Contacts of the helix formed by residues 697 - 729 (chain A) in PDB entry 6UZA
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 697 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A TYR* 3.1 34.4 + + - +
693A ILE* 3.4 23.0 - - + +
695A TYR* 3.3 25.3 - + + +
696A ASN* 1.3 80.0 + - + +
698A LYS* 1.3 63.6 + - - +
699A PHE 3.2 3.3 + - - +
700A ILE* 3.5 5.6 + - + +
701A GLU* 3.5 8.3 + - - +
583D ARG* 3.2 28.9 + - + -
584D ILE 5.0 2.3 + - - -
586D TRP* 3.9 22.7 + + + +
587D ASP 4.1 8.5 - - - -
588D PRO* 4.1 7.2 - - + -
593D ILE* 3.8 31.4 - - + +
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Residues in contact with LYS 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A VAL* 5.3 1.2 - - - +
693A ILE* 3.7 10.3 + - - +
694A ASN 5.2 0.2 - - - -
695A TYR 3.2 26.9 + - - -
696A ASN* 3.2 22.0 + - - +
697A HIS* 1.3 72.7 - - - +
699A PHE* 1.3 59.6 + - - +
700A ILE 3.4 0.2 - - - -
701A GLU* 2.7 38.6 + - - +
702A ASN* 2.9 38.3 + - - +
1006A Y01 3.7 28.9 + - + +
588D PRO* 5.6 0.6 - - - +
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Residues in contact with PHE 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A HIS* 3.2 0.4 - - - +
698A LYS* 1.3 76.7 - - - +
700A ILE* 1.3 58.6 + - + +
702A ASN* 3.2 4.5 + - - +
703A ILE* 3.0 37.3 + - + +
1006A Y01 3.5 67.5 + - + +
588D PRO 4.8 12.7 + - - +
593D ILE* 3.3 33.7 - - + +
594D ILE* 3.8 44.6 - - + -
597D GLY* 3.9 13.9 - - - -
598D LEU* 4.6 8.7 - - + -
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Residues in contact with ILE 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A LEU* 3.8 34.7 - - + +
656A TYR* 3.7 18.4 + - + -
659A TYR* 3.4 40.6 - - + +
693A ILE* 4.5 5.8 - - + -
697A HIS* 3.5 10.7 + - + +
699A PHE* 1.3 77.0 - - + +
701A GLU* 1.3 57.7 + - - +
703A ILE* 3.3 8.2 + - - +
704A GLY* 2.9 23.2 + - - -
593D ILE* 4.0 34.1 - - + +
596D GLU* 4.6 12.8 - - + +
597D GLY* 4.7 1.8 - - - -
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Residues in contact with GLU 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A TYR* 3.8 8.9 + - - -
691A VAL 3.6 14.8 - - - +
692A VAL* 4.2 18.4 - - - +
693A ILE* 3.8 18.5 + - + +
697A HIS 3.5 9.6 + - - +
698A LYS* 2.7 46.9 + - + +
699A PHE 3.3 0.8 - - - -
700A ILE* 1.3 80.5 - - - +
702A ASN* 1.3 59.2 + - - +
704A GLY* 3.3 1.6 + - - -
705A TYR* 2.9 55.7 + - + -
676D LYS* 5.7 0.5 + - - -
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Residues in contact with ASN 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A LYS* 2.9 26.8 + - - +
699A PHE 3.7 3.1 - - - +
701A GLU* 1.3 78.3 - - - +
703A ILE* 1.3 62.1 + - - +
705A TYR* 3.4 10.9 + - - +
706A VAL* 3.0 34.8 + - - +
1005A SBJ 3.4 37.4 + - - +
1006A Y01 2.6 47.6 + - + +
672D GLU* 5.0 2.6 + - - +
676D LYS* 5.4 2.1 + - - -
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Residues in contact with ILE 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A LEU* 3.8 18.8 - - + -
699A PHE* 3.0 32.2 + - + +
700A ILE* 3.6 10.3 - - - +
702A ASN* 1.3 77.3 - - - +
704A GLY* 1.3 56.9 + - - +
706A VAL* 3.4 4.1 + - + +
707A LEU* 2.9 35.6 + - + +
1006A Y01 3.6 39.9 - - + -
597D GLY* 3.7 22.7 - - - +
598D LEU* 5.7 0.2 - - + -
600D ALA* 4.8 0.4 - - + -
601D ILE* 3.7 31.6 - - + -
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Residues in contact with GLY 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A MET* 4.3 3.9 - - - +
655A LEU* 3.7 11.8 - - - +
656A TYR* 3.6 23.3 - - - -
691A VAL* 4.0 8.5 - - - +
700A ILE 2.9 12.0 + - - -
702A ASN 3.3 0.4 - - - -
703A ILE* 1.3 76.9 - - - +
705A TYR* 1.3 55.5 + - - +
707A LEU* 3.5 4.2 + - - +
708A TYR* 3.0 31.5 + - - +
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Residues in contact with TYR 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A VAL* 3.6 28.3 + - + +
691A VAL* 3.8 19.7 - - + +
692A VAL* 3.6 17.3 - - + +
701A GLU* 2.9 54.7 + - + +
702A ASN* 3.6 14.4 - - - +
703A ILE 3.3 0.2 - - - -
704A GLY* 1.3 76.5 - - - +
706A VAL* 1.3 57.0 + - - +
708A TYR* 3.9 3.2 - - - +
709A GLY 3.0 23.6 + - - -
1005A SBJ 3.7 41.7 - - + +
676D LYS* 4.4 25.6 + - + +
680D TRP* 4.0 15.0 - + - -
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Residues in contact with VAL 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ASN 3.0 21.4 + - - +
703A ILE* 3.9 3.6 - - - +
705A TYR* 1.3 75.1 - - - +
707A LEU* 1.3 64.0 + - + +
709A GLY* 3.4 0.7 + - - -
710A VAL* 3.0 39.4 + - + +
1005A SBJ 4.2 56.6 - - + +
1006A Y01 3.8 40.4 - - + -
601D ILE* 6.4 1.1 - - + -
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PHE* 3.6 15.7 - - + -
651A GLY 4.4 1.3 - - - +
652A MET* 3.9 30.3 - - + -
655A LEU* 4.6 4.3 - - + -
703A ILE* 2.9 28.4 + - + +
704A GLY 4.0 3.4 - - - +
706A VAL* 1.3 82.6 - - + +
708A TYR* 1.3 57.7 + - - +
710A VAL* 3.5 4.7 + - + -
711A TYR* 2.9 28.9 + - - +
600D ALA* 4.3 22.7 - - + +
601D ILE* 4.7 18.8 - - + -
604D VAL* 4.3 30.3 - - + -
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Residues in contact with TYR 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A MET* 3.9 19.8 - - + +
668A PHE* 4.5 8.5 - + - -
677A THR* 4.1 1.8 + - - +
678A LEU* 4.1 18.2 - - + -
681A ALA* 3.4 15.8 - - + +
686A SER* 3.3 35.6 + - - -
687A GLU 4.0 15.8 + - - -
688A VAL* 4.7 9.0 - - + -
690A SER* 4.5 7.3 + - - -
691A VAL* 4.1 17.5 - - + -
704A GLY 3.0 18.6 + - - +
705A TYR* 3.9 3.6 - - - +
707A LEU* 1.3 76.8 - - - +
709A GLY* 1.3 53.2 + - - +
711A TYR* 3.3 5.3 + + - +
712A ASN* 2.6 50.4 + - - -
680D TRP* 3.5 26.7 - + + -
685D LEU* 4.8 4.6 - - + +
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Residues in contact with GLY 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A TYR 3.0 14.3 + - - -
706A VAL 3.4 2.4 + - - -
708A TYR* 1.3 75.5 - - - +
710A VAL* 1.3 57.1 + - - +
712A ASN* 3.3 2.8 + - - +
713A VAL* 3.0 35.8 + - - +
1005A SBJ 4.3 7.4 - - - -
679D PHE* 3.9 16.5 - - - -
680D TRP* 3.6 16.5 - - - -
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Residues in contact with VAL 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PHE* 3.7 21.3 - - + -
706A VAL* 3.0 31.3 + - + +
707A LEU* 3.9 7.4 - - + +
709A GLY* 1.3 76.3 - - - +
711A TYR* 1.3 54.1 + - - +
713A VAL* 3.5 5.0 + - - +
714A THR* 2.5 44.1 + - - +
1005A SBJ 4.0 55.0 - - + -
604D VAL* 6.1 0.2 - - + -
1003D S9Y 5.5 5.6 - - + -
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Residues in contact with TYR 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A VAL* 4.9 0.4 - - + -
645A PHE* 3.4 17.9 - + - -
648A PHE* 3.8 38.8 - + + -
652A MET* 4.6 1.6 - - + -
678A LEU* 2.5 60.1 + - + -
681A ALA* 4.1 15.5 - - + -
682A ILE* 3.9 9.7 - - + +
707A LEU 2.9 18.7 + - - +
708A TYR* 3.5 9.0 - + - +
709A GLY 3.3 0.2 - - - -
710A VAL* 1.3 76.6 - - - +
712A ASN* 1.3 72.2 + - - +
714A THR* 3.4 1.7 + - - -
715A MET* 3.0 62.6 + - + +
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Residues in contact with ASN 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681A ALA* 4.0 19.8 - - - +
708A TYR* 2.6 52.4 + - - +
709A GLY* 3.8 4.3 - - - +
711A TYR* 1.3 82.0 - - - +
713A VAL* 1.3 62.8 + - - +
715A MET* 3.4 5.2 + - - +
716A VAL* 3.0 28.1 + - - +
680D TRP* 3.7 18.6 - - - -
683D PHE* 3.8 33.9 - - + +
685D LEU* 5.0 5.0 - - - +
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Residues in contact with VAL 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709A GLY 3.0 17.6 + - - +
710A VAL 4.0 2.7 - - - +
712A ASN* 1.3 74.8 - - - +
714A THR* 1.3 58.8 + - - +
716A VAL* 3.3 7.8 + - + +
717A ILE* 3.0 46.1 + - + +
1005A SBJ 3.8 33.0 - - + -
638D MET* 5.0 9.6 - - + -
679D PHE* 4.1 16.4 - - + -
683D PHE* 4.0 17.9 - - + -
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Residues in contact with THR 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A VAL* 3.8 32.8 - - + -
648A PHE* 4.5 5.4 - - + -
710A VAL* 2.5 30.5 + - - +
711A TYR* 3.8 4.3 - - - -
713A VAL* 1.3 77.7 - - - +
715A MET* 1.3 57.2 + - - +
717A ILE* 3.3 8.7 + - - +
718A VAL* 3.0 33.4 + - + +
1005A SBJ 3.7 30.9 - - + +
1003D S9Y 5.1 8.2 - - + +
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Residues in contact with MET 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A PHE* 3.5 62.8 - - + +
644A VAL* 3.7 22.0 - - + -
645A PHE* 3.9 7.0 - - + +
682A ILE* 5.4 7.2 - - + -
711A TYR* 3.0 58.2 + - + +
712A ASN* 4.0 4.9 - - - +
714A THR* 1.3 73.7 - - - +
716A VAL* 1.3 60.9 + - + +
718A VAL* 3.4 6.1 + - - +
719A LEU* 3.0 39.8 + - + +
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Residues in contact with VAL 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A ASN 3.0 22.1 + - - +
713A VAL* 3.3 7.2 + - + +
715A MET* 1.3 76.8 - - + +
717A ILE* 1.3 59.6 + - + +
719A LEU* 3.9 5.3 - - + +
720A LEU* 3.0 38.0 + - + +
683D PHE* 3.9 24.0 - - + -
722D MET* 6.3 2.2 - - + -
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Residues in contact with ILE 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713A VAL* 3.0 36.7 + - + +
714A THR* 3.6 5.4 - - - +
715A MET 3.3 0.2 - - - -
716A VAL* 1.3 80.4 - - + +
718A VAL* 1.3 58.7 + - + +
720A LEU* 3.4 11.1 + - + +
721A ASN* 2.9 28.9 + - + +
1005A SBJ 3.8 34.1 - - + -
627D LEU* 5.1 9.0 - - + -
630D THR* 4.9 9.2 - - - +
631D VAL* 4.6 19.7 - - + -
634D ILE* 3.7 31.6 - - + -
638D MET* 5.1 1.6 - - + -
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Residues in contact with VAL 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A PHE* 5.1 10.8 - - + +
640A ILE* 4.9 7.9 - - + -
641A PHE* 4.0 35.7 - - + +
644A VAL* 4.9 13.0 - - + -
714A THR* 3.0 31.3 + - + +
715A MET* 3.9 9.0 - - - +
717A ILE* 1.3 78.0 - - + +
719A LEU* 1.3 59.0 + - + +
721A ASN* 3.4 8.4 + - - +
722A MET* 3.0 27.8 + - + +
1005A SBJ 6.3 0.4 - - + -
627D LEU* 4.7 22.9 - - + -
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Residues in contact with LEU 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A PHE* 3.6 26.9 - - + -
682A ILE* 4.2 25.6 - - + +
715A MET* 3.0 24.1 + - + +
716A VAL* 4.1 4.7 - - + +
718A VAL* 1.3 76.7 - - + +
720A LEU* 1.3 57.6 + - - +
722A MET* 3.3 31.8 + - + +
723A LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716A VAL* 3.0 26.2 + - + +
717A ILE* 3.9 9.2 - - + +
719A LEU* 1.3 74.5 - - - +
721A ASN* 1.3 62.9 + - + +
723A LEU* 3.4 8.7 + - + +
724A ILE* 3.0 43.1 + - + +
630D THR* 5.5 2.2 - - - +
634D ILE* 5.0 6.1 - - + -
722D MET* 4.0 23.8 - - + -
723D LEU* 4.2 25.8 - - + -
726D MET* 3.7 33.4 - - + -
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Residues in contact with ASN 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A PHE* 3.9 18.3 - - - -
717A ILE* 2.9 18.8 + - + +
718A VAL* 3.7 6.0 + - - +
720A LEU* 1.3 80.0 - - - +
722A MET* 1.3 56.7 + - - +
724A ILE* 3.9 6.0 - - - +
725A ALA* 2.9 29.8 + - - +
623D LEU 4.8 0.4 + - - -
626D SER* 3.3 27.2 + - - +
627D LEU* 3.5 37.2 - - + +
630D THR* 3.9 22.0 - - - +
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Residues in contact with MET 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A ILE* 4.2 24.2 - - + +
637A PHE* 3.9 43.7 - - + -
641A PHE* 6.4 1.1 - - - -
718A VAL* 3.0 18.1 + - + +
719A LEU* 3.6 33.4 - - + +
720A LEU 3.3 0.2 - - - -
721A ASN* 1.3 77.9 - - - +
723A LEU* 1.3 57.3 + - - +
725A ALA* 3.4 1.2 + - - +
726A MET* 2.9 46.0 + - - +
716B VAL* 6.3 2.5 - - + -
720B LEU* 4.0 25.8 - - + -
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Residues in contact with LEU 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719A LEU 3.0 17.2 + - - +
720A LEU* 3.8 7.2 - - + +
722A MET* 1.3 76.9 - - - +
724A ILE* 1.3 57.2 + - - +
726A MET* 3.4 4.5 + - - +
727A ILE* 2.9 50.8 + - + +
720B LEU* 4.2 25.8 - - + -
723B LEU* 4.1 26.2 - - + -
724B ILE* 4.4 8.3 - - + -
723D LEU* 4.1 30.3 - - + -
727D ILE* 5.6 0.2 - - + -
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Residues in contact with ILE 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720A LEU* 3.0 32.5 + - + +
721A ASN* 4.0 6.3 - - - +
723A LEU* 1.3 76.2 - - + +
725A ALA* 1.3 58.5 + - - +
727A ILE* 3.3 8.6 + - + +
728A ASN* 2.9 27.3 + - + +
630D THR* 5.5 8.1 - - + -
723D LEU* 4.4 11.2 - - + -
726D MET* 3.8 49.1 - - + +
727D ILE* 3.9 21.3 - - + +
730D SER* 3.8 25.1 - - - +
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Residues in contact with ALA 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A PHE* 3.8 26.9 - - + -
721A ASN* 2.9 22.5 + - - +
722A MET 3.8 0.9 - - - +
724A ILE* 1.3 77.0 - - - +
726A MET* 1.3 58.5 + - - +
728A ASN* 3.3 6.4 + - - +
729A SER* 2.9 31.1 + - - -
626D SER* 5.4 7.0 - - - +
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Residues in contact with MET 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A THR* 3.7 35.4 - - + +
633A ASP* 4.2 24.9 - - + +
634A ILE* 3.6 22.0 - - + -
637A PHE* 5.0 4.0 - - + -
722A MET* 2.9 32.7 + - + +
723A LEU 4.0 1.3 - - - +
725A ALA* 1.3 75.0 - - - +
727A ILE* 1.3 63.8 + - - +
729A SER* 3.6 11.3 + - - +
730A SER* 3.2 20.4 + - - -
720B LEU* 3.7 29.4 - - + -
724B ILE* 3.8 19.6 - - + +
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Residues in contact with ILE 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A LEU* 2.9 39.1 + - + +
724A ILE* 3.7 5.4 - - - +
726A MET* 1.3 76.2 - - - +
728A ASN* 1.3 61.1 + - - +
730A SER* 3.5 7.4 + - - -
731A PHE* 3.4 32.0 - - + -
723B LEU* 5.6 0.2 - - + -
724B ILE* 3.9 24.0 - - + -
727B ILE* 3.8 32.5 - - + -
727D ILE* 3.8 40.4 - - + -
731D PHE* 4.5 8.3 - - + -
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Residues in contact with ASN 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A ILE* 2.9 17.5 + - + +
725A ALA* 3.7 7.2 - - - +
726A MET 3.3 0.2 - - - -
727A ILE* 1.3 79.0 - - - +
729A SER* 1.3 55.9 + - - +
730A SER 3.1 5.5 + - - -
731A PHE* 3.6 4.2 + - - +
732A GLN* 3.4 27.9 + - - +
730D SER* 4.0 29.1 + - - +
731D PHE* 3.4 34.9 - - + +
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Residues in contact with SER 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633A ASP* 3.9 19.1 + - - +
725A ALA 2.9 19.7 + - - -
726A MET* 3.6 10.7 + - - +
727A ILE 3.4 0.4 - - - -
728A ASN* 1.3 74.7 - - - +
730A SER* 1.3 62.5 + - - +
732A GLN* 4.3 13.5 - - - -
733A GLU* 6.2 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