Contacts of the helix formed by residues 646 - 672 (chain A) in PDB entry 3IKM
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 VAL 646 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A GLY 2.9 9.5 + - - -
645A VAL* 1.3 97.5 - - - +
647A CYS* 1.3 80.5 + - + +
649A TYR* 4.9 0.3 - - - +
650A ARG* 4.0 22.2 + - + +
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Residues in contact with CYS 647 (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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645A VAL* 2.7 32.4 - - - +
646A VAL* 1.3 84.8 - - + +
648A PRO* 1.4 71.7 - - + +
649A TYR* 2.9 24.3 + - + +
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Residues in contact with PRO 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A CYS* 1.4 91.3 - - + +
649A TYR* 1.3 56.6 + - + +
651A ALA* 2.9 12.3 + - + +
652A ILE* 2.3 60.6 + - + +
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Residues in contact with TYR 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646A VAL 4.9 0.4 - - - +
647A CYS* 2.9 20.7 - - + -
648A PRO* 1.3 78.4 - - + +
650A ARG* 1.3 54.0 + - + +
651A ALA 2.9 4.5 - - - -
652A ILE* 2.7 24.5 + - + -
653A GLU* 2.1 47.5 + - - +
656A TYR* 4.8 11.7 - + - +
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Residues in contact with ARG 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A GLU* 3.4 38.9 + - - +
642A SER* 3.7 15.4 - - - +
645A VAL* 2.5 63.3 + - + +
646A VAL* 4.0 13.9 + - + +
647A CYS 3.5 4.0 + - - -
649A TYR* 1.3 77.7 - - + +
651A ALA* 1.3 48.0 + - - +
653A GLU* 3.7 18.6 + - - +
654A SER* 2.8 34.7 + - - -
657A ARG* 5.5 6.4 + - - +
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Residues in contact with ALA 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A GLU* 6.0 1.8 - - - +
645A VAL* 3.9 14.6 - - + +
648A PRO* 2.9 17.8 + - + +
649A TYR 2.9 0.6 - - - -
650A ARG* 1.3 73.9 - - - +
652A ILE* 1.3 52.1 + - + +
654A SER* 2.6 22.3 + - - -
655A LEU* 2.8 27.2 + - + +
713A PRO* 5.9 0.5 - - - +
722A ARG* 5.8 1.8 - - - +
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Residues in contact with ILE 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A PRO* 2.3 59.3 + - + +
649A TYR* 3.5 20.4 - - + +
651A ALA* 1.3 65.2 - - + +
653A GLU* 1.3 51.1 + - - +
655A LEU* 2.5 45.0 - - + +
656A TYR* 2.7 33.3 + - + -
719A LEU 4.6 0.4 - - - +
720A THR 4.5 8.5 - - - +
722A ARG* 4.1 29.6 - - + +
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Residues in contact with GLU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A TYR* 2.1 37.5 + - - +
650A ARG* 3.7 16.0 + - - +
652A ILE* 1.3 66.0 - - - +
654A SER* 1.3 58.2 + - - +
655A LEU 2.9 1.6 - - - -
656A TYR* 2.9 39.4 + - + +
657A ARG* 2.6 81.4 + - - +
744A ILE* 4.2 2.5 - - + -
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Residues in contact with SER 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A ARG 2.8 21.0 + - - -
651A ALA* 2.6 29.1 + - - -
653A GLU* 1.3 75.5 - - - +
655A LEU* 1.3 49.7 + - - +
657A ARG* 3.1 14.4 + - - +
658A LYS* 2.6 48.1 + - - +
713A PRO* 4.8 3.8 - - - +
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Residues in contact with LEU 655 (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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651A ALA* 2.8 18.6 - - + +
652A ILE* 2.5 42.8 - - + +
653A GLU 2.9 0.8 - - - -
654A SER* 1.3 77.0 + - - +
656A TYR* 1.3 46.9 + - - -
657A ARG 2.8 4.3 - - - -
659A HIS* 2.5 35.4 + - - +
712A VAL 4.7 0.2 - - - +
713A PRO* 3.8 21.7 - - + +
719A LEU* 2.6 58.3 - - + +
720A THR* 3.1 5.6 - - - +
722A ARG* 3.0 41.3 - - - +
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Residues in contact with TYR 656 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A TYR* 4.1 12.9 + + - +
652A ILE* 2.7 39.7 + - + -
653A GLU* 2.9 57.4 + - + +
655A LEU* 1.3 73.1 - - - +
657A ARG* 1.3 54.7 + - - +
659A HIS* 3.1 12.8 - - + +
660A CYS* 3.0 20.1 + - - +
663A GLN* 3.6 6.3 - - - +
720A THR* 2.5 47.6 - - + +
743A ASP* 4.7 10.5 + - + +
744A ILE* 2.9 45.5 - - + +
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Residues in contact with ARG 657 (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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630A ASN* 3.6 12.8 - - - +
631A LEU 4.5 1.8 + - - -
632A ALA* 3.2 42.1 - - - +
642A SER* 5.5 7.5 + - - -
650A ARG* 5.5 8.3 + - - +
653A GLU* 2.6 57.7 + - - +
654A SER* 3.1 13.5 - - - +
655A LEU 2.8 1.2 - - - -
656A TYR* 1.3 77.8 - - - +
658A LYS* 1.3 68.4 + - - +
659A HIS 3.1 0.4 - - - -
660A CYS* 2.5 27.9 - - + +
661A LEU* 3.4 2.4 + - - +
744A ILE* 3.3 29.9 - - + +
745A PRO* 5.7 0.2 - - - -
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Residues in contact with LYS 658 (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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654A SER* 2.6 27.0 + - - +
657A ARG* 1.3 76.4 - - - +
659A HIS* 1.3 53.2 + - - +
660A CYS* 2.5 10.7 + - - -
661A LEU* 3.3 1.4 + - - +
662A GLU* 2.5 33.2 - - - +
710A ALA* 6.3 2.9 - - + -
713A PRO* 2.6 54.7 - - + +
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Residues in contact with HIS 659 (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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612A LEU* 4.6 3.0 - - + +
613A HIS* 4.4 1.6 - - - -
614A TYR 5.7 0.8 + - - -
655A LEU 2.5 22.7 + - - +
656A TYR* 3.1 5.6 - - - -
658A LYS* 1.3 74.3 - - - +
660A CYS* 1.3 48.8 + - - +
662A GLU* 2.9 10.1 - - - +
663A GLN* 2.7 82.8 + - - +
713A PRO 3.3 2.8 + - - -
716A PRO* 2.6 53.5 + - + +
717A LEU* 3.5 4.5 + - - -
719A LEU* 3.0 9.6 - - + -
720A THR* 2.8 50.2 - - + +
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Residues in contact with CYS 660 (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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630A ASN* 5.5 2.7 - - - -
656A TYR 3.0 4.4 + - - +
657A ARG* 2.5 29.0 + - - +
658A LYS 2.5 4.2 + - - -
659A HIS* 1.3 70.9 - - - +
661A LEU* 1.3 98.1 + - - -
662A GLU 3.0 1.3 - - - -
663A GLN* 3.1 18.7 + - - +
664A GLY* 3.1 10.7 + - - -
745A PRO* 2.8 44.6 - - + +
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Residues in contact with LEU 661 (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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657A ARG 4.8 0.9 - - - +
658A LYS 3.3 4.4 + - - +
660A CYS* 1.3 90.8 - - - +
662A GLU* 1.3 65.6 + - - +
664A GLY* 3.3 3.2 + - - -
665A LYS* 2.8 34.9 + - + +
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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
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658A LYS* 2.5 57.1 - - - +
659A HIS* 2.9 13.5 - - - +
661A LEU* 1.3 85.2 - - - +
663A GLN* 1.3 50.3 + - - +
665A LYS* 3.2 18.6 - - + +
666A GLN* 2.5 45.1 + - + +
713A PRO 3.5 4.7 - - - +
714A GLY* 4.2 17.4 - - - +
716A PRO* 5.3 4.7 - - + -
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Residues in contact with GLN 663 (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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612A LEU* 2.8 39.7 - - + +
613A HIS* 4.1 9.6 - - + -
621A GLY* 4.7 6.5 - - - -
622A TYR 5.3 7.7 + - - +
656A TYR* 3.6 12.1 - - - +
659A HIS* 2.7 66.6 + - + +
660A CYS* 3.1 8.8 + - - +
662A GLU* 1.3 71.3 - - - +
664A GLY* 1.3 53.7 + - - +
666A GLN* 3.3 8.4 + - - +
667A GLN* 2.6 41.4 + - - +
716A PRO* 3.7 4.9 - - + -
720A THR* 5.2 1.1 - - - +
745A PRO* 5.4 3.1 - - - +
746A GLY* 5.9 1.3 + - - -
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Residues in contact with GLY 664 (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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623A LEU* 4.2 10.1 - - - +
660A CYS 3.1 9.8 + - - -
661A LEU* 3.6 3.8 - - - -
663A GLN* 1.3 76.6 - - - +
665A LYS* 1.3 54.3 + - - +
667A GLN* 2.7 39.1 - - - +
668A LEU* 2.7 21.5 - - - +
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Residues in contact with LYS 665 (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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661A LEU* 2.8 20.5 + - + +
662A GLU* 3.2 25.1 - - + +
664A GLY* 1.3 68.8 - - - -
666A GLN* 1.3 91.1 + - - +
667A GLN 3.2 0.3 + - - -
668A LEU* 3.4 14.6 - - + +
669A MET* 3.0 50.3 + - + +
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Residues in contact with GLN 666 (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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607A TRP* 5.7 3.5 + - - -
611A PRO* 5.3 2.2 - - - +
612A LEU 3.5 8.5 + - - -
613A HIS* 3.0 42.6 + - + +
662A GLU* 2.5 23.0 + - + +
663A GLN* 3.4 6.3 + - - +
665A LYS* 1.3 81.1 - - + +
667A GLN* 1.3 51.7 - - - +
669A MET* 3.3 26.2 - - + +
670A PRO* 2.1 47.2 - - + +
716A PRO* 5.4 2.7 - - + -
783A PRO* 5.1 13.2 - - - +
363C ARG* 5.4 7.8 + - - +
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Residues in contact with GLN 667 (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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611A PRO* 3.5 28.4 - - + +
612A LEU* 5.6 1.3 - - - +
622A TYR* 4.0 5.7 - - - +
623A LEU* 2.7 65.6 - - - +
663A GLN* 2.6 15.1 + - - +
664A GLY* 2.7 31.0 - - - +
666A GLN* 1.3 74.3 - - - +
668A LEU* 1.3 70.5 + - + +
670A PRO* 2.5 22.9 - - - +
671A GLN* 2.7 22.4 + - + +
672A GLU* 5.5 2.7 - - - +
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Residues in contact with LEU 668 (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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623A LEU* 4.7 10.5 - - + -
664A GLY 2.7 26.5 - - - +
665A LYS* 3.4 17.5 - - - +
667A GLN* 1.3 87.1 - - + +
669A MET* 1.3 71.6 + - + +
672A GLU* 2.9 50.5 + - + +
673A ALA 3.4 0.3 + - - -
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Residues in contact with MET 669 (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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665A LYS* 3.0 45.7 + - + +
666A GLN* 3.3 42.2 - - + +
668A LEU* 1.3 78.2 - - + +
670A PRO* 1.3 49.1 - - + -
672A GLU 5.1 0.2 - - - -
673A ALA* 2.1 46.1 + - + +
363C ARG 5.7 4.3 - - - +
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Residues in contact with PRO 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A TRP* 3.1 23.4 - - + +
666A GLN* 2.1 42.4 - - + +
667A GLN* 2.5 18.2 - - - +
669A MET* 1.3 77.0 - - + +
671A GLN* 1.3 89.8 + - - +
673A ALA* 2.8 24.0 + - + +
783A PRO* 5.8 6.7 - - + -
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Residues in contact with GLN 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A TRP* 2.6 60.5 - - - +
610A PHE* 3.0 37.1 - - + +
611A PRO* 3.2 39.4 - - + +
666A GLN* 5.5 0.4 - - - +
667A GLN* 2.7 26.3 + - + +
670A PRO* 1.3 82.9 - - - +
672A GLU* 1.3 70.6 + - + +
673A ALA 3.3 2.8 + - - -
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Residues in contact with GLU 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A GLN* 5.5 2.6 - - - +
668A LEU* 2.9 35.9 + - + +
669A MET 3.4 2.0 - - - -
671A GLN* 1.3 81.7 - - + +
673A ALA* 1.3 60.6 + - - +
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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