +
434A SER* 1.3 63.0 + - - +
435A MET 3.3 0.4 - - - -
436A GLY* 3.5 14.4 + - - +
437A GLN* 4.5 5.0 + - - +
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASN* 3.9 4.5 + - - +
416A VAL* 3.6 13.0 - - - +
419A VAL* 3.6 27.6 - - - -
430A ALA 2.9 17.8 + - - -
431A THR 2.6 22.4 + - - -
433A LYS* 1.3 78.7 - - - +
435A MET* 1.3 56.7 + - - +
436A GLY 3.1 5.6 + - - -
437A GLN* 3.2 14.3 + - - +
438A ILE* 3.1 33.1 + - - +
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Residues in contact with MET 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP* 5.7 4.5 - - - +
412A VAL* 4.3 14.6 - - + -
416A VAL* 5.4 0.2 - - + -
431A THR* 3.0 39.5 - - + +
432A ARG* 3.2 16.8 + - - +
434A SER* 1.3 82.0 + - - +
436A GLY* 1.3 58.2 + - - +
437A GLN 3.4 0.2 - - - -
438A ILE* 3.7 26.7 - - + -
439A GLN* 3.0 28.9 + - + +
442A LEU* 5.2 4.3 - - + -
485A ALA 4.9 2.7 - - - +
486A LEU* 6.0 1.6 - - - -
490A PRO* 3.6 43.3 - - + +
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Residues in contact with GLY 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ARG 3.7 1.9 + - - -
433A LYS* 3.5 14.7 + - - -
434A SER 3.1 2.8 - - - -
435A MET* 1.3 79.8 - - - +
437A GLN* 1.3 61.5 + - - +
439A GLN* 4.3 5.2 + - - +
440A GLY* 4.5 6.2 + - - -
951A ASP* 4.6 1.9 - - - +
955A LYS* 4.5 9.2 + - - -
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Residues in contact with GLN 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASN* 5.3 0.4 - - - +
433A LYS 5.1 4.3 - - - +
434A SER 3.2 9.2 + - - +
436A GLY* 1.3 77.8 - - - +
438A ILE* 1.3 60.6 + - - +
439A GLN 3.6 0.2 - - - -
440A GLY* 4.3 1.8 + - - -
441A ALA* 4.1 1.9 + - - +
947A GLU* 3.8 17.5 - - - +
948A PHE* 3.5 39.8 - - + +
951A ASP* 3.5 44.7 + - - +
952A LEU* 4.8 12.4 - - - +
955A LYS* 3.7 19.1 - - - +
956A GLU* 5.5 3.4 - - - +
970A MET* 5.4 5.7 - - - +
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Residues in contact with ILE 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A VAL* 4.2 20.0 - - + +
412A VAL* 4.5 11.7 - - + +
415A ASN* 3.1 42.8 - - + +
434A SER* 3.1 36.7 + - - +
435A MET* 3.6 14.6 - - + +
436A GLY 3.4 0.2 - - - -
437A GLN* 1.3 78.1 - - - +
439A GLN* 1.3 60.2 + - - +
440A GLY 3.4 0.9 - - - -
441A ALA* 3.1 8.3 + - + +
442A LEU* 2.9 50.7 + - + +
948A PHE* 4.8 4.7 - - + -
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Residues in contact with GLN 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A MET* 3.0 26.0 + - + +
436A GLY* 4.8 3.9 + - - +
437A GLN 3.6 0.2 - - - -
438A ILE* 1.3 77.3 - - - +
440A GLY* 1.3 68.9 + - - +
442A LEU* 4.4 9.6 - - + -
443A VAL* 3.2 41.4 + - + +
486A LEU* 4.9 8.5 - - + -
891A LEU* 5.4 3.8 - - - +
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Residues in contact with GLY 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLY 4.5 6.7 + - - -
437A GLN 4.3 2.6 + - - -
438A ILE 3.4 0.6 - - - -
439A GLN* 1.3 88.2 + - - +
441A ALA* 1.3 59.5 + - - +
444A GLY* 3.3 17.5 + - - -
891A LEU* 3.9 13.7 - - - +
892A TYR* 3.9 0.2 + - - -
947A GLU* 3.1 25.2 - - - +
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Residues in contact with ALA 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A VAL* 5.9 1.3 - - + -
437A GLN 4.4 2.0 - - - +
438A ILE* 3.1 17.3 + - + +
440A GLY* 1.3 74.6 - - - +
442A LEU* 1.3 57.3 + - + +
444A GLY 2.8 7.3 + - - -
445A ILE* 2.7 38.4 + - + +
892A TYR* 4.1 5.2 - - - -
943A ILE* 4.9 3.1 - - + -
944A LEU* 4.5 20.6 - - + -
947A GLU* 3.6 27.2 - - + +
948A PHE* 6.4 1.1 - - + -
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASP* 3.1 33.4 - - - +
411A VAL* 4.8 7.6 - - + -
412A VAL* 3.9 15.5 - - + -
435A MET* 5.2 7.2 - - - -
438A ILE* 2.9 43.6 + - + +
439A GLN* 3.3 6.0 + - - +
441A ALA* 1.3 74.1 - - + +
443A VAL* 1.3 58.2 + - - +
445A ILE* 3.6 11.3 - - + +
446A ALA* 3.1 25.1 + - - +
482A VAL* 3.9 12.3 - - + +
485A ALA* 3.6 23.6 - - + +
486A LEU* 3.9 20.9 - - + -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLN* 3.2 30.5 + - + +
442A LEU* 1.3 75.3 - - - +
444A GLY* 1.3 65.8 - - - +
446A ALA* 3.5 6.9 - - + +
447A MET* 3.4 28.1 + - + +
482A VAL* 5.1 2.2 - - + -
486A LEU* 4.3 27.8 - - + -
891A LEU* 3.9 16.1 - - + +
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Residues in contact with GLY 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A GLY 3.3 6.5 + - - -
441A ALA 2.8 7.9 + - - -
443A VAL* 1.3 74.2 - - - +
445A ILE* 1.3 67.0 + - - +
447A MET* 2.9 17.5 + - - +
448A VAL* 3.2 14.4 + - - +
891A LEU* 3.5 23.3 - - - +
892A TYR* 3.2 16.2 - - - -
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Residues in contact with ILE 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASP* 3.5 23.1 - - - +
441A ALA* 2.7 28.1 + - + +
442A LEU* 3.6 16.4 - - + +
444A GLY* 1.3 69.1 - - - -
446A ALA* 1.3 55.5 + - - +
448A VAL* 2.8 10.7 + - - -
449A LEU* 2.7 47.4 + - + +
482A VAL* 5.6 0.2 - - + -
892A TYR* 3.1 5.5 + - - -
939A ALA* 5.4 0.4 - - + -
940A LYS* 3.4 50.7 - - + +
943A ILE* 3.5 35.9 - - + -
944A LEU* 5.5 2.5 - - + -
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A LEU 3.1 21.7 + - - +
443A VAL* 3.5 12.1 - - + +
444A GLY 3.1 0.4 - - - -
445A ILE* 1.3 79.5 - - - +
447A MET* 1.3 71.3 + - + +
449A LEU* 3.4 11.0 + - - +
450A SER* 3.4 6.9 + - - -
478A MET* 3.3 26.7 - - + +
479A ALA* 6.3 0.4 - - - -
482A VAL* 3.6 23.6 - - + -
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Residues in contact with MET 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A VAL* 3.4 21.8 - - + +
444A GLY 2.9 13.2 + - - +
446A ALA* 1.3 82.4 - - + +
448A VAL* 1.3 56.9 + - - +
450A SER* 2.8 25.6 + - - +
451A ALA 3.0 10.6 + - - -
478A MET* 6.4 0.4 - - - -
887A CYS* 3.3 36.2 - - + +
890A ALA* 5.1 6.1 - - + -
891A LEU* 4.3 10.8 - - + -
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A GLY 3.2 19.3 - - - +
445A ILE* 2.8 13.6 + - - +
447A MET* 1.3 69.6 - - - +
449A LEU* 1.3 62.6 + - - +
451A ALA* 3.5 13.7 + - - +
452A VAL* 3.9 12.3 + - - +
884A VAL* 3.8 31.9 - - + +
887A CYS* 3.9 10.5 - - + +
888A LEU* 3.4 37.5 - - + -
892A TYR* 4.3 1.1 - - + -
901A VAL* 5.0 3.4 - - + -
936A GLY* 5.9 0.7 - - - -
939A ALA* 5.0 11.1 - - + +
943A ILE* 3.8 12.6 - - + -
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 3.8 32.5 - - + -
408A ASP* 5.3 4.0 - - - +
445A ILE* 2.7 50.5 + - + +
446A ALA* 3.7 3.8 - - - +
448A VAL* 1.3 70.7 - - - +
450A SER* 1.3 60.4 + - - +
451A ALA 3.1 5.3 + - - -
452A VAL* 3.7 5.1 + - - +
453A PHE* 3.4 32.3 + - + +
478A MET* 3.4 31.0 - - + +
481A SER* 5.9 0.9 - - - +
482A VAL* 5.4 1.6 - - + -
936A GLY* 3.5 35.9 - - - +
939A ALA* 5.1 3.8 - - + -
940A LYS* 5.2 6.7 - - + +
----------------------------------------------------------
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Residues in contact with SER 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ALA 3.4 2.6 + - - -
447A MET* 2.8 30.5 + - - +
449A LEU* 1.3 74.4 - - - +
451A ALA* 1.3 57.1 + - - +
452A VAL 3.4 0.9 - - - -
453A PHE 4.0 0.7 - - - -
454A VAL* 3.4 25.8 - - - +
455A PRO* 3.0 21.3 - - - +
475A VAL* 4.6 2.2 - - - -
478A MET* 3.2 27.3 - - - +
883A VAL* 4.4 5.0 - - - +
887A CYS* 4.9 2.4 - - - -
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A MET 3.0 15.1 + - - +
448A VAL* 3.5 13.9 - - - +
449A LEU 3.1 1.0 - - - -
450A SER* 1.3 77.1 - - - +
452A VAL* 1.3 59.2 + - - +
455A PRO* 3.0 16.3 - - - +
880A SER* 3.2 18.7 - - - +
883A VAL* 3.3 38.2 - - + +
884A VAL* 3.4 13.3 + - + +
----------------------------------------------------------
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Residues in contact with VAL 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL 4.3 8.1 - - - +
449A LEU 3.7 5.2 - - - +
451A ALA* 1.3 77.9 - - - +
453A PHE* 1.3 82.5 + - + +
455A PRO* 3.8 1.1 - - - -
456A MET* 3.6 3.3 - - - +
877A TYR* 6.4 0.4 - - + -
880A SER* 3.2 27.9 + - - +
884A VAL* 3.2 28.0 - - + -
932A LEU* 3.6 33.2 - - + +
935A ILE* 3.9 27.1 - - + -
936A GLY* 4.8 6.3 - - - +
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Residues in contact with PHE 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A LEU* 5.2 5.2 - - + -
449A LEU* 3.4 18.9 + - + +
452A VAL* 1.3 89.0 - - + +
454A VAL* 1.3 54.9 + - - +
456A MET* 3.1 5.9 + - - +
457A ALA 2.8 24.1 + - - -
471A SER* 2.7 43.4 + - - -
474A ILE* 3.4 40.6 - - + -
475A VAL* 3.3 19.1 - - + -
478A MET* 5.2 1.1 - - + -
929A VAL* 4.8 1.8 - - + -
932A LEU* 3.5 40.6 - - + -
933A THR* 3.5 28.7 - - + -
936A GLY* 5.1 5.4 - - - -
----------------------------------------------------------
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Residues in contact with VAL 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A SER* 3.4 23.5 + - - +
453A PHE* 1.3 69.5 - - - +
455A PRO* 1.3 72.3 - - + +
457A ALA* 3.0 23.7 + - + +
458A PHE* 3.7 22.3 + - + -
471A SER* 4.6 0.2 - - - +
472A ILE* 6.1 0.4 - - - -
475A VAL* 3.4 37.0 - - + -
----------------------------------------------------------
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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
------------------------------------------------------------
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