Contacts of the helix formed by residues 647 - 671 (chain D) in PDB entry 3F7F
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 PHE 647 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579D ILE* 3.6 32.8 - - + -
580D PRO* 3.8 29.4 - - + -
583D LEU* 3.9 5.2 - - + -
637D PHE* 3.6 29.4 - + + -
642D LEU* 4.0 28.3 - - + -
643D ASP 3.0 20.3 + - - +
644D THR 4.1 1.1 - - - -
646D ILE* 1.3 95.0 - - + +
648D GLY* 1.3 54.8 + - - +
649D GLN 3.1 3.3 + - - -
650D HIS* 3.2 22.6 + + + +
651D ILE* 2.7 41.6 + - + +
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Residues in contact with GLY 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D THR 3.2 20.0 + - - -
645D GLU* 3.2 9.2 + - - -
646D ILE 3.1 5.5 - - - -
647D PHE* 1.3 77.6 - - - +
649D GLN* 1.3 62.0 + - - +
651D ILE* 3.9 4.8 - - - +
652D SER* 3.1 24.8 + - - -
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Residues in contact with GLN 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645D GLU 4.8 0.6 + - - -
646D ILE 4.3 5.6 + - - +
647D PHE 3.1 0.6 - - - -
648D GLY* 1.3 74.9 - - - +
650D HIS* 1.3 71.8 - - + +
652D SER* 3.0 15.3 + - - -
653D THR* 2.9 46.2 + - - +
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Residues in contact with HIS 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580D PRO* 4.4 5.7 + - + +
583D LEU* 4.2 14.5 - - + +
584D ASN* 4.1 39.6 + - - -
587D ILE* 3.4 31.0 - - + +
588D ASN* 4.2 10.1 - - - -
637D PHE* 5.0 1.1 - - + -
646D ILE 5.7 0.9 - - - -
647D PHE* 3.2 36.6 + + + +
649D GLN* 1.3 84.7 - - + +
651D ILE* 1.3 57.9 + - - +
653D THR* 3.1 4.1 + - - -
654D LEU* 2.8 41.0 + - + +
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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
----------------------------------------------------------
546D THR* 4.4 8.7 - - + +
550D PHE* 3.7 32.3 - - + -
634D LEU* 4.1 3.9 - - + +
637D PHE* 3.9 33.9 - - + -
642D LEU 5.4 1.1 - - - +
644D THR* 4.0 29.2 - - - +
647D PHE* 2.7 35.9 + - + +
648D GLY* 3.9 4.5 - - - +
650D HIS* 1.3 71.9 - - - +
652D SER* 1.3 58.3 + - - +
654D LEU* 3.7 7.6 - - - +
655D LEU* 3.0 40.1 + - + +
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Residues in contact with SER 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D GLY 3.1 13.7 + - - -
649D GLN* 3.0 24.6 + - - -
651D ILE* 1.3 78.9 - - - +
653D THR* 1.3 63.9 + - - +
655D LEU* 4.1 8.2 - - - +
656D ASP* 3.2 23.0 + - - +
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Residues in contact with THR 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D ILE* 3.8 27.4 - - + -
592D LYS* 3.9 31.0 + - - +
649D GLN* 2.9 37.0 + - - +
650D HIS* 3.7 8.1 + - - -
652D SER* 1.3 74.8 - - - +
654D LEU* 1.3 62.1 + - - +
656D ASP* 3.4 6.0 + - + +
657D LEU* 2.9 32.4 + - + +
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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
----------------------------------------------------------
583D LEU* 5.2 0.4 - - + -
586D LEU* 5.7 1.3 - - + -
587D ILE* 3.7 29.6 - - + -
591D MET* 5.0 8.7 - - - -
630D THR* 3.7 22.8 - - + +
633D VAL* 3.8 31.4 - - + -
634D LEU* 3.5 25.6 - - + -
637D PHE* 4.0 13.7 - - + -
650D HIS* 2.8 26.8 + - + +
651D ILE* 3.7 0.7 - - - +
653D THR* 1.3 74.9 - - - +
655D LEU* 1.3 60.0 + - - +
657D LEU* 3.0 9.5 + - + +
658D HIS* 2.8 32.1 + - - +
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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
----------------------------------------------------------
532D PHE* 3.6 45.5 - - + +
535D ILE* 4.1 28.5 - - + -
536D ILE* 3.6 20.6 - - + +
546D THR* 6.4 0.2 - - + -
550D PHE* 4.7 4.7 - - + -
634D LEU* 3.7 19.3 - - + -
651D ILE* 3.0 38.1 + - + +
652D SER* 4.1 7.4 - - - +
654D LEU* 1.3 76.0 - - - +
656D ASP* 1.3 60.7 + - - +
658D HIS* 3.9 5.8 + - - +
659D TYR* 3.2 21.8 + - - +
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Residues in contact with ASP 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536D ILE* 4.4 10.7 - - + +
592D LYS* 6.0 0.9 - - - -
652D SER 3.2 19.5 + - - +
653D THR* 3.6 6.8 - - - +
654D LEU 3.1 0.4 - - - -
655D LEU* 1.3 77.1 - - - +
657D LEU* 1.3 69.4 + - - +
659D TYR* 3.5 4.5 + - - +
660D LYS* 2.6 61.8 + - - +
714D ILE* 3.7 15.1 - - - +
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Residues in contact with LEU 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D ILE* 4.9 5.2 - - + -
591D MET* 4.4 22.7 - - + -
592D LYS* 4.3 22.9 - - + -
630D THR* 4.7 1.6 - - + -
653D THR* 2.9 37.6 + - + +
654D LEU* 3.0 9.4 + - + +
656D ASP* 1.3 80.4 - - - +
658D HIS* 1.3 60.9 + - - +
660D LYS* 3.4 4.5 + - + +
661D GLN* 2.8 45.3 + - - +
710D TYR* 3.4 51.0 - - + +
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Residues in contact with HIS 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D SER* 2.8 48.2 + - - -
532D PHE* 3.6 17.1 - - + +
533D LEU* 4.0 17.6 - - + +
627D TYR* 3.4 24.5 - + - -
630D THR* 3.7 8.9 - - + +
631D LEU* 3.7 21.9 - - + +
634D LEU* 3.9 13.7 - - + -
654D LEU 2.8 16.3 + - - +
655D LEU 3.9 5.6 + - - +
657D LEU* 1.3 78.1 - - - +
659D TYR* 1.3 59.2 + - - +
661D GLN* 3.1 14.5 + - - +
662D PHE* 2.8 30.8 + - + +
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Residues in contact with TYR 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D LEU* 3.4 29.6 - - + -
536D ILE* 3.6 33.2 - - + -
537D THR* 3.9 19.7 - - + +
655D LEU 3.2 15.8 + - - +
656D ASP* 3.7 5.6 - - - +
657D LEU 3.3 0.2 - - - -
658D HIS* 1.3 80.2 + - - +
660D LYS* 1.3 63.8 + - - +
662D PHE* 3.4 2.1 + - - +
663D LEU* 3.0 51.4 + - + +
714D ILE* 3.6 36.9 + - + -
716D GLU* 3.7 6.9 + - - -
725D ARG* 3.1 30.8 - - - +
729D ILE* 4.1 10.1 - - + -
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Residues in contact with LYS 660 (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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656D ASP* 2.6 48.2 + - - +
657D LEU* 3.9 4.3 - - + +
659D TYR* 1.3 79.5 - - + +
661D GLN* 1.3 56.7 + - - +
663D LEU* 3.4 5.6 + - - +
664D LEU* 2.9 32.1 + - - +
709D VAL* 3.6 31.7 - - + +
710D TYR* 3.0 34.0 + - + +
711D ASN 4.9 0.6 - - - -
712D ALA* 3.5 20.0 + - + +
714D ILE* 3.9 26.5 - - + -
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Residues in contact with GLN 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591D MET* 3.5 8.3 - - - +
623D LEU* 4.2 21.1 - - + +
626D HIS* 3.7 1.2 + - - +
627D TYR* 3.2 35.7 - - + -
630D THR* 2.8 28.1 + - - -
657D LEU* 2.8 30.9 + - - +
658D HIS* 3.3 15.5 - - - +
660D LYS* 1.3 73.6 - - - +
662D PHE* 1.3 66.5 + - - +
664D LEU* 3.3 4.5 + - - +
665D LEU* 2.9 30.7 + - - +
710D TYR* 3.0 31.1 + - + +
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Residues in contact with PHE 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D ILE* 5.0 3.8 - - + -
398D VAL* 4.1 26.9 - - + -
529D SER* 4.1 9.2 - - - -
533D LEU* 3.5 37.7 - - + -
627D TYR* 3.7 33.3 - + + -
658D HIS* 2.8 18.9 + - + +
659D TYR 3.6 3.6 - - - +
661D GLN* 1.3 74.8 - - - +
663D LEU* 1.3 67.7 + - - +
665D LEU* 2.9 6.5 + - - +
666D ASN* 2.7 43.2 + - + +
729D ILE* 3.8 27.1 - - + -
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Residues in contact with LEU 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659D TYR* 3.0 47.4 + - + +
660D LYS* 3.6 6.1 - - - +
662D PHE* 1.3 78.4 - - + +
664D LEU* 1.3 57.9 + - - +
666D ASN* 3.0 8.5 + - + +
667D LEU* 2.8 44.1 + - + +
714D ILE* 4.9 8.7 - - + -
725D ARG* 5.3 6.1 - - + -
729D ILE* 3.3 41.7 - - + -
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Residues in contact with LEU 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D LEU* 6.3 0.2 - - + -
619D LEU* 4.0 20.2 - - + +
620D HIS* 5.4 2.7 - - + -
623D LEU* 2.9 40.4 - - + -
660D LYS 2.9 20.2 + - - +
661D GLN 3.7 3.4 - - - +
663D LEU* 1.3 72.5 - - - +
665D LEU* 1.3 61.3 + - + +
667D LEU* 3.1 10.4 + - + +
668D TYR* 2.8 29.5 + - + +
675D LEU* 4.0 31.4 - - + -
679D LEU* 4.4 7.9 - - + -
709D VAL* 4.1 22.0 - - + -
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Residues in contact with LEU 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D VAL* 3.8 30.5 - - + -
620D HIS* 3.3 28.3 - - + +
623D LEU* 4.3 10.5 - - + +
624D SER* 3.3 33.9 - - - +
627D TYR* 3.9 30.7 - - + -
661D GLN 2.9 21.1 + - - +
662D PHE* 3.4 3.6 - - - +
664D LEU* 1.3 79.0 - - + +
666D ASN* 1.3 61.7 + - - +
668D TYR* 3.5 4.8 + - - +
669D ARG* 3.0 35.5 + - - +
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Residues in contact with ASN 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D VAL* 4.1 14.5 - - + +
400D LYS* 4.0 15.6 + - - +
662D PHE* 2.7 35.9 + - + +
663D LEU* 3.2 14.8 - - - +
665D LEU* 1.3 75.6 - - - +
667D LEU* 1.3 65.1 + - + +
669D ARG* 3.5 8.1 + - - +
670D GLN* 3.1 47.5 + - - +
728D ILE* 3.4 27.0 + - - +
729D ILE* 4.2 4.9 - - + +
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Residues in contact with LEU 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663D LEU* 2.8 34.0 + - + +
664D LEU* 3.7 8.5 - - + +
666D ASN* 1.3 73.6 - - + +
668D TYR* 1.3 65.0 + - - +
670D GLN* 3.8 7.0 - - + +
671D ASP* 3.1 26.5 + - - +
675D LEU* 4.2 27.4 - - + +
678D VAL* 5.8 4.0 - - + -
728D ILE* 4.2 28.7 - - + -
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Residues in contact with TYR 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D VAL* 4.1 12.1 - - + +
616D LEU* 4.1 25.6 - - + -
617D GLU* 2.5 41.0 + - - -
620D HIS* 3.1 56.5 - + + -
664D LEU* 2.8 18.3 + - + +
665D LEU* 3.5 4.5 - - - +
666D ASN 3.2 0.2 - - - -
667D LEU* 1.3 79.2 - - - +
669D ARG* 1.3 72.7 + - + +
672D LYS* 3.3 54.9 + - + +
675D LEU* 3.6 13.6 - - + +
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Residues in contact with ARG 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390D GLN* 5.0 5.1 + - - -
396D ASP* 2.9 33.1 + - - -
398D VAL* 3.5 16.5 - - + +
399D THR* 3.1 38.1 + - + +
400D LYS 5.7 0.2 - - - +
406D ARG* 5.5 3.1 + - - -
410D ASN* 5.7 2.6 - - - +
413D SER* 2.8 28.5 + - - +
414D ARG* 6.5 0.4 - - - -
620D HIS* 2.6 38.3 + - - -
624D SER* 4.5 2.0 + - - -
665D LEU* 3.0 30.4 + - - +
666D ASN* 3.8 9.9 - - - +
668D TYR* 1.3 86.5 - - + +
670D GLN* 1.3 59.8 + - - +
672D LYS* 4.4 2.7 - - - +
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Residues in contact with GLN 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D LYS* 3.5 14.9 - - - +
406D ARG* 3.8 33.1 - - - +
413D SER* 4.7 3.8 + - - -
666D ASN* 3.1 35.3 + - - +
667D LEU* 3.2 10.0 + - + +
669D ARG* 1.3 81.6 - - - +
671D ASP* 1.3 66.2 + - + +
728D ILE* 3.9 20.1 - - + +
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Residues in contact with ASP 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D SER* 5.3 2.0 - - - -
667D LEU 3.1 10.2 + - - +
669D ARG 3.4 1.0 - - - -
670D GLN* 1.3 85.5 - - + +
672D LYS* 1.3 63.4 + - - +
673D CYS* 3.4 9.0 + - - +
674D LEU* 3.0 40.7 + - + +
675D LEU* 3.0 18.2 + - - +
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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