Contacts of the helix formed by residues 629 - 660 (chain D) in PDB entry 3A8P
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 ASP 629 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627D LYS* 4.5 5.4 - - + +
628D GLU* 1.3 75.0 - - - +
630D THR* 1.3 63.4 + - - +
631D VAL* 3.4 8.3 + - - +
632D ARG* 3.0 42.2 + - + +
633D LEU* 3.1 20.6 + - - +
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Residues in contact with THR 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D ALA* 3.5 30.7 + - + +
619D SER* 4.5 6.0 - - - +
622D ALA* 3.6 21.3 - - + +
628D GLU 3.2 8.7 + - - -
629D ASP* 1.3 72.5 + - - +
631D VAL* 1.3 64.2 + - - +
633D LEU* 3.1 5.1 + - + +
634D LEU* 2.9 32.7 + - + +
699D LEU* 3.7 25.8 - - + -
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Residues in contact with VAL 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D ASP* 3.4 6.6 + - - +
630D THR* 1.3 78.0 - - - +
632D ARG* 1.3 58.8 + - - +
634D LEU* 3.3 9.9 + - - +
635D LYS* 2.9 55.0 + - + +
696D LEU* 4.3 5.4 - - + -
699D LEU* 4.4 19.3 - - + -
700D GLN* 3.9 25.1 - - + +
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Residues in contact with ARG 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D ASP* 3.0 39.2 + - - +
631D VAL* 1.3 77.3 - - - +
633D LEU* 1.3 60.5 + - - +
635D LYS* 3.9 6.6 - - - +
636D SER* 2.9 32.4 + - - -
639D ARG* 4.7 4.8 + - - +
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Residues in contact with LEU 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D PHE* 4.0 15.7 - - + -
622D ALA* 3.4 33.4 - - + -
625D HIS* 3.5 40.8 - - + -
627D LYS* 4.0 25.4 - - + +
629D ASP 3.1 10.9 + - - +
630D THR* 3.1 7.7 + - - +
632D ARG* 1.3 74.0 - - - +
634D LEU* 1.3 56.4 + - + +
636D SER* 3.1 9.9 + - - +
637D GLN* 2.7 46.1 + - + +
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Residues in contact with LEU 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618D ALA* 4.3 1.3 - - + -
621D PHE* 4.1 14.4 - - + -
630D THR* 2.9 25.7 + - + +
631D VAL* 3.6 2.5 - - - +
633D LEU* 1.3 77.0 - - - +
635D LYS* 1.3 62.2 + - - +
637D GLN* 3.2 6.4 + - - +
638D THR* 2.9 28.5 + - - +
692D MET* 3.8 25.3 - - - +
695D TYR* 3.7 38.1 - - + -
696D LEU* 3.4 33.0 - - + +
699D LEU* 3.9 23.6 - - + -
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Residues in contact with LYS 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D VAL* 2.9 39.1 + - + +
632D ARG* 4.0 6.1 - - - +
634D LEU* 1.3 75.8 - - - +
636D SER* 1.3 64.1 + - - +
638D THR* 2.7 25.4 + - - +
639D ARG* 2.9 33.8 + - - +
696D LEU* 3.9 15.9 - - + -
700D GLN* 3.8 17.7 - - - +
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Residues in contact with SER 636 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632D ARG* 2.9 22.4 + - - -
633D LEU* 3.3 12.5 - - - +
635D LYS* 1.3 76.3 - - - +
637D GLN* 1.3 64.9 + - - +
639D ARG* 3.4 21.7 + - - +
640D SER* 3.2 21.8 + - - -
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Residues in contact with GLN 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D PHE* 3.8 34.4 - - + -
625D HIS* 4.4 13.4 + - - -
633D LEU* 2.7 31.9 + - + +
634D LEU 3.4 5.6 - - - +
635D LYS 3.1 0.2 - - - -
636D SER* 1.3 76.8 + - - +
638D THR* 1.3 56.8 + - - +
640D SER* 3.3 10.7 + - - -
641D LEU* 3.0 42.6 + - + +
692D MET* 3.7 15.8 - - + -
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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
----------------------------------------------------------
634D LEU 2.9 15.4 + - - +
635D LYS* 2.7 20.8 + - - +
637D GLN* 1.3 71.9 - - - +
639D ARG* 1.3 66.2 + - - +
641D LEU* 3.3 4.2 + - - +
642D LEU* 2.9 34.4 + - - +
689D LEU* 3.9 21.6 - - + +
692D MET* 3.5 25.6 - - + -
693D ARG* 4.7 5.2 - - + +
696D LEU* 3.9 19.5 - - + +
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Residues in contact with ARG 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632D ARG* 4.7 4.8 + - - +
635D LYS* 2.9 30.7 + - - +
636D SER* 3.4 33.0 - - - +
638D THR* 1.3 79.8 + - - +
640D SER* 1.3 62.0 + - - +
642D LEU* 3.3 10.8 + - - +
643D GLN* 3.1 38.0 + - + +
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Residues in contact with SER 640 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636D SER 3.2 10.1 + - - -
637D GLN* 3.5 15.7 - - - -
638D THR 3.3 0.2 - - - -
639D ARG* 1.3 81.6 - - - +
641D LEU* 1.3 63.8 + - - +
643D GLN* 3.2 13.0 + - - +
644D LYS* 3.1 43.1 + - - +
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Residues in contact with LEU 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D GLN* 3.0 33.1 + - + +
638D THR* 3.3 5.6 + - - +
640D SER* 1.3 75.4 - - - +
642D LEU* 1.3 60.9 + - - +
644D LYS* 3.3 9.2 + - + +
645D ILE* 2.8 37.0 + - - +
685D PHE* 4.1 28.0 - - + +
688D ASP* 3.7 26.9 - - + +
689D LEU* 3.5 41.5 - - + +
692D MET* 3.9 12.8 - - + -
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Residues in contact with LEU 642 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638D THR* 2.9 27.6 + - - +
639D ARG* 3.5 9.2 - - - +
641D LEU* 1.3 77.0 - - - +
643D GLN* 1.3 58.0 + - + +
645D ILE* 3.9 7.9 - - + +
646D ASP* 3.0 30.3 + - - +
689D LEU* 3.6 29.8 - - + -
693D ARG* 4.1 19.3 - - - +
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Residues in contact with GLN 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D ARG* 3.1 28.0 + - + +
640D SER* 3.5 9.9 + - - +
641D LEU 3.2 0.2 - - - -
642D LEU* 1.3 79.4 - - + +
644D LYS* 1.3 61.9 + - + +
646D ASP* 3.4 6.0 + - - +
647D MET* 3.0 24.6 + - - +
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Residues in contact with LYS 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640D SER* 3.1 29.2 + - - +
641D LEU* 3.7 12.4 - - + +
643D GLN* 1.3 74.4 - - + +
645D ILE* 1.3 61.8 + - - +
647D MET* 3.4 4.6 + - - +
648D ASP* 2.9 35.1 + - - +
685D PHE* 3.8 43.5 - - + -
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Residues in contact with ILE 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641D LEU 2.8 22.6 + - - +
642D LEU* 3.9 8.7 - - + +
644D LYS* 1.3 76.1 - - - +
646D ASP* 1.3 53.7 + - - +
649D SER* 2.7 43.7 + - - +
682D LEU* 3.7 13.6 - - + +
685D PHE* 3.6 32.3 - - + +
686D HIS* 3.4 38.1 - - + +
689D LEU* 3.7 31.2 - - + -
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Residues in contact with ASP 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642D LEU 3.0 19.4 + - - +
643D GLN* 3.6 7.4 - - - +
644D LYS 3.3 0.2 - - - -
645D ILE* 1.3 78.0 - - - +
647D MET* 1.3 61.2 + - - +
649D SER* 3.0 18.3 + - - -
650D LYS* 3.1 50.1 + - - +
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Residues in contact with MET 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D GLN 3.0 17.1 + - - +
644D LYS* 3.9 4.7 - - - +
646D ASP* 1.3 77.2 + - - +
648D ASP* 1.3 62.7 + - - +
650D LYS* 3.3 20.4 + - - +
651D MET* 2.9 53.8 + - - +
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Residues in contact with ASP 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D LYS* 2.9 23.2 + - - +
647D MET* 1.3 78.1 - - - +
649D SER* 1.3 60.3 + - - +
651D MET* 3.9 8.5 - - - +
652D LYS* 3.0 28.8 + - - +
678D TRP* 3.8 21.6 + - + -
681D ASN* 3.8 22.0 + - - +
682D LEU* 3.8 19.2 - - + +
685D PHE* 3.8 20.5 - - + -
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Residues in contact with SER 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645D ILE* 2.7 29.0 + - - +
646D ASP* 3.0 13.7 + - - -
648D ASP* 1.3 77.9 - - - +
650D LYS* 1.3 59.8 + - - +
652D LYS* 3.2 5.8 + - - +
653D LYS* 2.9 27.5 + - - +
682D LEU* 3.8 21.2 - - - +
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Residues in contact with LYS 650 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646D ASP* 3.1 49.2 + - - +
647D MET* 3.7 19.2 - - - +
649D SER* 1.3 83.0 + - - +
651D MET* 1.3 65.1 + - + +
653D LYS* 2.6 55.5 + - + +
654D MET* 3.0 4.5 + - - +
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Residues in contact with MET 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D MET* 2.9 45.8 + - - +
648D ASP* 4.0 8.5 - - - +
650D LYS* 1.3 77.1 - - + +
652D LYS* 1.3 61.3 + - - +
654D MET* 3.2 9.4 + - - +
655D ALA* 3.1 22.2 + - - +
678D TRP* 3.5 39.5 - - + +
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Residues in contact with LYS 652 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D ASP 3.0 18.7 + - - +
649D SER* 3.3 6.1 - - - +
650D LYS 3.1 0.2 - - - -
651D MET* 1.3 75.5 - - - +
653D LYS* 1.3 64.3 + - - +
655D ALA 3.2 1.6 + - - -
656D GLU* 2.9 57.6 + - - +
675D ILE* 3.5 16.6 - - + +
678D TRP* 3.9 28.0 - - + -
679D GLU* 3.4 36.5 + - + +
682D LEU* 4.0 21.5 - - + -
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Residues in contact with LYS 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649D SER 2.9 10.8 + - - +
650D LYS* 2.6 59.4 + - + +
652D LYS* 1.3 76.9 - - - +
654D MET* 1.3 83.6 + - - +
656D GLU* 3.1 16.7 + - - +
657D LEU* 2.8 41.4 + - + +
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Residues in contact with MET 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D LYS 3.0 7.6 + - - +
651D MET* 3.5 13.7 - - + +
652D LYS 3.2 0.2 - - - -
653D LYS* 1.3 101.0 - - - +
655D ALA* 1.3 56.2 + - - +
657D LEU* 3.6 18.0 + - + +
658D GLN* 3.1 29.6 + - + +
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Residues in contact with ALA 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651D MET 3.1 5.1 + - - +
652D LYS 3.6 1.8 - - - +
653D LYS 3.1 0.8 - - - -
654D MET* 1.3 75.2 - - - +
656D GLU* 1.3 59.8 + - - +
657D LEU 3.1 1.3 - - - -
658D GLN* 3.1 9.7 + - - +
659D LEU 2.8 22.9 + - - -
671D ILE* 2.9 23.7 - - + +
675D ILE* 3.2 22.2 - - + -
678D TRP* 3.4 26.5 - - + -
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Residues in contact with GLU 656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D LYS* 2.9 45.0 + - - +
653D LYS* 3.6 16.4 - - - +
655D ALA* 1.3 76.3 - - - +
657D LEU* 1.3 59.8 + - + +
659D LEU* 3.1 14.1 + - + +
660D SER* 2.9 26.9 + - - -
671D ILE* 4.4 0.2 - - - -
675D ILE* 3.4 23.0 - - + +
679D GLU* 5.2 0.3 - - - +
----------------------------------------------------------
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Residues in contact with LEU 657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653D LYS* 2.8 24.5 + - + +
654D MET* 3.7 23.8 - - + +
656D GLU* 1.3 78.9 - - + +
658D GLN* 1.3 64.2 + - - +
660D SER* 2.5 29.6 + - - +
661D VAL* 3.6 9.8 - - - +
----------------------------------------------------------
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Residues in contact with GLN 658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654D MET* 3.1 20.3 + - + +
655D ALA* 3.1 14.4 - - - +
657D LEU* 1.3 75.2 - - - +
659D LEU* 1.3 62.1 + - - +
661D VAL* 3.2 18.5 + - - +
662D VAL* 3.1 31.9 + - + +
671D ILE* 4.5 7.2 - - + -
----------------------------------------------------------
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Residues in contact with LEU 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655D ALA 2.8 12.4 + - - +
656D GLU* 3.2 15.3 - - + +
657D LEU 3.1 0.2 - - - -
658D GLN* 1.3 73.7 - - - +
660D SER* 1.3 57.1 + - - +
661D VAL 2.9 11.3 + - - -
662D VAL* 3.1 18.3 + - - +
668D ARG* 3.4 53.6 + - + +
671D ILE* 3.3 35.2 - - + +
672D GLU* 3.9 22.4 - - + +
675D ILE* 5.5 2.7 - - + -
----------------------------------------------------------
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Residues in contact with SER 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656D GLU 2.9 12.7 + - - -
657D LEU* 2.5 33.6 + - - +
659D LEU* 1.3 74.6 - - - +
661D VAL* 1.3 68.7 + - - +
668D ARG* 5.6 0.2 - - - +
----------------------------------------------------------
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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