Contacts of the helix formed by residues 603 - 623 (chain A) in PDB entry 5I35
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 PRO 603 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A PHE* 3.7 29.8 - - + -
544A MSE 4.0 7.4 - - - +
545A LYS* 3.6 32.3 - - + +
601A PRO 3.5 4.1 - - - +
602A PRO* 1.3 84.3 - - + +
604A GLU* 1.3 65.4 + - - +
605A GLU* 3.1 14.1 - - - +
606A THR* 2.8 31.9 + - + +
607A TYR* 3.8 1.9 + - - -
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Residues in contact with GLU 604 (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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280A MSE 5.2 0.9 - - - +
393A HIS* 4.4 8.8 - - + -
397A VAL* 3.8 34.4 - - + +
401A GLU* 5.2 8.0 - - - +
514A TYR* 4.9 4.7 - - + +
596A ARG* 2.7 43.3 + - - -
602A PRO 3.4 3.5 + - - +
603A PRO* 1.3 71.0 - - - +
605A GLU* 1.3 67.3 + - - +
606A THR 3.1 0.2 + - - -
607A TYR* 3.2 26.0 + - - +
608A SER* 3.1 22.4 + - - -
611A LYS* 5.1 1.4 - - - -
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Residues in contact with GLU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A TYR* 3.2 47.3 - - + -
515A ASP* 5.6 1.6 + - - +
518A PHE* 3.3 47.0 - - + -
603A PRO* 3.6 9.2 - - - +
604A GLU* 1.3 83.4 + - - +
606A THR* 1.3 62.6 + - - +
608A SER* 3.3 3.5 - - - -
609A LEU* 3.1 29.6 + - + +
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Residues in contact with THR 606 (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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518A PHE* 3.9 14.1 - - + -
544A MSE 3.7 53.3 - - + +
546A PHE* 3.2 29.2 - - - +
602A PRO* 3.5 8.3 - - - +
603A PRO* 2.8 22.7 + - + +
605A GLU* 1.3 76.2 - - - +
607A TYR* 1.3 63.2 + - - +
609A LEU* 3.1 15.8 + - - +
610A HIS* 3.2 18.7 + - - -
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Residues in contact with TYR 607 (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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546A PHE* 4.1 14.3 - + - -
591A ILE* 3.3 37.2 - - + +
592A PRO 4.4 2.0 + - - -
595A LEU* 3.6 11.1 - - - +
596A ARG* 2.9 53.0 + - + +
601A PRO* 5.7 0.7 - - + -
602A PRO* 3.6 34.9 - - + +
603A PRO 4.2 4.3 - - - -
604A GLU* 3.2 39.9 + - - +
606A THR* 1.3 81.6 + - - +
608A SER* 1.3 59.0 + - - +
609A LEU 3.3 0.2 + - - -
610A HIS* 3.4 2.3 + - - +
611A LYS* 2.8 54.5 + - - +
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Residues in contact with SER 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A MSE 4.9 1.5 - - - +
487A THR* 3.9 18.7 - - - +
514A TYR* 2.7 39.7 + - - -
604A GLU 3.1 6.1 + - - -
605A GLU 3.3 9.9 - - - -
607A TYR* 1.3 79.9 - - - +
609A LEU* 1.3 54.9 + - - +
611A LYS* 3.2 9.8 + - - +
612A LYS* 2.7 36.8 + - - +
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Residues in contact with LEU 609 (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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479A LEU* 3.7 25.3 - - + +
480A PHE* 6.5 0.2 - - + -
485A MSE 3.7 22.0 - - + -
514A TYR* 4.8 6.1 - - + -
518A PHE* 4.1 26.7 - - + +
519A THR* 4.4 11.7 - - + +
522A TYR* 3.6 51.3 + - + -
544A MSE 4.5 6.1 - - - -
605A GLU 3.1 17.9 + - - +
606A THR* 3.1 5.8 + - - +
608A SER* 1.3 77.5 - - - +
610A HIS* 1.3 63.5 + - - +
612A LYS* 3.3 5.4 + - - +
613A MSE 3.1 19.2 + - - +
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Residues in contact with HIS 610 (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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522A TYR* 3.1 34.1 + + - -
525A ILE* 4.9 7.0 - - + +
541A SER* 5.3 1.0 + - - -
544A MSE 4.3 12.8 - - + +
546A PHE* 4.1 21.0 - + - +
559A HIS* 3.9 10.9 + + - -
563A ILE* 3.9 29.7 - - + +
590A LEU* 3.6 33.8 - - + +
591A ILE* 3.4 21.3 - - + +
606A THR 3.2 15.3 + - - +
607A TYR 3.9 1.3 - - - +
609A LEU* 1.3 76.8 - - - +
611A LYS* 1.3 59.7 + - - +
613A MSE 4.2 0.2 - - - +
614A GLY* 2.9 27.7 + - - -
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Residues in contact with LYS 611 (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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279A GLN 4.2 3.7 + - - +
280A MSE 3.1 34.2 + - - +
282A SER* 5.4 3.8 + - - -
487A THR* 6.5 0.2 - - - -
488A ASP* 3.5 31.9 - - - +
489A PRO* 4.0 5.6 - - - +
591A ILE* 4.3 19.3 - - + +
596A ARG* 3.7 11.4 - - - +
604A GLU* 5.1 1.3 - - - -
607A TYR* 2.8 53.5 + - - +
608A SER* 3.7 7.4 - - - +
610A HIS* 1.3 69.8 - - - +
612A LYS* 1.3 62.8 + - - +
614A GLY* 5.0 0.2 - - - -
615A GLY* 2.8 30.1 + - - +
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Residues in contact with LYS 612 (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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475A CYS* 3.8 28.3 - - - +
478A GLU* 2.9 40.7 + - - -
479A LEU* 3.9 20.0 - - + -
485A MSE 4.4 10.5 - - - -
486A GLN* 2.6 36.4 + - - +
487A THR* 5.2 2.5 - - - -
488A ASP 5.2 0.6 - - - +
489A PRO* 3.6 23.0 - - + +
494A PHE* 5.9 3.6 - - - -
608A SER 2.7 21.5 + - - +
609A LEU 3.7 4.7 - - - +
610A HIS 3.2 0.4 - - - -
611A LYS* 1.3 73.7 - - - +
613A MSE 1.3 60.7 + - - +
616A SER* 2.9 34.3 + - - -
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Residues in contact with MSE 613 (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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472A LEU* 4.7 2.2 - - - -
475A CYS* 4.2 20.0 - - - -
476A LEU* 4.2 12.1 - - + -
479A LEU* 4.0 18.1 - - + +
480A PHE* 4.6 2.7 - - + -
522A TYR* 3.6 21.8 - - + +
526A ILE* 3.7 32.1 - - + -
566A LEU* 3.5 25.8 - - + -
570A PHE* 4.0 20.2 - - + -
609A LEU 3.1 7.5 + - - +
610A HIS 4.2 0.9 - - - +
612A LYS* 1.3 74.3 - - - +
614A GLY* 1.3 65.8 + - - +
616A SER* 3.1 3.5 + - - -
617A PHE* 3.0 48.8 + - + -
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Residues in contact with GLY 614 (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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566A LEU* 5.2 0.7 - - - -
587A ILE* 3.8 9.5 - - - +
590A LEU* 3.6 20.1 - - - +
610A HIS 2.9 18.6 + - - -
611A LYS* 5.0 0.4 - - - -
613A MSE 1.3 76.5 - - - +
615A GLY* 1.3 58.8 + - - +
617A PHE* 3.2 7.7 + - - +
618A LEU* 2.9 34.4 + - - +
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Residues in contact with GLY 615 (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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489A PRO* 4.0 17.4 - - - +
611A LYS* 2.8 18.5 + - - +
614A GLY* 1.3 79.5 - - - +
616A SER* 1.4 59.1 + - - +
618A LEU* 3.2 14.0 + - - +
619A ILE* 3.2 26.9 + - - +
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Residues in contact with SER 616 (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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471A ILE* 4.9 11.3 - - - +
472A LEU* 3.9 22.2 - - - -
475A CYS* 3.4 19.8 - - - +
489A PRO* 4.0 9.2 - - - +
612A LYS* 2.9 21.1 + - - -
613A MSE 3.1 5.8 + - - -
615A GLY* 1.4 71.5 - - - +
617A PHE* 1.3 69.1 + - - +
618A LEU 3.3 0.2 + - - -
619A ILE* 3.3 14.2 + - - +
620A CYS* 3.3 26.4 + - - -
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Residues in contact with PHE 617 (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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472A LEU* 4.1 14.8 - - + -
565A ILE 5.9 0.2 - - - -
566A LEU* 3.4 33.7 - - + -
569A ALA* 3.9 21.8 - - + -
570A PHE* 3.9 36.1 - + - -
576A PHE* 4.1 3.8 - + - -
578A PHE* 3.6 28.7 - + - -
582A SER* 3.2 24.7 + - - +
587A ILE* 4.1 9.0 - - + -
613A MSE 3.0 35.3 + - + +
614A GLY 3.2 8.9 + - - +
616A SER* 1.3 78.1 - - - +
618A LEU* 1.3 56.2 + - - +
620A CYS* 3.2 6.3 + - - +
621A SER* 3.1 23.6 + - - -
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Residues in contact with LEU 618 (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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284A GLN* 3.6 25.8 - - - +
582A SER 3.5 19.7 - - - +
583A THR* 4.6 0.2 - - - -
584A THR* 3.7 33.9 - - + +
587A ILE* 3.6 17.9 - - + -
614A GLY 2.9 18.3 + - - +
615A GLY* 3.2 15.2 + - - +
617A PHE* 1.3 70.8 - - - +
619A ILE* 1.3 58.6 + - + +
620A CYS 3.1 1.1 - - - -
621A SER* 3.5 4.2 - - - -
622A LYS* 2.7 50.6 + - + +
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Residues in contact with ILE 619 (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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453A LEU* 4.9 1.1 - - + -
468A CYS* 4.5 3.4 - - - -
471A ILE* 4.2 24.7 - - + -
489A PRO* 4.1 18.8 - - + +
491A TRP* 3.9 37.2 - - + +
494A PHE* 4.0 22.0 - - + -
615A GLY 3.2 16.3 + - - +
616A SER* 3.7 10.5 - - - +
618A LEU* 1.3 76.0 - - + +
620A CYS* 1.3 57.5 + - - +
622A LYS* 3.8 8.5 - - + +
623A LEU* 3.1 45.7 + - + +
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Residues in contact with CYS 620 (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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468A CYS* 3.6 43.1 - - + -
471A ILE* 5.6 2.5 - - - -
472A LEU* 4.7 9.0 - - - -
578A PHE* 3.4 36.8 - - + +
616A SER 3.3 17.6 + - - -
617A PHE 3.2 2.3 + - - +
618A LEU 3.1 0.8 - - - -
619A ILE* 1.3 79.4 - - - +
621A SER* 1.3 62.7 + - - +
623A LEU 3.6 0.5 + - - -
624A LYS 3.1 3.3 + - - -
625A ALA* 3.0 29.3 + - + +
627A PHE* 4.0 11.7 - - - -
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Residues in contact with SER 621 (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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578A PHE* 2.7 33.5 + - - +
579A GLY* 3.5 11.3 + - - -
582A SER 3.5 19.8 + - - -
583A THR* 3.6 18.4 + - - +
617A PHE 3.1 8.1 + - - -
618A LEU* 3.2 10.1 + - - -
620A CYS* 1.3 72.8 - - - +
622A LYS* 1.3 67.7 + - - +
624A LYS* 3.0 20.4 + - - +
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Residues in contact with LYS 622 (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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284A GLN* 4.5 20.8 + - - +
457A GLU* 4.2 18.0 - - - +
491A TRP* 3.7 57.0 - - + +
584A THR* 6.0 4.9 - - - +
618A LEU* 2.7 36.1 + - + +
619A ILE* 3.8 7.6 - - + +
621A SER* 1.3 73.7 - - - +
623A LEU* 1.3 59.1 + - - +
624A LYS* 3.5 10.3 + - - +
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Residues in contact with LEU 623 (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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453A LEU* 3.9 42.0 - - + +
456A ALA* 4.1 9.2 - - + +
457A GLU* 4.0 24.2 - - + +
464A ARG* 2.8 45.9 + - + +
467A ILE* 5.0 3.8 - - + -
468A CYS* 3.5 30.5 - - - -
491A TRP* 4.0 12.8 - - + -
619A ILE* 3.1 28.2 + - + +
620A CYS 4.3 0.2 - - - +
621A SER 3.2 0.2 - - - -
622A LYS* 1.3 74.0 - - - +
624A LYS* 1.3 63.8 + - - +
625A ALA 3.3 1.4 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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