Contacts of the helix formed by residues 588 - 614 (chain D) in PDB entry 1P93
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 HIS 588 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D LEU* 1.3 73.7 - - - +
589D LEU* 1.3 80.3 + - + +
590D ASP* 2.8 41.2 + - + -
591D ASP* 2.4 44.0 + - - +
592D GLN* 2.8 9.2 + - - -
681D LYS* 3.0 33.2 - - + +
682D SER* 3.4 15.6 + - - +
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Residues in contact with LEU 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D LEU 3.3 0.4 + - - -
588D HIS* 1.3 78.7 - - + +
590D ASP* 1.3 59.4 + - - +
592D GLN* 3.2 23.6 - - + +
593D MET* 2.6 56.9 + - + +
945H ARG* 4.9 5.8 - - + +
948H LEU* 4.3 13.2 - - + -
949H ASP* 3.6 37.7 - - + +
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Residues in contact with ASP 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588D HIS* 2.8 28.9 + - + +
589D LEU* 1.3 84.2 - - - +
591D ASP* 1.3 58.2 + - - +
593D MET* 4.1 3.1 - - - +
594D THR* 3.0 38.2 + - + +
681D LYS* 2.7 36.7 + - - +
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Residues in contact with ASP 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D LEU* 4.1 8.8 - - + +
588D HIS* 2.4 36.7 + - - +
590D ASP* 1.3 70.7 - - - +
592D GLN* 1.3 54.3 + - - +
594D THR* 3.2 7.4 + - - -
595D LEU* 2.7 41.3 + - - +
680D LEU* 3.0 31.9 - - + +
681D LYS* 3.3 26.3 - - - +
682D SER* 2.8 34.8 + - - -
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Residues in contact with GLN 592 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579D LYS* 5.5 2.6 - - - +
584D PHE* 3.1 54.7 - - + +
585D ARG* 3.3 21.5 + - - -
587D LEU* 2.7 28.9 + - + +
588D HIS 2.8 10.8 + - - +
589D LEU* 3.2 29.1 - - + +
591D ASP* 1.3 77.2 - - - +
593D MET* 1.3 60.3 + - - +
595D LEU* 4.8 1.1 - - - -
596D LEU* 3.2 31.6 + - + +
948H LEU* 5.8 6.2 - - + +
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Residues in contact with MET 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589D LEU* 2.6 32.2 + - + +
590D ASP* 4.1 5.4 - - - +
592D GLN* 1.3 72.1 - - - +
594D THR* 1.3 63.5 + - + +
596D LEU* 3.5 9.5 + - + +
597D GLN* 2.8 48.7 + - + +
755D GLU* 5.8 0.2 - - + -
942H ALA* 3.5 18.2 - - - +
944H LEU* 3.3 20.6 - - + -
945H ARG* 3.0 53.6 - - + +
948H LEU* 5.2 4.0 - - + +
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Residues in contact with THR 594 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590D ASP* 3.0 29.3 + - + +
591D ASP* 3.2 8.7 + - - -
593D MET* 1.3 76.3 - - + +
595D LEU* 1.3 58.9 + - - +
597D GLN* 2.8 42.6 + - - +
598D TYR* 3.3 8.0 + - - +
676D PRO* 5.7 3.8 - - + -
680D LEU* 3.6 15.6 - - - +
681D LYS* 6.5 0.4 - - - -
760D GLN* 5.6 0.2 + - - -
763D LYS* 5.5 2.9 - - - +
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Residues in contact with LEU 595 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584D PHE* 4.5 6.7 - - + -
587D LEU* 3.7 30.1 - - + -
591D ASP 2.7 25.1 + - - +
592D GLN* 4.0 4.3 - - - +
594D THR* 1.3 69.9 + - - +
596D LEU* 1.3 61.1 + - - +
597D GLN 2.8 5.5 + - - -
598D TYR* 3.2 11.0 + - - +
599D SER* 2.9 21.7 + - - -
671D LEU* 3.6 32.5 - - + +
672D LEU* 4.7 3.8 - - + -
674D SER 3.6 24.2 - - - +
675D VAL* 5.4 0.9 - - - -
680D LEU* 4.3 21.1 - - + -
686D PHE* 4.2 18.8 - - + -
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Residues in contact with LEU 596 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D ALA* 4.8 5.4 - - + +
575D VAL* 4.5 35.9 - - + +
577D TRP* 6.1 0.9 - - + -
578D ALA* 3.6 25.8 - - + -
584D PHE* 3.7 17.7 - - + -
592D GLN* 3.2 22.5 + - + +
593D MET* 3.9 7.4 - - + +
595D LEU* 1.3 80.3 - - - +
597D GLN* 1.3 62.4 + - - +
599D SER* 3.7 6.3 - - - +
600D TRP* 3.2 28.1 + - - +
603D LEU* 5.5 4.7 - - + -
671D LEU* 4.8 9.6 - - + -
756D ILE* 5.7 0.2 - - - +
944H LEU* 6.6 0.2 - - + -
948H LEU* 5.7 7.0 - - + -
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Residues in contact with GLN 597 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593D MET* 2.8 55.1 + - + +
594D THR* 2.8 30.9 + - - +
595D LEU 2.8 1.6 - - - -
596D LEU* 1.3 79.5 - - - +
598D TYR* 1.3 57.0 + - - -
600D TRP* 3.5 13.6 - - - -
756D ILE* 4.5 8.0 - - + +
759D ASN* 3.4 22.0 + - - +
760D GLN* 3.1 32.8 - - + +
763D LYS* 3.2 24.1 + - - +
944H LEU* 5.9 0.2 - - - +
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Residues in contact with TYR 598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594D THR 3.3 6.9 + - - +
595D LEU* 3.2 5.2 + - - +
597D GLN* 1.3 77.1 - - - +
599D SER* 1.3 74.1 + - - +
600D TRP* 3.0 5.7 + - - -
601D MET* 3.7 9.9 + - - +
602D SER* 3.9 20.1 + - - -
673D SER* 4.7 1.8 - - - -
674D SER* 3.1 46.9 - - - +
726D HIS* 2.9 44.2 + + - +
729D VAL* 4.3 17.2 - - + +
733D LEU* 5.5 4.7 - - + +
760D GLN* 4.1 20.8 - - - +
764D TYR* 5.1 11.9 - + - -
769D ILE* 4.3 16.6 - - + -
771D LYS* 4.1 7.5 - - + +
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Residues in contact with SER 599 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595D LEU 2.9 20.4 + - - -
596D LEU* 3.7 7.6 - - - -
598D TYR* 1.3 87.9 - - - +
600D TRP* 1.3 56.8 + - - +
601D MET 3.2 0.4 - - - -
602D SER* 2.8 7.5 + - - -
603D LEU* 2.6 47.9 + - - +
670D LEU 3.5 7.0 - - - -
671D LEU* 3.4 37.9 - - - +
674D SER 6.1 0.4 - - - -
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Residues in contact with TRP 600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D VAL* 4.1 23.3 - - + -
596D LEU* 3.2 15.0 + - - +
597D GLN 3.5 21.8 - - - -
598D TYR 3.0 5.9 + - - -
599D SER* 1.3 79.1 + - - +
601D MET* 1.3 97.0 + - + +
603D LEU* 3.7 9.4 + - - +
604D MET* 2.9 39.0 + - + +
733D LEU* 4.6 11.3 - - + +
736D CYS* 4.9 1.8 - - - -
753D LEU* 3.9 27.8 - - + -
756D ILE* 3.4 28.2 - - + +
757D ILE* 4.7 16.2 - - + +
760D GLN* 5.2 3.4 + - + +
761D ILE* 6.3 0.6 - - - +
4999D DEX 3.8 30.5 - - + -
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Residues in contact with MET 601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598D TYR 3.7 3.0 + - - +
599D SER 3.0 1.0 + - - -
600D TRP* 1.3 111.2 - - + +
602D SER* 1.3 70.0 + - - +
603D LEU 2.8 3.5 + - - -
604D MET* 2.9 12.4 + - - +
605D ALA* 2.9 13.9 + - - +
729D VAL* 3.9 23.1 - - + -
732D LEU* 3.7 19.1 - - + +
733D LEU* 3.5 29.8 - - + -
736D CYS* 3.7 12.8 - - + -
4999D DEX 3.5 56.1 - - + -
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Residues in contact with SER 602 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598D TYR* 3.9 17.7 + - - -
599D SER* 3.1 23.7 - - - -
601D MET* 1.3 78.2 - - - +
603D LEU* 1.3 57.4 + - - +
605D ALA* 4.0 0.7 - - - +
606D PHE 3.8 6.8 + - - -
670D LEU* 3.2 36.0 + - - +
673D SER* 4.6 3.1 - - - -
725D MET* 3.8 20.6 - - - +
726D HIS 5.0 0.2 + - - -
729D VAL* 3.3 28.9 - - - +
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Residues in contact with LEU 603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D ALA* 5.5 10.1 - - + -
577D TRP* 4.0 22.2 - - + -
596D LEU* 5.5 5.8 - - + -
599D SER* 2.6 48.2 + - - +
600D TRP* 3.9 8.5 - - - +
601D MET 2.8 0.4 + - - -
602D SER* 1.3 72.2 - - - +
604D MET* 1.3 76.6 + - + +
606D PHE* 2.7 15.5 + - - +
607D ALA* 3.0 12.9 + - - +
667D LYS* 2.9 38.0 - - + +
670D LEU* 4.1 6.5 - - + -
671D LEU* 4.0 18.4 - - + +
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Residues in contact with MET 604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567D GLY 4.6 2.5 - - - +
570D GLN* 3.9 48.5 - - + +
571D VAL* 4.6 3.1 - - - -
574D ALA* 4.8 10.3 - - + -
600D TRP* 2.9 39.3 - - + +
601D MET* 2.9 8.5 + - - +
603D LEU* 1.3 82.4 - - + +
605D ALA* 1.3 64.7 + - - +
606D PHE 2.8 1.7 + - - -
607D ALA* 3.1 12.8 + - + +
608D LEU* 2.8 25.5 + - - +
4999D DEX 3.5 34.4 - - + +
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Residues in contact with ALA 605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D MET* 2.9 15.4 + - + +
602D SER* 4.0 7.2 - - - +
604D MET* 1.3 75.6 - - - +
606D PHE* 1.3 56.2 + - - +
608D LEU* 3.8 8.3 - - - +
609D GLY* 3.2 17.7 + - - -
646D MET* 5.4 3.8 - - + +
649D VAL* 3.7 17.0 - - + +
725D MET* 4.3 11.2 - - + -
728D VAL* 4.9 7.9 - - + -
729D VAL* 5.2 2.2 - - + -
732D LEU* 4.1 24.7 - - + -
4999D DEX 3.9 8.8 - - + +
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Residues in contact with PHE 606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D SER 3.8 0.2 + - - -
603D LEU* 2.7 11.7 + - - +
605D ALA* 1.3 77.3 - - - +
607D ALA* 1.3 67.5 + - - +
608D LEU 3.0 0.9 - - - -
609D GLY* 3.1 2.3 + - - -
610D TRP* 2.9 23.7 + - - +
649D VAL* 4.0 11.2 - - + +
653D LEU* 3.6 26.0 - - + +
663D TYR* 3.6 34.1 - + - -
666D MET* 3.7 33.7 - - + -
667D LYS* 3.7 33.4 - - + -
670D LEU* 3.6 25.4 - - + -
721D LEU* 4.5 10.3 - - + -
722D LEU* 4.8 3.8 - - + -
725D MET* 4.0 13.2 - - + -
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Residues in contact with ALA 607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D GLU* 5.5 2.5 - - - +
570D GLN* 6.2 0.4 - - - +
603D LEU 3.0 7.7 + - - +
604D MET* 3.8 18.6 - - + +
606D PHE* 1.3 78.5 - - - +
608D LEU* 1.3 67.0 + - - +
610D TRP* 3.2 2.6 + - - +
611D ARG* 2.9 35.5 + - - +
663D TYR* 3.2 22.6 + - - +
667D LYS* 5.3 7.3 - - + +
4999D DEX 5.5 0.7 - - - +
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Residues in contact with LEU 608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D MET 2.8 18.0 + - - +
605D ALA* 3.8 5.6 - - - +
607D ALA* 1.3 73.7 - - - +
609D GLY* 1.3 58.6 + - - +
611D ARG* 2.6 45.8 + - - +
612D SER* 2.7 20.0 + - - +
621D LEU* 4.7 3.8 - - + -
622D CYS 3.3 30.1 - - - +
623D PHE* 3.8 25.6 - - + -
646D MET* 3.3 46.4 - - + -
4999D DEX 3.6 11.6 + - + +
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Residues in contact with GLY 609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D ALA 3.2 11.5 + - - -
606D PHE 3.1 7.0 + - - -
608D LEU* 1.3 79.5 - - - +
610D TRP* 1.3 50.2 + - - +
612D SER* 3.2 7.7 + - - -
613D TYR* 2.7 28.8 + - - +
621D LEU* 6.0 0.2 - - - -
646D MET 4.8 2.9 - - - -
649D VAL* 3.9 5.4 - - - -
650D SER* 2.9 30.7 - - - -
653D LEU* 3.7 5.8 - - - -
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Residues in contact with TRP 610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D PHE 2.9 6.2 + - - +
607D ALA 3.5 7.9 - - - +
608D LEU 2.7 3.6 + - - -
609D GLY* 1.3 68.6 - - - +
611D ARG* 1.3 73.1 + - + +
612D SER 3.0 1.1 - - - -
613D TYR* 3.0 19.5 + + - -
614D ARG* 3.0 63.4 + - + +
653D LEU* 3.0 34.2 - - + +
658D VAL* 3.5 25.1 - - + -
659D SER 3.5 1.8 - - - -
660D TYR* 3.3 58.1 - + + -
663D TYR* 3.6 48.0 - + + -
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Residues in contact with ARG 611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543D VAL* 3.2 40.2 - - + +
570D GLN* 4.3 11.8 + - - +
607D ALA* 2.9 33.8 + - - +
608D LEU* 2.6 19.2 + - - +
610D TRP* 1.3 82.0 - - + +
612D SER* 1.3 61.1 + - - +
614D ARG* 3.3 9.5 + - - +
615D GLN* 3.2 17.8 + - - +
622D CYS* 3.3 36.6 + - - +
623D PHE* 2.6 30.5 + - - +
624D ALA* 4.6 1.2 - - - +
625D PRO* 5.3 1.3 - - - -
4999D DEX 2.9 23.4 + - - -
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Residues in contact with SER 612 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D LEU* 2.7 24.2 + - - +
609D GLY* 3.2 13.0 - - - -
611D ARG* 1.3 78.8 - - - +
613D TYR* 1.3 55.6 + - - +
614D ARG 3.3 0.7 - - - -
616D SER* 2.8 32.4 - - - +
619D ASN 3.9 1.0 - - - +
620D LEU 3.6 13.7 - - - +
621D LEU* 3.6 9.1 - - - +
622D CYS* 2.9 26.4 + - - +
650D SER* 3.4 14.7 - - - -
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Residues in contact with TYR 613 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609D GLY 2.7 15.8 + - - +
610D TRP* 3.0 17.6 + + - -
612D SER* 1.3 72.0 - - - +
614D ARG* 1.3 87.4 + - - +
615D GLN 3.3 9.5 + - - -
616D SER 4.7 4.0 - - - -
650D SER* 3.2 20.9 - - - +
653D LEU* 3.3 30.5 - - + -
654D HIS* 3.3 48.7 + + + -
657D GLN* 3.5 23.6 + - - -
658D VAL 3.4 14.8 + - - -
----------------------------------------------------------
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Residues in contact with ARG 614 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610D TRP* 3.0 66.9 + - + +
611D ARG* 3.3 13.5 + - - +
612D SER 3.3 0.2 - - - -
613D TYR* 1.3 110.2 + - - +
615D GLN* 1.3 73.0 + - - +
658D VAL 5.0 1.6 + - - -
659D SER* 6.1 0.2 - - - +
660D TYR* 5.5 1.4 - - - +
----------------------------------------------------------
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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