Contacts of the helix formed by residues 785 - 814 (chain A) in PDB entry 2XT6
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 SER 785 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A ILE* 3.5 5.9 - - - +
784A ILE* 1.3 74.5 - - - +
786A MET* 1.3 66.5 + - - +
787A LYS* 3.2 9.6 - - - -
788A GLU* 2.9 23.3 + - - -
789A ALA 3.0 18.0 + - - -
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Residues in contact with MET 786 (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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779A ILE* 3.8 36.8 - - + +
785A SER* 1.3 72.8 - - - +
787A LYS* 1.4 51.7 + - - +
789A ALA* 3.3 5.5 + - - +
790A GLU* 2.8 52.2 + - + +
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Residues in contact with LYS 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A SER* 3.2 7.0 - - - -
786A MET* 1.4 74.2 - - - +
788A GLU* 1.4 59.6 + - + +
790A GLU* 3.1 14.9 + - - +
791A ASP* 2.9 38.1 + - - +
794A ARG* 4.6 0.2 + - - -
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Residues in contact with GLU 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A VAL* 4.4 12.3 - - - +
783A ASP 4.1 3.4 - - - +
784A ILE* 3.2 26.8 - - + +
785A SER* 2.9 40.3 + - - +
787A LYS* 1.4 77.1 - - + +
789A ALA* 1.4 56.6 + - - +
791A ASP* 3.6 13.7 - - - +
792A ALA* 3.3 21.1 + - - +
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Residues in contact with ALA 789 (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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775A THR* 4.0 13.9 - - + +
779A ILE* 3.2 33.9 - - + -
784A ILE* 3.8 11.6 - - + +
785A SER 3.0 5.1 + - - -
786A MET* 3.5 9.2 - - - +
787A LYS 3.2 0.2 - - - -
788A GLU* 1.4 75.2 - - - +
790A GLU* 1.4 60.1 + - + +
791A ASP 3.2 0.4 - - - -
792A ALA* 3.1 8.8 + - - +
793A LEU* 3.0 26.0 + - - +
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Residues in contact with GLU 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A MET* 2.8 34.0 + - + +
787A LYS* 3.1 14.1 + - - +
789A ALA* 1.4 75.8 - - + +
791A ASP* 1.4 56.3 + - - +
793A LEU* 3.3 10.0 + - + +
794A ARG* 2.9 54.8 + - - +
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Residues in contact with ASP 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A LYS* 2.9 25.4 + - - +
788A GLU* 3.6 14.1 - - - +
790A GLU* 1.4 74.2 - - - +
792A ALA* 1.4 51.6 + - - +
794A ARG* 2.6 32.5 + - - +
795A ASP* 2.8 33.0 + - - +
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Residues in contact with ALA 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU* 3.8 30.5 - - + -
487A ASN* 2.8 29.9 + - - +
771A ARG* 5.7 0.7 - - - -
775A THR* 4.7 6.3 - - + +
784A ILE* 5.6 0.2 - - + -
788A GLU 3.3 10.3 + - - +
789A ALA* 3.1 14.5 + - - +
791A ASP* 1.4 76.5 - - - +
793A LEU* 1.4 59.0 + - - +
795A ASP* 3.4 2.9 + - - -
796A TYR* 3.0 12.6 + - - +
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Residues in contact with LEU 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A ARG* 3.9 26.0 - - - +
789A ALA 3.0 11.3 + - - +
790A GLU* 3.3 11.0 + - + +
792A ALA* 1.4 72.8 - - - +
794A ARG* 1.3 60.3 + - - +
796A TYR* 3.4 13.8 + - + +
797A GLN* 3.1 48.7 + - + +
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Residues in contact with ARG 794 (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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790A GLU* 2.9 45.8 + - - +
791A ASP* 2.6 51.3 + - - +
792A ALA 3.3 0.2 - - - -
793A LEU* 1.3 75.9 - - - +
795A ASP* 1.4 55.2 + - - +
797A GLN* 3.5 14.8 + - - +
798A GLY* 3.0 24.9 + - - -
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Residues in contact with ASP 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A SER* 4.1 14.7 - - - -
487A ASN* 2.8 27.1 + - - +
791A ASP 2.8 18.9 + - - +
792A ALA* 3.5 8.5 - - - +
794A ARG* 1.4 70.3 - - - +
796A TYR* 1.3 64.1 + - - +
798A GLY* 3.1 2.9 + - - -
799A GLN* 2.9 42.1 + - - +
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Residues in contact with TYR 796 (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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487A ASN* 3.4 32.6 - - - +
490A GLU* 3.8 10.9 - - + +
491A ALA* 3.4 25.5 - - + +
494A THR* 3.0 25.5 + - - +
771A ARG* 3.7 40.6 - - - +
792A ALA 3.0 14.8 + - - +
793A LEU* 3.7 11.4 - - + +
795A ASP* 1.3 76.2 - - - +
797A GLN* 1.3 69.5 + - + +
799A GLN* 3.4 3.8 + - - +
800A LEU* 3.0 54.7 + - + +
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Residues in contact with GLN 797 (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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793A LEU* 3.1 42.4 + - + +
794A ARG* 3.6 18.7 - - - +
796A TYR* 1.3 83.2 - - + +
798A GLY* 1.3 58.9 + - - +
800A LEU* 3.4 7.2 + - + +
801A GLU* 2.8 43.5 + - + +
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Residues in contact with GLY 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A ARG 3.0 15.6 + - - -
795A ASP* 3.1 4.7 + - - -
797A GLN* 1.3 74.3 - - - +
799A GLN* 1.3 57.3 + - - +
801A GLU* 3.2 14.5 + - - +
802A ARG* 2.9 32.9 + - - +
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Residues in contact with GLN 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A SER* 3.8 12.1 + - - +
487A ASN 4.6 1.3 - - - +
488A ALA* 3.5 31.8 - - - +
491A ALA* 3.8 16.6 - - + +
554A TYR* 4.9 2.1 + - - +
795A ASP* 2.9 35.9 + - - +
796A TYR* 3.5 9.6 - - - +
798A GLY* 1.3 74.3 - - - +
800A LEU* 1.4 60.6 + - - +
802A ARG* 2.8 42.0 + - - +
803A VAL* 3.2 25.8 + - - +
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Residues in contact with LEU 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ALA* 3.3 29.5 - - + +
494A THR* 3.8 19.3 - - + -
495A PHE* 3.9 3.8 - - + +
796A TYR* 3.0 46.7 + - + +
797A GLN* 3.7 7.6 - - + +
799A GLN* 1.4 73.4 - - - +
801A GLU* 1.3 61.8 + - - +
803A VAL* 3.2 10.1 - - - +
804A PHE* 3.1 51.6 + - + -
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Residues in contact with GLU 801 (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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797A GLN* 2.8 30.8 + - + +
798A GLY* 3.2 11.0 + - - +
800A LEU* 1.3 73.3 - - - +
802A ARG* 1.4 59.9 + - - +
804A PHE* 3.1 8.9 + - - +
805A ASN* 2.8 37.0 + - - +
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Residues in contact with ARG 802 (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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554A TYR* 3.4 38.1 + - - -
798A GLY 2.9 26.4 + - - +
799A GLN* 2.8 41.3 + - - +
801A GLU* 1.4 69.4 - - - +
803A VAL* 1.3 58.9 + - - +
805A ASN* 4.1 7.4 - - + -
806A GLU* 2.8 56.8 + - + +
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Residues in contact with VAL 803 (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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491A ALA* 4.5 6.7 - - + +
492A PHE* 4.4 7.0 - - + -
495A PHE* 3.6 46.9 - - + -
554A TYR* 3.6 44.9 - - + +
799A GLN 3.2 14.7 + - - +
800A LEU* 3.2 25.1 - - + +
802A ARG* 1.3 77.8 - - - +
804A PHE* 1.3 61.0 + - - +
807A VAL* 3.2 31.7 + - + +
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Residues in contact with PHE 804 (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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494A THR* 5.3 1.1 - - + -
495A PHE* 3.6 33.2 - + - -
498A THR* 3.7 32.8 - - + -
499A LYS* 4.0 23.7 + - + -
800A LEU* 3.1 47.1 + - + -
801A GLU* 3.1 9.9 + - - +
803A VAL* 1.3 76.7 - - - +
805A ASN* 1.3 55.9 + - - +
807A VAL* 4.0 1.4 - - - +
808A ARG* 3.0 47.3 + - - +
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Residues in contact with ASN 805 (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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801A GLU* 2.8 23.9 + - - +
802A ARG* 3.9 8.7 - - + +
803A VAL 3.4 0.2 - - - -
804A PHE* 1.3 73.7 - - - +
806A GLU* 1.4 64.5 + - + +
808A ARG* 3.2 36.6 + - - +
809A GLU* 3.4 31.7 + - - +
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Residues in contact with GLU 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A PRO* 5.1 4.3 - - - +
554A TYR* 3.3 44.5 + - + +
555A SER* 4.8 7.4 + - - +
802A ARG* 2.8 48.6 + - + +
805A ASN* 1.4 73.6 - - + +
807A VAL* 1.3 63.2 + - - +
809A GLU* 3.5 8.7 + - - +
810A LEU* 3.3 21.5 + - - +
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Residues in contact with VAL 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A PHE* 3.6 16.6 - - + -
499A LYS* 3.7 15.5 - - - +
500A TYR* 3.5 24.9 - - - +
554A TYR* 4.1 11.2 - - + +
558A PHE* 3.5 37.7 - - + +
803A VAL* 3.2 19.5 + - + +
804A PHE 4.3 0.7 - - - +
806A GLU* 1.3 74.3 - - - +
808A ARG* 1.4 64.7 + - - +
810A LEU* 3.6 10.9 + - + +
811A GLU* 3.2 26.5 + - + +
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Residues in contact with ARG 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A LYS* 4.4 4.9 - - - +
804A PHE* 3.0 27.8 + - - +
805A ASN* 3.2 57.4 + - - +
806A GLU 3.3 0.4 - - - -
807A VAL* 1.4 76.6 - - - +
809A GLU* 1.4 64.3 + - + +
811A GLU* 3.4 23.5 + - - +
812A LYS* 3.4 10.4 + - - +
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Residues in contact with GLU 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A ASN* 3.4 18.5 + - - +
806A GLU* 3.7 9.9 - - - +
807A VAL 3.4 0.2 - - - -
808A ARG* 1.4 75.7 + - - +
810A LEU* 1.3 64.0 + - - +
812A LYS* 3.2 19.2 + - - +
813A HIS* 3.2 13.2 + - - +
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Residues in contact with LEU 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A TYR 4.1 5.6 - - - +
555A SER* 3.7 33.2 - - - +
558A PHE* 3.3 42.4 - - + +
559A SER* 4.1 10.8 - - - -
806A GLU 3.3 12.4 + - - +
807A VAL* 3.7 13.0 - - + +
808A ARG 3.4 0.2 - - - -
809A GLU* 1.3 77.5 - - - +
811A GLU* 1.3 58.8 + - + +
813A HIS* 4.5 6.1 - - + +
814A GLU* 2.8 50.8 + - + +
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Residues in contact with GLU 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A LYS* 3.2 38.4 + - - -
500A TYR* 4.1 12.9 + - - +
807A VAL* 3.2 16.5 + - + +
808A ARG* 3.5 15.6 - - - +
809A GLU 3.2 0.2 - - - -
810A LEU* 1.3 78.3 - - + +
812A LYS* 1.4 58.9 + - - +
814A GLU* 3.8 16.3 - - - +
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Residues in contact with LYS 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A ARG 3.4 8.5 + - - +
809A GLU* 3.2 15.6 + - - +
811A GLU* 1.4 76.8 - - - +
813A HIS* 1.4 63.9 + - - +
814A GLU 4.3 1.7 - - - +
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Residues in contact with HIS 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A GLU 3.2 11.9 + - - +
810A LEU* 3.9 9.9 - - + +
812A LYS* 1.4 78.4 - - - +
814A GLU* 1.4 63.2 + - + +
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Residues in contact with GLU 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A SER* 5.5 1.3 - - - -
560A GLU* 3.4 31.2 - - + +
810A LEU* 2.8 36.0 + - + +
811A GLU* 3.8 18.0 - - - +
812A LYS 4.3 1.7 - - - +
813A HIS* 1.4 77.7 - - - +
----------------------------------------------------------
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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