Contacts of the helix formed by residues 636 - 658 (chain D) in PDB entry 1JFZ
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 TYR 636 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623D LYS 3.3 8.1 - - - +
624D ALA 3.5 18.8 - - - +
626D THR 2.8 24.8 + - - -
627D HIS* 3.0 45.0 + + + -
628D VAL* 4.8 3.8 - - + -
635D HIS* 1.3 76.5 - + + +
637D GLU* 1.3 60.8 + - + +
638D THR 3.4 2.0 - - - -
639D LEU* 3.1 7.7 + - - +
640D GLU* 2.6 42.7 + - + +
704D ILE* 3.3 23.2 - - + +
707D ASP* 3.5 32.1 + - + -
708D VAL* 3.8 20.0 - - + -
711D ALA* 3.5 11.2 - - + -
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Residues in contact with GLU 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C LYS 4.9 5.6 - - - +
463C ARG* 4.6 5.6 - - - +
464C GLU* 3.3 43.1 + - + +
467C LEU* 6.0 0.4 - - + -
628D VAL* 6.1 0.4 - - + -
635D HIS* 2.9 34.9 + - + +
636D TYR* 1.3 86.8 - - + +
638D THR* 1.3 68.5 + - - +
640D GLU* 3.1 16.5 + - + +
641D PHE* 3.1 11.4 + - - +
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Residues in contact with THR 638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C VAL* 3.4 29.6 - - + +
462C LYS* 3.5 39.2 + - + +
467C LEU* 5.3 5.6 - - + -
623D LYS* 5.4 11.9 + - - -
635D HIS* 4.9 1.6 + - - -
636D TYR 3.4 0.2 - - - -
637D GLU* 1.3 78.4 - - - +
639D LEU* 1.3 63.6 + - + +
641D PHE* 2.9 31.4 + - + +
642D LEU* 3.3 6.2 + - - +
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Residues in contact with LEU 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D LEU* 3.9 18.6 - - + +
623D LYS* 3.9 24.9 - - + +
624D ALA* 3.6 35.2 - - + +
635D HIS 5.3 0.2 + - - -
636D TYR* 3.1 10.6 + - - +
638D THR* 1.3 81.9 - - + +
640D GLU* 1.3 57.1 + - - +
642D LEU* 3.5 3.3 + - + +
643D GLY* 2.9 22.9 + - - -
711D ALA* 3.9 13.6 - - + +
714D ALA* 3.0 13.2 - - + +
715D ALA* 4.3 15.7 - - + +
718D ILE* 3.5 31.9 - - + -
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Residues in contact with GLU 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C GLU* 5.3 4.1 - - - +
636D TYR* 2.6 31.1 + - + +
637D GLU* 3.4 10.8 - - + +
639D LEU* 1.3 70.2 - - - +
641D PHE* 1.3 72.7 + - - +
644D ASP* 2.9 27.4 + - - +
707D ASP* 3.2 26.1 - - + +
710D GLU* 2.4 12.3 - - - +
711D ALA* 3.9 11.6 - - - +
764D MN 2.4 35.5 + - - -
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Residues in contact with PHE 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C VAL* 3.9 28.9 - - + +
455C LEU* 4.8 9.4 - - + -
456C VAL* 4.8 8.3 - - + -
464C GLU* 2.8 43.1 - - - +
467C LEU* 3.4 48.9 - - + -
468C SER* 4.4 7.4 - - - -
471C LYS* 4.1 23.6 - - + -
637D GLU 3.1 3.1 + - - +
638D THR* 2.9 19.6 + - + +
640D GLU* 1.3 87.9 - - - +
642D LEU* 1.3 60.6 + - - +
644D ASP* 3.6 17.1 + - - +
645D ALA* 3.7 3.3 + - - +
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Residues in contact with LEU 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C PHE* 4.3 16.2 - - + -
452C VAL* 3.8 11.9 - - + -
453C ASP* 3.6 35.2 - - + +
456C VAL* 3.8 24.4 - - + +
638D THR 3.3 6.2 + - - +
639D LEU* 3.9 7.6 - - + +
641D PHE* 1.3 79.8 - - - +
643D GLY* 1.3 64.5 + - - +
645D ALA* 3.1 4.9 + - - +
646D LEU* 2.9 21.9 + - + +
714D ALA* 4.3 4.7 - - + -
717D TYR* 4.0 21.5 - - + -
718D ILE* 4.3 15.5 - - + -
722D ARG* 3.9 14.4 - - - +
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Residues in contact with GLY 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639D LEU 2.9 10.5 + - - -
640D GLU 3.2 2.0 + - - -
642D LEU* 1.3 75.9 - - - +
644D ASP* 1.3 54.4 + - - +
646D LEU* 3.0 7.1 + - - +
647D VAL* 2.6 37.9 + - - +
710D GLU* 3.1 32.5 - - - -
713D TRP 5.3 0.2 - - - -
714D ALA* 3.5 9.6 - - - +
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Residues in contact with ASP 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C ASN* 5.7 2.0 + - - -
471C LYS* 5.5 6.2 - - - -
640D GLU* 2.9 21.6 + - - +
641D PHE* 3.6 10.6 - - - +
643D GLY* 1.3 74.5 - - - +
645D ALA* 1.3 59.4 + - - +
647D VAL* 4.5 0.6 - - - +
648D ASN* 3.0 33.4 + - - +
675D ILE* 6.0 2.3 - - - +
680D PHE* 5.9 0.2 - - - -
710D GLU* 3.2 30.5 - - - +
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Residues in contact with ALA 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C ALA 4.5 1.4 - - - +
448C ASN* 3.8 22.2 - - - +
449C PHE* 3.8 16.4 - - - +
452C VAL* 3.7 33.4 - - + -
471C LYS* 5.9 0.2 - - - -
641D PHE 3.7 1.7 + - - +
642D LEU* 3.1 10.8 + - + +
644D ASP* 1.3 81.4 - - - +
646D LEU* 1.3 61.4 + - - +
648D ASN* 3.7 5.0 + - - +
649D PHE* 3.2 22.9 + - - +
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Residues in contact with LEU 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C PHE* 4.0 32.7 - - + -
642D LEU* 2.9 14.7 + - + +
643D GLY* 3.2 8.5 - - - +
645D ALA* 1.3 74.7 - - - +
647D VAL* 1.3 67.5 + - - +
649D PHE* 3.3 5.3 + - + +
650D PHE* 3.1 62.5 + - + -
713D TRP* 3.1 38.4 - - + +
714D ALA* 3.9 2.9 - - - +
717D TYR* 3.6 26.0 - - + -
724D ALA* 5.5 0.4 - - + -
727D THR* 4.6 0.7 - - + -
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Residues in contact with VAL 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D GLY 2.6 20.6 + - - +
644D ASP 4.5 0.7 - - - +
646D LEU* 1.3 75.0 - - - +
648D ASN* 1.3 61.4 + - - +
650D PHE* 3.1 8.5 + - + +
651D ILE* 2.8 47.7 + - + +
675D ILE* 5.9 0.2 - - + -
680D PHE* 3.3 34.5 - - + -
709D PHE* 4.6 3.6 - - + -
710D GLU* 4.9 7.2 - - + -
713D TRP* 3.7 33.0 - - + -
731D PHE* 3.9 21.1 - - + -
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Residues in contact with ASN 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444C ASP* 5.5 1.8 + - - -
445C ALA* 3.6 26.9 - - - +
448C ASN* 4.4 11.3 - - - +
644D ASP* 3.0 24.8 + - - +
645D ALA* 3.7 7.0 + - - +
647D VAL* 1.3 78.9 - - - +
649D PHE* 1.3 58.0 + - - +
651D ILE* 3.1 7.0 + - - +
652D VAL* 2.7 35.5 + - - +
671D LYS* 3.2 27.3 + - - +
675D ILE* 4.0 21.4 - - + +
680D PHE* 5.6 0.6 - - - -
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Residues in contact with PHE 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C LEU* 4.7 5.6 - - + -
445C ALA* 3.9 23.1 - - - +
446C LEU* 4.1 24.0 - - + -
449C PHE* 4.1 24.5 - + + -
517C TYR* 3.6 41.3 - + - -
524C ALA* 4.0 22.0 - - + -
645D ALA 3.2 11.6 + - - +
646D LEU* 3.3 6.5 + - + +
648D ASN* 1.3 79.5 - - - +
650D PHE* 1.3 97.8 + + - +
652D VAL* 3.7 0.2 - - - +
653D ASP* 2.9 31.8 + - + +
724D ALA* 5.0 1.8 - - + -
728D ARG* 4.6 5.4 - - + -
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Residues in contact with PHE 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646D LEU* 3.1 36.7 + - + -
647D VAL* 3.1 14.4 + - + +
649D PHE* 1.3 106.6 - + - +
651D ILE* 1.3 59.8 + - - +
653D ASP* 4.8 0.4 - - - -
654D LEU* 3.4 6.6 + - - +
713D TRP* 5.0 2.2 - + - -
724D ALA* 3.9 7.4 - - - -
727D THR* 3.6 27.6 - - + -
728D ARG* 3.6 34.5 - - + -
731D PHE* 3.7 41.7 - + + -
732D TYR* 2.7 33.5 + - + -
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Residues in contact with ILE 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647D VAL* 2.8 46.6 + - + +
648D ASN 3.6 5.6 - - - +
650D PHE* 1.3 74.3 - - - +
652D VAL* 1.3 71.2 + - + +
653D ASP 3.2 0.2 - - - -
654D LEU* 3.3 5.8 + - - +
655D LEU* 3.1 25.1 + - + +
671D LYS* 5.2 2.9 - - + +
674D LEU* 3.7 45.8 - - + +
675D ILE* 4.0 17.5 - - + -
679D PHE* 5.5 0.2 - - + -
680D PHE* 4.9 1.3 - - + -
683D LEU* 5.9 0.2 - - + -
731D PHE* 3.5 25.8 - - + -
739D ILE* 3.8 17.5 - - + +
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Residues in contact with VAL 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C PHE* 3.4 38.1 - - + +
442C LEU* 3.8 13.9 - - + -
445C ALA* 3.3 27.8 - - + -
648D ASN* 2.7 39.4 + - - +
649D PHE 3.7 1.3 - - - +
651D ILE* 1.3 78.9 - - + +
653D ASP* 1.3 62.5 - - - +
655D LEU* 3.4 8.3 + - - +
656D VAL* 3.1 22.6 + - + +
671D LYS* 4.3 18.4 - - + +
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Residues in contact with ASP 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C LEU* 3.7 16.6 - - + +
517C TYR* 2.8 37.0 + - - -
522C ARG* 3.0 38.7 + - - -
649D PHE* 2.9 22.6 + - + +
650D PHE* 4.8 0.2 - - - -
652D VAL* 1.3 75.9 - - - +
654D LEU* 1.3 66.9 + - - +
656D VAL* 3.5 5.3 + - - +
657D GLN* 3.2 25.4 + - - +
728D ARG* 4.8 2.1 + - - -
732D TYR* 3.6 16.6 + - - +
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Residues in contact with LEU 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D PHE 3.4 5.9 + - - +
651D ILE* 3.3 8.6 + - - +
653D ASP* 1.3 78.7 - - - +
655D LEU* 1.3 54.0 + - - +
657D GLN* 2.9 11.9 + - - +
658D TYR* 2.8 44.5 + - + -
732D TYR* 3.4 45.8 - - + +
736D LYS* 3.8 44.6 - - + +
739D ILE* 4.2 28.3 - - + -
740D LEU* 3.9 14.6 - - + -
743D ILE* 4.4 2.2 - - + -
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Residues in contact with LEU 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C PHE* 4.0 13.9 - - + -
651D ILE* 3.1 10.6 + - + +
652D VAL* 3.4 11.9 - - - +
654D LEU* 1.3 79.3 - - - +
656D VAL* 1.3 63.2 + - + +
657D GLN 3.2 0.5 + - - -
659D SER* 3.0 46.7 + - - +
667D LEU* 3.6 30.9 - - + +
670D LEU* 3.9 23.8 - - + -
671D LYS* 3.7 26.5 - - + +
674D LEU* 4.0 15.0 - - + -
739D ILE* 5.6 0.2 - - - +
743D ILE* 3.9 12.2 - - + +
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Residues in contact with VAL 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C THR* 3.6 28.5 - - + +
439C LEU* 6.1 2.0 - - + -
441C PHE* 3.9 25.4 - - + -
442C LEU* 4.2 28.0 - - + -
518C ILE* 5.9 3.1 - - + -
522C ARG* 5.1 6.1 - - - +
652D VAL* 3.1 17.3 + - + +
653D ASP* 4.1 5.4 - - - +
654D LEU 3.2 0.6 + - - -
655D LEU* 1.3 77.8 - - - +
657D GLN* 1.3 51.4 + - + +
662D LYS* 2.5 36.9 + - - +
667D LEU* 4.4 9.9 - - + -
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Residues in contact with GLN 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522C ARG* 3.3 51.5 + - - +
653D ASP* 3.2 24.2 + - - +
654D LEU* 2.9 14.6 + - - +
656D VAL* 1.3 80.1 - - + +
658D TYR* 1.3 86.2 + - + +
659D SER 3.5 2.2 + - - +
662D LYS* 4.2 8.7 + - - +
732D TYR* 5.2 2.6 + - - -
736D LYS* 5.8 0.4 - - - +
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Residues in contact with TYR 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654D LEU* 2.8 33.2 + - + +
655D LEU 3.9 1.1 - - - -
657D GLN* 1.3 96.8 + - + +
659D SER* 1.3 57.8 + - - +
660D PRO* 4.1 2.3 - - - +
736D LYS* 3.3 32.7 + - - -
740D LEU* 3.4 45.7 - - + +
743D ILE* 2.9 26.6 - - + +
744D LYS* 5.5 0.7 + - - -
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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