Contacts of the helix formed by residues 640 - 665 (chain A) in PDB entry 5XJY
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 MET 640 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A MET* 2.9 11.3 + - + +
637A SER* 3.8 13.2 - - - +
638A ARG 3.5 1.2 - - - -
639A SER* 1.3 76.7 - - - +
641A PRO* 1.3 64.4 - - + +
642A LEU 2.9 7.1 + - - -
643A PHE* 3.3 39.1 + - + -
644A MET* 3.1 40.0 + - + +
700A LEU* 5.5 3.8 - - + -
704A LEU* 4.7 12.8 - - + -
709A LEU* 6.2 0.2 - - + -
710A LEU* 3.9 29.2 - - + -
787A PHE* 4.4 8.5 - - + -
791A CYS* 3.5 34.5 - - - -
794A PHE* 5.6 1.6 - - + -
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Residues in contact with PRO 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ARG 4.6 1.3 - - - +
639A SER* 3.6 4.5 - - - -
640A MET* 1.3 90.2 - - + +
642A LEU* 1.3 55.0 + - - +
644A MET* 4.0 2.7 - - + -
645A THR* 2.2 40.9 + - - +
725A PHE* 5.9 0.2 - - + -
758A TYR* 3.5 33.3 - - + +
761A TYR* 3.9 19.1 - - + +
784A PRO* 4.8 2.9 - - + +
787A PHE* 3.6 33.0 - - + -
788A GLY* 4.2 14.6 - - - -
791A CYS* 5.2 1.8 - - + -
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Residues in contact with LEU 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A SER* 3.9 21.5 + - - +
640A MET 2.9 3.4 + - - -
641A PRO* 1.3 77.7 - - - +
643A PHE* 1.3 61.7 + - + +
645A THR* 2.8 22.1 + - + +
646A LEU* 2.9 13.9 + - - +
649A ILE* 5.7 0.2 - - - +
755A PHE* 5.9 7.6 - - + -
758A TYR* 3.5 37.2 - - + +
759A LEU* 6.0 1.1 - - + -
762A VAL* 4.8 9.0 - - + -
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Residues in contact with PHE 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.5 14.5 - - + +
36A PHE* 3.2 39.0 - + + -
39A LEU* 3.6 29.2 - - + -
636A MET* 3.6 32.8 - - + -
639A SER* 3.2 26.0 - - - -
640A MET* 3.5 38.1 - - + -
642A LEU* 1.3 77.5 - - + +
644A MET* 1.3 63.4 + - - +
646A LEU* 3.8 16.7 + - + +
647A ALA 4.3 3.3 + - - -
700A LEU* 6.0 1.3 - - + -
704A LEU* 6.5 0.2 - - + -
709A LEU* 5.8 4.3 - - + -
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Residues in contact with MET 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE* 3.5 25.6 - - + -
640A MET* 3.1 43.9 + - + +
641A PRO* 4.0 7.4 - - + -
643A PHE* 1.3 77.4 - - + +
645A THR* 1.3 63.6 + - - +
646A LEU 3.3 0.4 + - - -
647A ALA* 4.2 2.3 + - - +
648A TRP* 4.0 45.4 + - + +
700A LEU* 3.8 21.5 - - + -
722A LEU* 3.7 36.8 - - + -
725A PHE* 5.2 3.3 - - + -
787A PHE* 4.1 14.1 - - + -
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Residues in contact with THR 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A PRO* 2.2 29.2 + - - +
642A LEU* 2.8 12.0 + - + +
644A MET* 1.3 77.4 - - - +
646A LEU* 1.3 49.8 + - - +
648A TRP* 3.0 7.5 + - - +
649A ILE* 2.7 52.5 + - + +
725A PHE* 4.9 12.0 - - - -
754A TYR* 3.8 22.1 + - + +
755A PHE* 5.4 4.0 - - + -
758A TYR* 4.2 27.1 - - + -
784A PRO* 5.4 1.7 - - - +
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Residues in contact with LEU 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TRP* 3.5 24.7 + - + +
35A ILE* 3.8 39.9 - - + -
642A LEU 2.9 11.8 + - - +
643A PHE* 4.1 10.8 - - + +
644A MET 3.3 1.2 - - - -
645A THR* 1.3 76.1 - - - +
647A ALA* 1.3 63.6 + - - +
649A ILE* 3.0 38.7 + - + +
650A TYR 3.3 4.7 + - - -
755A PHE* 5.9 2.7 - - + -
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Residues in contact with ALA 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 5.3 1.7 - - - +
31A TRP* 3.4 14.4 - - + +
32A PRO* 3.8 38.1 - - + -
35A ILE* 6.0 1.9 - - + +
36A PHE* 5.1 5.4 - - + -
643A PHE 4.3 6.0 + - - +
644A MET 4.2 4.1 + - - +
645A THR 3.5 0.2 - - - -
646A LEU* 1.3 78.4 - - - +
648A TRP* 1.3 72.0 + - + +
650A TYR* 3.4 6.8 + - - +
651A SER* 2.9 25.6 + - - -
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Residues in contact with TRP 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 5.9 0.2 - - - +
644A MET* 4.0 30.6 - - + +
645A THR 3.0 8.5 + - - +
647A ALA* 1.3 93.7 - - + +
649A ILE* 1.3 59.8 + - - +
651A SER* 3.7 9.9 - - - -
652A VAL* 2.9 33.1 + - + +
693A LEU* 3.6 28.9 - - + +
696A SER* 3.2 28.8 + - - -
697A ALA* 4.1 13.9 - - + -
722A LEU* 3.7 21.1 - - + -
725A PHE* 3.4 39.3 - + - -
726A ALA* 3.8 20.0 - - + -
729A THR* 3.9 15.9 - - + -
754A TYR* 3.4 13.2 - - - +
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Residues in contact with ILE 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A THR* 2.7 24.0 + - + +
646A LEU* 3.0 34.7 + - + +
648A TRP* 1.3 76.5 - - - +
650A TYR* 1.3 63.2 + - - +
652A VAL* 4.0 1.7 - - - +
653A ALA* 3.0 24.1 + - + +
751A GLY* 4.1 23.6 - - - +
754A TYR* 3.5 21.1 - - + -
755A PHE* 3.5 35.0 - - + -
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Residues in contact with TYR 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.3 39.3 + - - +
27A LEU* 3.4 36.3 - - + +
28A GLU* 3.3 51.4 - - - -
31A TRP* 4.5 14.4 - - + +
646A LEU 3.3 7.9 + - - +
647A ALA 3.4 8.0 + - - +
648A TRP 3.3 0.2 - - - -
649A ILE* 1.3 81.3 - - - +
651A SER* 1.3 60.5 + - - +
653A ALA* 3.3 8.6 + - + +
654A VAL* 3.0 37.8 + - + +
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Residues in contact with SER 651 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 2.4 39.6 + - - -
647A ALA 2.9 18.0 + - - -
648A TRP* 3.8 7.4 - - - -
649A ILE 3.3 0.2 - - - -
650A TYR* 1.3 74.1 - - - +
652A VAL* 1.3 63.9 + - - +
654A VAL* 3.2 3.3 + - - +
655A ILE* 3.0 26.2 + - - +
693A LEU* 3.6 30.7 - - - +
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Residues in contact with VAL 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TRP* 2.9 21.7 + - + +
649A ILE 4.0 2.9 - - - +
651A SER* 1.3 75.7 - - - +
653A ALA* 1.3 59.6 + - - +
655A ILE* 3.3 8.5 - - + +
656A ILE* 2.9 31.1 + - + +
693A LEU* 6.1 2.9 - - + -
729A THR* 3.8 28.5 - - + +
730A ILE* 5.9 0.2 - - - -
733A CYS* 3.7 27.4 - - + -
736A ILE* 4.4 16.2 - - + -
750A GLY 4.7 8.7 - - - +
751A GLY 5.0 0.2 - - - +
754A TYR* 4.1 20.4 - - + +
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Residues in contact with ALA 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ILE* 3.0 21.2 + - + +
650A TYR* 3.5 11.4 - - + +
652A VAL* 1.3 78.3 - - - +
654A VAL* 1.3 64.0 + - + +
656A ILE* 3.3 11.0 - - - +
657A LYS* 3.0 24.7 + - - +
747A ALA* 4.1 20.3 - - - +
751A GLY* 5.2 10.1 - - - +
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Residues in contact with VAL 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.9 26.0 + - + +
21A GLN* 5.6 1.6 - - - +
24A GLN* 4.5 22.4 - - + +
28A GLU* 4.4 7.6 - - + +
650A TYR* 3.0 50.2 + - + +
651A SER 3.2 6.5 + - - +
653A ALA* 1.3 77.8 - - + +
655A ILE* 1.3 57.6 + - - +
657A LYS* 3.2 14.9 + - - +
658A GLY* 3.0 24.3 + - - -
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Residues in contact with ILE 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ARG* 3.4 24.9 - - - +
651A SER 3.0 17.8 + - - +
652A VAL* 3.3 11.7 - - + +
654A VAL* 1.3 77.3 - - - +
656A ILE* 1.3 60.5 + - - +
658A GLY 3.2 1.6 + - - +
659A ILE* 3.0 27.1 + - + +
685A TRP* 3.9 26.0 - - + +
689A SER* 3.3 39.5 - - - +
693A LEU* 5.8 3.8 - - + -
730A ILE* 5.8 2.0 - - + -
733A CYS* 3.6 18.6 - - + -
734A PHE* 4.9 13.0 - - + -
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Residues in contact with ILE 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A VAL* 2.9 22.8 + - + +
653A ALA* 3.3 13.5 - - - +
655A ILE* 1.3 75.2 - - - +
657A LYS* 1.3 67.5 + - - +
659A ILE* 3.9 4.2 - - - +
660A VAL* 3.1 27.9 + - + +
733A CYS* 3.7 8.5 - - - +
736A ILE* 3.6 46.9 - - + +
737A SER* 3.5 23.6 - - - +
740A PHE* 4.8 6.7 - - + -
746A ALA* 4.1 25.1 - - + +
747A ALA* 4.6 0.2 - - - -
750A GLY* 4.5 11.2 - - - -
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Residues in contact with LYS 657 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 5.0 10.7 - - - +
24A GLN* 4.5 24.8 - - - +
653A ALA 3.0 20.4 + - - +
654A VAL* 3.2 13.0 + - - +
656A ILE* 1.3 73.6 - - - +
658A GLY* 1.3 54.1 + - - +
660A VAL* 4.3 4.4 - - - +
661A TYR* 2.7 46.9 + - + +
743A ALA* 4.6 8.5 - - + +
744A ASN* 4.3 10.8 - - - +
747A ALA* 3.7 28.5 - - + +
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Residues in contact with GLY 658 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 6.0 1.9 - - - -
18A ARG* 5.8 2.2 - - - -
654A VAL 3.0 14.2 + - - -
655A ILE* 3.2 5.5 + - - -
657A LYS* 1.3 77.2 - - - +
659A ILE* 1.3 61.8 + - - +
661A TYR* 3.5 4.7 - - - +
662A GLU* 3.1 26.7 + - - +
685A TRP* 4.1 19.6 - - - -
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Residues in contact with ILE 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A ILE* 3.0 17.9 + - + +
656A ILE* 3.3 1.8 + - - +
658A GLY* 1.3 77.2 - - - +
660A VAL* 1.3 61.3 + - + +
662A GLU* 3.3 11.8 + - - +
663A LYS* 2.9 29.4 + - + +
668A LYS* 5.6 4.5 - - + +
682A TRP* 4.6 20.2 - - + -
685A TRP* 3.4 50.5 - - + +
733A CYS* 6.4 0.4 - - - -
734A PHE* 4.1 20.0 - - + -
737A SER* 3.2 29.2 - - - +
738A THR* 6.0 0.4 - - - -
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Residues in contact with VAL 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A ILE* 3.1 15.8 + - + +
657A LYS* 4.3 2.0 - - - +
659A ILE* 1.3 76.3 - - + +
661A TYR* 1.3 61.8 + - - +
663A LYS* 3.5 13.7 - - + +
664A GLU* 2.9 27.2 + - - +
737A SER* 3.4 32.1 - - - +
740A PHE* 4.0 25.4 - - + +
741A SER 5.8 1.1 - - - -
742A ARG 3.9 13.4 + - - +
743A ALA* 4.0 12.1 + - - +
746A ALA* 3.6 23.8 - - + -
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Residues in contact with TYR 661 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 5.9 10.1 - + - -
657A LYS* 2.7 31.1 + - + +
658A GLY* 3.5 7.6 - - - +
660A VAL* 1.3 78.0 - - - +
662A GLU* 1.3 68.6 + - + +
664A GLU* 3.2 34.2 + - - +
665A ALA* 3.5 12.5 + - + +
667A LEU* 5.8 5.2 - - + -
743A ALA* 4.6 13.2 - - + -
986A ASP* 3.3 32.7 - - + +
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Residues in contact with GLU 662 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 4.9 7.2 + - - +
17A PHE* 5.2 7.0 - - + -
658A GLY 3.1 14.8 + - - +
659A ILE* 3.5 10.6 - - - +
661A TYR* 1.3 82.9 - - + +
663A LYS* 1.3 62.7 + - - +
665A ALA* 4.3 2.9 - - - +
666A ARG 3.6 0.2 + - - -
667A LEU* 3.0 52.4 + - + +
668A LYS* 3.2 43.7 + - - +
681A LEU* 6.1 0.6 - - - +
685A TRP* 3.6 35.6 + - + -
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Residues in contact with LYS 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A ILE* 2.9 21.7 + - + +
660A VAL* 3.7 14.4 - - + +
661A TYR 3.1 0.4 - - - -
662A GLU* 1.3 78.5 - - - +
664A GLU* 1.3 64.6 + - - +
666A ARG* 3.4 13.7 + - - +
668A LYS* 4.8 24.7 - - + +
669A GLU* 4.5 15.7 - - - +
737A SER 5.6 1.3 - - - +
738A THR* 3.5 32.4 + - - +
739A LEU 5.7 0.2 - - - -
740A PHE 4.3 17.9 + - - +
741A SER* 6.2 0.4 - - - +
846A PHE* 5.6 8.7 - - - +
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Residues in contact with GLU 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660A VAL 2.9 13.0 + - - +
661A TYR* 3.2 21.1 + - - +
663A LYS* 1.3 76.6 - - - +
665A ALA* 1.3 61.1 + - + +
666A ARG* 3.1 19.2 + - - +
741A SER 5.4 11.0 - - - +
742A ARG* 5.5 4.5 - - - +
743A ALA* 3.4 34.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A TYR* 3.5 17.6 + - + +
662A GLU* 4.3 0.4 + - - -
664A GLU* 1.3 78.7 - - + +
666A ARG* 1.3 70.2 + - - +
667A LEU* 3.3 17.2 + - + +
981A HIS* 4.8 6.4 - - - +
982A ASN 4.7 12.9 - - - +
983A VAL* 5.5 0.7 - - - -
986A ASP* 6.3 2.7 - - + -
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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