Contacts of the helix formed by residues 770 - 803 (chain D) in PDB entry 1S77
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 770 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739D TYR* 3.0 12.2 + - + -
740D LYS 4.0 4.3 - - - -
741D LYS* 3.4 42.1 + - - +
742D PRO* 5.2 1.7 - - - +
768D GLU 3.7 0.8 + - - -
769D ILE* 1.3 74.6 - - - +
771D ALA* 1.3 62.9 + - - +
772D HIS* 3.1 13.2 + - - +
773D LYS* 2.8 58.3 + - + +
774D GLN* 2.9 21.8 + - - +
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Residues in contact with ALA 771 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
704D LYS* 5.6 0.5 - - - -
707D ALA* 3.6 26.0 - - + +
708D ALA* 5.0 0.7 - - - +
722D ARG* 3.5 29.2 - - - +
741D LYS* 4.3 5.6 - - - +
769D ILE* 3.2 6.5 + - - +
770D ASP* 1.3 72.1 - - - +
772D HIS* 1.3 62.5 + - - +
774D GLN* 3.8 2.4 - - - +
775D GLU* 3.4 22.3 + - - +
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Residues in contact with HIS 772 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741D LYS* 4.5 8.8 - - - +
770D ASP* 3.0 9.4 + - - +
771D ALA* 1.3 76.1 - - - +
773D LYS* 1.3 75.8 + - + +
775D GLU* 3.0 14.5 + - - +
776D SER* 3.1 28.0 + - - -
121T A 3.2 18.4 + - - -
122T C 2.9 44.1 + - - -
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Residues in contact with LYS 773 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739D TYR* 3.5 52.0 - - + +
740D LYS 5.3 5.2 + - - +
742D PRO* 6.2 2.2 - - - -
770D ASP* 2.8 38.8 + - - +
772D HIS* 1.3 80.1 + - - +
774D GLN* 1.3 63.2 + - - +
776D SER* 3.2 10.6 + - - +
777D GLY* 3.0 22.9 + - - -
9R C 5.1 9.8 + - - -
10R A 5.1 11.7 + - - -
119T T 4.7 7.2 - - - +
121T A 5.2 5.6 - - - +
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Residues in contact with GLN 774 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703D ALA* 3.2 17.4 - - + +
707D ALA* 4.3 10.1 - - + -
723D CYS 4.1 1.9 - - - +
724D ALA* 3.8 4.7 - - - -
725D VAL* 3.5 17.9 + - + +
737D GLN* 2.6 42.8 + - - +
738D GLU* 2.9 10.6 - - - +
739D TYR* 2.5 48.8 - - - +
769D ILE* 3.5 22.2 - - + -
770D ASP 2.9 19.7 + - - +
771D ALA* 3.8 8.5 - - - +
772D HIS 3.2 0.2 - - - -
773D LYS* 1.3 76.7 - - - +
775D GLU* 1.3 57.8 + - - +
778D ILE* 3.5 5.7 + - - +
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Residues in contact with GLU 775 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700D LYS* 3.4 49.3 + - + +
703D ALA* 3.8 7.9 - - + -
704D LYS* 3.0 45.7 + - + +
771D ALA 3.4 10.9 + - - +
772D HIS* 3.0 9.7 + - - +
774D GLN* 1.3 77.3 - - - +
776D SER* 1.3 60.9 + - - +
777D GLY 3.2 2.2 - - - -
778D ILE* 3.3 18.4 - - - +
779D ALA 4.8 0.2 + - - -
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Residues in contact with SER 776 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D TYR 4.0 7.7 - - - +
700D LYS* 4.6 12.5 - - - +
772D HIS* 3.1 26.8 + - - -
773D LYS* 3.3 12.1 + - - -
775D GLU* 1.3 76.2 - - - +
777D GLY* 1.3 59.4 + - - +
780D PRO* 3.8 8.8 - - - +
119T T 2.5 31.5 + - - +
120T T 3.1 23.8 - - - +
121T A 6.0 0.4 - - - -
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Residues in contact with GLY 777 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737D GLN* 3.3 7.2 - - - -
739D TYR* 4.7 2.5 - - - -
773D LYS 3.0 13.3 + - - -
776D SER* 1.3 79.1 + - - +
778D ILE* 1.3 66.3 + - - +
779D ALA 3.1 3.4 - - - -
780D PRO* 2.9 4.8 - - - +
781D ASN* 2.8 30.0 + - - +
119T T 3.5 20.9 - - - -
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Residues in contact with ILE 778 (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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699D LEU* 3.8 44.0 - - + +
700D LYS* 3.9 4.5 - - + +
703D ALA* 3.8 10.8 - - + -
725D VAL* 3.5 31.4 - - + -
727D TRP* 3.6 20.0 - - + -
737D GLN* 3.1 14.8 - - - +
774D GLN 3.5 12.1 + - - +
775D GLU 3.3 19.5 - - - +
777D GLY* 1.3 75.4 - - - +
779D ALA* 1.3 65.9 + - - +
781D ASN* 4.5 0.7 - - - -
782D PHE* 2.9 30.9 + - + +
845D PHE* 4.1 6.5 - - + -
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Residues in contact with ALA 779 (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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546D PHE* 4.9 1.6 - - + -
638D ALA 4.1 15.7 - - - +
639D TYR* 4.0 11.7 - - - +
696D MET* 4.1 23.3 - - + +
699D LEU* 4.1 12.8 - - + -
700D LYS* 5.3 3.8 - - + -
775D GLU 4.8 1.0 + - - +
777D GLY 3.0 1.2 + - - -
778D ILE* 1.3 85.3 - - + +
780D PRO* 1.3 72.9 - - + +
782D PHE* 3.5 0.9 - - - +
783D VAL* 3.0 29.0 + - - +
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Residues in contact with PRO 780 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D TYR* 3.6 42.6 - - + +
776D SER 3.8 2.9 - - - +
777D GLY 2.9 21.5 - - - +
779D ALA* 1.3 89.5 - - + +
781D ASN* 1.3 59.4 + - - +
784D HIS* 2.8 44.7 + - + +
119T T 3.2 38.1 - - - +
120T T 4.2 5.2 - - - +
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Residues in contact with ASN 781 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422D TRP* 3.0 17.6 - - + -
423D ARG* 3.1 36.0 - - + +
727D TRP* 3.7 8.7 - - + -
737D GLN* 2.6 29.0 + - - +
739D TYR* 2.8 17.0 + - - -
777D GLY* 2.8 20.2 + - - +
778D ILE 4.2 0.7 - - - +
780D PRO* 1.3 73.8 - - - +
782D PHE* 1.3 58.1 + - - +
784D HIS* 5.0 0.2 + - - -
785D SER* 3.0 29.8 + - - -
118T C 3.4 16.0 - - - -
119T T 3.6 7.2 + - - -
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Residues in contact with PHE 782 (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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549D MET* 3.9 19.7 - - + -
699D LEU* 3.8 27.4 - - + -
727D TRP* 3.5 49.1 - + + -
778D ILE* 2.9 22.4 + - + +
779D ALA 3.5 3.1 - - - +
781D ASN* 1.3 75.7 - - - +
783D VAL* 1.3 68.4 + - + +
785D SER* 2.8 19.4 + - - -
786D GLN* 3.0 29.9 + - + +
841D VAL* 3.7 26.7 - - + -
842D LEU* 3.5 23.1 - - + -
845D PHE* 4.4 13.7 - + + -
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Residues in contact with VAL 783 (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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542D GLY* 3.9 21.5 - - - +
545D HIS* 4.0 18.2 - - + -
546D PHE* 3.5 38.4 - - + -
549D MET* 5.3 2.2 - - + -
639D TYR* 3.8 25.8 - - + +
779D ALA 3.0 17.3 + - - +
780D PRO 4.0 0.4 - - - +
782D PHE* 1.3 81.0 - - + +
784D HIS* 1.3 55.1 + - - +
786D GLN* 2.7 28.3 + - - +
787D ASP* 2.8 14.0 + - - +
1R 3DA 5.1 0.9 - - - +
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Residues in contact with HIS 784 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D ARG* 2.7 37.9 + - - +
425D ARG* 3.4 27.2 - - - +
639D TYR* 3.8 6.8 + + - -
780D PRO* 2.8 32.8 + - + +
781D ASN* 3.9 2.4 + - - +
783D VAL* 1.3 73.3 - - - +
785D SER* 1.3 57.2 + - - +
787D ASP* 2.9 13.1 - - - +
788D GLY 2.9 23.2 + - - -
1R 3DA 2.8 62.4 + + - -
119T T 3.5 17.9 + - - -
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Residues in contact with SER 785 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D ARG* 3.1 33.6 - - - +
727D TRP* 2.9 25.0 + - - -
729D THR* 3.3 23.9 - - - +
735D VAL* 4.0 3.1 - - - -
781D ASN 3.0 16.5 + - - -
782D PHE 2.8 12.5 + - - -
784D HIS* 1.3 78.0 - - - +
786D GLN* 1.3 59.3 + - - +
788D GLY* 3.8 1.4 - - - +
789D SER* 3.1 19.2 + - - -
792D ARG* 4.6 0.5 + - - -
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Residues in contact with GLN 786 (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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545D HIS* 3.8 7.3 - - + +
549D MET* 4.1 9.6 - - + -
727D TRP* 4.5 2.0 - - - -
728D VAL 4.9 1.6 + - - -
729D THR* 4.4 5.7 - - - +
730D PRO* 3.4 30.8 - - - +
782D PHE* 3.0 54.8 + - + +
783D VAL* 2.7 13.4 + - - +
785D SER* 1.3 84.2 + - - +
787D ASP* 1.3 62.5 + - - +
789D SER* 3.5 3.8 + - - -
790D HIS* 3.1 21.7 + - - +
835D THR* 5.2 0.5 - - - +
836D TYR* 3.7 20.5 + - - +
841D VAL* 3.5 21.3 - - - +
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Residues in contact with ASP 787 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D ARG* 2.8 41.5 + - - -
541D SER* 5.0 7.9 - - - +
545D HIS* 3.3 31.8 - - + +
783D VAL* 2.8 8.0 + - + +
784D HIS* 2.9 24.8 - - - -
786D GLN* 1.3 75.6 - - - +
788D GLY* 1.3 74.4 + - - +
790D HIS* 2.9 5.3 + - + +
791D LEU* 2.7 29.1 + - - +
811D HIS 3.6 16.2 - - - +
812D ASP* 5.6 2.5 - - + -
814D PHE* 5.6 0.2 - - - -
1R 3DA 4.2 3.2 + - - +
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Residues in contact with GLY 788 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424D GLY 4.6 0.8 - - - +
425D ARG* 4.3 15.9 - - - -
426D VAL* 5.3 1.2 - - - +
784D HIS 2.9 12.3 + - - -
785D SER 4.1 1.3 - - - -
786D GLN 3.3 0.2 - - - -
787D ASP* 1.3 89.1 + - - +
789D SER* 1.3 56.5 + - - +
791D LEU* 3.3 9.2 + - - +
792D ARG* 3.0 44.4 + - - +
811D HIS 5.3 0.2 - - - -
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Residues in contact with SER 789 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729D THR* 3.4 9.4 - - - -
730D PRO* 3.6 11.6 - - - +
731D ASP* 3.1 35.7 + - - +
785D SER 3.1 18.3 + - - -
786D GLN 3.7 5.6 - - - -
787D ASP 3.0 0.4 - - - -
788D GLY* 1.3 73.8 - - - +
790D HIS* 1.3 57.0 + - - +
792D ARG* 3.2 17.9 + - - +
793D LYS* 2.8 38.2 + - - +
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Residues in contact with HIS 790 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D HIS* 3.9 16.8 - + + -
786D GLN 3.1 14.2 + - - +
787D ASP* 2.9 8.9 + - + +
789D SER* 1.3 77.1 - - - +
791D LEU* 1.3 54.2 + - - +
793D LYS* 3.8 6.4 - - - -
794D THR* 2.7 44.2 + - - -
814D PHE* 4.0 13.2 - + - -
828D VAL* 2.9 24.8 + - + +
831D THR* 2.7 33.0 + - - -
832D MET* 3.5 27.2 + - - -
835D THR* 5.2 7.5 + - + +
836D TYR* 5.8 2.0 - - + -
883D ALA* 3.0 28.5 + - + -
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Residues in contact with LEU 791 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426D VAL* 4.3 25.6 - - + +
787D ASP 2.7 12.5 + - - +
788D GLY* 3.4 11.7 - - - +
790D HIS* 1.3 78.9 - - - +
792D ARG* 1.3 60.5 + - + +
794D THR* 3.3 2.3 + - - -
795D VAL* 3.0 34.7 + - + +
809D LEU* 3.5 40.8 - - + -
811D HIS* 3.0 46.0 - - - +
813D SER 4.4 6.3 - - - +
814D PHE* 3.8 20.1 - - + -
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Residues in contact with ARG 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D GLU 5.1 1.1 - - - +
316D VAL* 3.7 23.8 - - - +
319D ALA* 3.5 26.9 - - + +
320D ILE* 4.9 0.7 - - - -
420D MET* 4.1 9.1 - - - -
423D ARG 5.0 0.6 + - - -
424D GLY* 2.7 35.3 + - - -
426D VAL* 4.3 16.2 - - + -
729D THR* 3.1 16.6 + - - +
731D ASP* 2.4 50.8 + - - +
733D PHE* 3.3 14.2 - - - +
788D GLY* 3.0 29.1 + - - +
789D SER* 3.2 10.5 + - - +
791D LEU* 1.3 77.5 - - + +
793D LYS* 1.3 64.9 + - - +
795D VAL* 3.2 3.9 + - - +
796D VAL* 3.0 28.9 + - - +
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Residues in contact with LYS 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D GLU* 5.2 10.9 - - + +
730D PRO* 3.8 38.5 + - + -
731D ASP* 3.9 14.5 - - + +
789D SER* 2.8 25.2 + - - +
790D HIS* 3.8 4.9 - - - +
792D ARG* 1.3 73.1 - - - +
794D THR* 1.3 57.8 + - - +
796D VAL* 3.4 5.6 + - - +
797D TRP* 2.9 37.7 + - + +
831D THR* 3.6 14.5 - - + +
834D ASP* 5.7 3.6 + - + -
835D THR* 3.2 28.5 - - + +
839D CYS* 6.2 1.1 - - - -
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Residues in contact with THR 794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790D HIS* 2.7 26.7 + - - -
791D LEU 3.7 4.0 - - - -
793D LYS* 1.3 75.2 - - - +
795D VAL* 1.3 60.6 + - - +
798D ALA* 2.8 30.1 + - - +
814D PHE* 3.8 22.5 - - + -
824D LEU* 4.3 14.4 - - + -
827D ALA* 4.1 3.1 - - + -
828D VAL* 3.6 28.5 - - + +
831D THR* 2.6 28.1 + - - -
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Residues in contact with VAL 795 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D ALA* 3.9 16.4 - - + +
322D ILE* 3.6 31.6 - - + -
323D ALA* 4.1 4.5 - - + +
791D LEU* 3.0 22.7 + - + +
792D ARG* 3.2 6.9 + - - +
794D THR* 1.3 76.6 - - + +
796D VAL* 1.3 62.8 + - - +
799D HIS* 3.1 23.4 + - - +
807D PHE* 3.6 20.8 - - + -
809D LEU* 3.4 42.6 - - + -
814D PHE* 5.8 0.7 - - + -
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Residues in contact with VAL 796 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D GLU* 3.5 24.9 - - + +
318D LYS* 3.4 15.9 - - - +
319D ALA* 3.7 28.5 - - - +
322D ILE* 3.9 11.4 - - + -
792D ARG 3.0 20.3 + - - +
793D LYS* 4.0 5.8 - - - +
795D VAL* 1.3 78.0 - - - +
797D TRP* 1.3 55.5 + - - +
799D HIS* 3.5 0.3 + - - +
800D GLU* 2.8 67.0 + - + +
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Residues in contact with TRP 797 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793D LYS* 2.9 25.8 + - + +
794D THR 3.7 1.3 - - - +
796D VAL* 1.3 76.2 - - - +
798D ALA* 1.3 60.6 + - - +
800D GLU* 4.5 0.7 - - - +
801D LYS* 2.7 65.2 + - + +
802D TYR* 3.9 12.3 - + - -
827D ALA* 4.1 10.1 - - + -
830D GLU* 2.8 44.1 + - + +
831D THR* 3.5 22.0 - - + -
834D ASP* 3.4 39.9 - - + -
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Residues in contact with ALA 798 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794D THR 2.8 20.5 + - - +
797D TRP* 1.3 73.8 - - - +
799D HIS* 1.3 58.6 + - - +
802D TYR* 3.0 34.6 + - - +
803D GLY 3.1 6.1 + - - -
804D ILE* 3.2 29.7 + - + +
807D PHE* 3.6 15.9 - - + -
824D LEU* 4.0 6.3 - - + -
827D ALA* 4.0 13.4 - - + +
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Residues in contact with HIS 799 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322D ILE* 3.9 40.1 - - + +
795D VAL 3.1 19.0 + - - +
796D VAL 3.8 2.7 - - - +
797D TRP 3.1 0.4 - - - -
798D ALA* 1.3 78.7 - - - +
800D GLU* 1.3 69.6 + - + +
803D GLY* 2.9 28.4 + - - -
804D ILE 2.7 28.6 + - - +
805D GLU* 4.2 13.8 - - + -
807D PHE* 4.0 1.0 - - + -
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Residues in contact with GLU 800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D GLU* 4.0 6.6 - - - +
318D LYS* 3.2 27.5 - - - +
322D ILE* 5.0 1.0 - - + +
796D VAL* 2.8 46.1 + - + +
797D TRP* 4.9 0.6 - - - -
799D HIS* 1.3 86.7 - - + +
801D LYS* 1.3 82.6 + - + +
803D GLY 4.5 0.8 + - - -
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Residues in contact with LYS 801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797D TRP* 2.7 52.9 + - + +
800D GLU* 1.3 97.5 + - + +
802D TYR* 1.3 81.3 - - + +
803D GLY 3.6 0.4 - - - -
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Residues in contact with TYR 802 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797D TRP* 3.9 7.0 - + - -
798D ALA* 3.0 24.4 + - - +
801D LYS* 1.3 96.6 - - + +
803D GLY* 1.3 65.4 + - - +
804D ILE* 3.2 8.1 + - + +
820D ASP* 5.7 0.3 - - - +
823D ASN* 3.3 42.3 + - + +
826D LYS* 2.9 32.3 - - + +
827D ALA* 3.9 13.2 - - + -
830D GLU* 2.6 33.1 + - - -
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Residues in contact with GLY 803 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D LYS* 5.6 2.8 + - - -
799D HIS* 2.9 21.7 + - - -
800D GLU 4.5 0.6 - - - -
801D LYS 3.6 1.4 - - - -
802D TYR* 1.3 78.1 - - - +
804D ILE* 1.3 63.8 + - - +
805D GLU* 3.6 12.7 + - - +
820D ASP* 5.4 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) + - + + + + + -
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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