Contacts of the helix formed by residues 598 - 621 (chain A) in PDB entry 4REC
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 ASP 598 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A LEU 5.5 0.9 - - - -
395A LEU* 3.6 18.3 - - - +
596A PHE* 3.3 1.3 - - - +
597A GLN* 1.3 85.2 - - - +
599A ARG* 1.3 69.4 + - + +
600A ASP* 3.2 14.4 + - - +
601A ASP* 2.9 38.3 + - - +
602A LEU* 3.1 10.9 + - - +
604A ARG* 4.6 3.9 + - - -
646A SER* 6.1 0.2 - - - -
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Residues in contact with ARG 599 (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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394A LEU 4.7 3.8 + - - +
395A LEU* 3.3 35.0 - - - +
396A PHE 4.5 0.4 - - - -
397A ASP* 3.4 31.4 + - - +
399A GLN* 6.0 0.4 - - - +
400A GLU* 2.9 38.4 + - - -
547A ARG* 4.2 2.3 + - - +
598A ASP* 1.3 73.7 - - + +
600A ASP* 1.3 71.4 + - - +
602A LEU* 3.4 3.9 + - - +
603A ILE* 3.1 45.1 + - + +
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Residues in contact with ASP 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ASP* 3.1 13.9 + - - +
599A ARG* 1.3 91.2 + - - +
601A ASP* 1.3 55.9 + - - +
603A ILE* 3.1 12.1 + - - +
604A ARG* 2.8 61.4 + - + +
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Residues in contact with ASP 601 (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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595A ILE 3.8 0.2 - - - +
596A PHE* 3.2 14.5 - - - -
597A GLN* 2.6 34.8 + - + +
598A ASP* 2.9 21.8 + - - +
600A ASP* 1.3 74.7 - - - +
602A LEU* 1.3 57.4 + - - +
604A ARG* 3.3 14.3 + - - +
605A TYR* 2.9 29.1 + - - +
646A SER* 4.2 8.3 + - - -
650A HIS* 3.0 40.8 + - - -
662A VAL* 4.5 6.2 + - - +
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Residues in contact with LEU 602 (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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395A LEU* 3.9 26.2 - - + +
396A PHE* 4.3 3.8 - - + -
547A ARG* 4.0 34.3 - - + +
550A LEU* 4.8 9.0 - - + -
551A LEU* 4.0 28.7 - - + -
596A PHE* 3.8 40.0 - - + -
598A ASP 3.1 8.1 + - - +
599A ARG 3.7 7.6 - - - +
601A ASP* 1.3 78.3 - - - +
603A ILE* 1.3 57.5 + - - +
605A TYR* 3.2 7.9 + - + +
606A ALA* 2.8 26.9 + - - +
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Residues in contact with ILE 603 (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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547A ARG* 3.5 39.9 - - - +
599A ARG* 3.1 49.4 + - + +
600A ASP* 3.1 14.9 + - - +
602A LEU* 1.3 71.7 - - - +
604A ARG* 1.3 69.8 + - + +
606A ALA* 3.3 3.0 + - - +
607A ALA* 3.0 24.6 + - + +
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Residues in contact with ARG 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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598A ASP* 4.6 3.6 + - - -
600A ASP* 2.8 38.7 + - - +
601A ASP* 3.8 21.8 + - - +
603A ILE* 1.3 75.4 - - + +
605A TYR* 1.3 63.8 + - - +
607A ALA* 3.2 6.9 + - - +
608A ALA* 3.0 23.0 + - - +
641A LEU* 3.8 29.8 - - + +
644A HIS* 3.1 41.3 + - - -
646A SER* 3.9 11.3 + - - -
662A VAL* 4.1 19.4 - - + +
666A TYR* 4.9 1.7 + - - -
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Residues in contact with TYR 605 (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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550A LEU* 4.1 24.7 - - + -
554A LEU* 4.3 5.6 - - + -
557A SER* 3.5 20.3 + - - -
558A MET* 5.5 0.7 - - - +
596A PHE* 3.6 31.2 - + + -
601A ASP* 2.9 15.3 + - - +
602A LEU* 3.3 9.0 - - + +
604A ARG* 1.3 76.3 - - - +
606A ALA* 1.3 63.1 + - - +
608A ALA* 3.2 5.9 + - - +
609A THR* 3.0 34.6 + - - -
659A CYS 4.1 0.5 + - - -
660A PHE* 3.4 37.1 - - + -
661A THR* 3.4 21.8 - - - -
662A VAL* 3.7 11.3 - - - +
665A ILE* 3.4 30.0 - - + +
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Residues in contact with ALA 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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546A SER 6.3 0.2 - - - -
547A ARG* 4.2 17.5 - - + -
550A LEU* 3.7 28.3 - - + -
602A LEU 2.8 19.5 + - - +
603A ILE* 3.8 5.2 - - - +
604A ARG 3.3 0.2 - - - -
605A TYR* 1.3 72.8 - - - +
607A ALA* 1.3 61.9 + - - +
609A THR* 3.2 4.7 + - - -
610A HIS* 3.0 40.3 + - + -
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Residues in contact with ALA 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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603A ILE* 3.0 18.9 + - + +
604A ARG* 3.2 6.5 + - - +
606A ALA* 1.3 73.8 - - - +
608A ALA* 1.3 67.0 + - - +
610A HIS* 3.4 10.8 + - - +
611A MET* 3.1 23.2 + - - +
666A TYR* 4.8 5.4 - - - +
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Residues in contact with ALA 608 (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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604A ARG 3.0 12.0 + - - +
605A TYR 3.5 9.2 - - - +
607A ALA* 1.3 77.0 - - - +
609A THR* 1.3 63.4 + - - +
611A MET* 3.1 6.2 + - - +
612A LEU* 2.9 23.4 + - - +
662A VAL* 4.3 4.7 - - + -
665A ILE* 3.6 25.8 - - + +
666A TYR* 3.7 38.7 + - + -
669A ILE* 3.8 1.2 - - - +
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Residues in contact with THR 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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550A LEU* 4.6 17.4 - - + +
557A SER* 4.0 25.4 + - - +
605A TYR* 3.0 36.1 + - - -
606A ALA* 3.2 13.4 + - - +
608A ALA* 1.3 76.7 - - - +
610A HIS* 1.3 69.8 + - + +
612A LEU* 3.2 5.0 + - - +
613A SER* 2.9 29.8 + - - -
665A ILE* 3.9 12.4 - - - +
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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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542A ARG* 6.0 3.4 - - - -
543A ALA* 6.5 0.9 - - + -
546A SER* 4.2 21.2 + - - -
550A LEU* 5.3 4.2 - - - +
606A ALA* 3.0 32.6 + - + +
607A ALA* 3.9 8.2 - - - +
609A THR* 1.3 85.6 - - + +
611A MET* 1.3 58.5 + - - +
613A SER* 3.2 8.5 + - - -
614A ASP* 2.8 34.7 + - - +
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Residues in contact with MET 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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607A ALA 3.1 13.8 + - - +
608A ALA* 3.4 10.5 - - - +
610A HIS* 1.3 77.4 - - - +
612A LEU* 1.3 57.2 + - - +
614A ASP* 3.0 10.1 + - - +
615A ILE* 2.9 40.9 + - + +
630A LEU* 3.7 42.0 - - + +
633A CYS* 4.5 9.0 - - + -
634A ALA* 3.6 30.7 - - + +
637A ASP* 4.6 8.1 - - - +
666A TYR* 5.3 2.2 - - + +
669A ILE* 3.9 5.6 - - + -
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Residues in contact with LEU 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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557A SER 4.9 3.1 - - - +
558A MET* 4.7 6.7 - - + -
560A ASP* 3.9 12.1 - - - +
561A GLU* 3.7 12.8 - - - +
608A ALA 2.9 12.9 + - - +
609A THR* 3.6 7.9 - - - +
611A MET* 1.3 76.0 - - - +
613A SER* 1.3 55.2 + - - +
615A ILE* 3.9 4.4 - - + +
616A SER* 2.7 50.1 + - - +
665A ILE* 4.2 16.8 - - + +
668A ARG* 3.5 38.8 - - + +
669A ILE* 3.8 24.8 - - + +
672A ARG* 3.7 17.5 - - + -
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Residues in contact with SER 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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560A ASP* 4.4 16.1 + - - -
609A THR* 2.9 16.2 + - - -
610A HIS* 3.4 13.0 - - - -
612A LEU* 1.3 76.4 - - - +
614A ASP* 1.3 66.4 + - - +
616A SER* 3.8 3.5 - - - -
617A SER* 3.0 23.9 + - - -
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Residues in contact with ASP 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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610A HIS* 2.8 21.6 + - - +
611A MET* 3.3 13.0 - - - +
613A SER* 1.3 76.4 + - - +
615A ILE* 1.3 62.6 + - - +
617A SER* 3.2 9.1 + - - -
618A ALA* 3.0 22.3 + - - +
630A LEU* 4.0 24.5 - - + +
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Residues in contact with ILE 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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611A MET* 2.9 35.4 + - + +
612A LEU* 3.9 4.5 - - + +
614A ASP* 1.3 70.3 - - - +
616A SER* 1.3 63.9 + - - +
618A ALA* 3.1 5.9 + - - +
619A MET* 3.0 38.0 + - + +
627A ALA* 4.2 3.8 - - + +
630A LEU* 3.7 26.2 - - + -
631A ALA* 3.7 20.6 - - + +
669A ILE* 3.5 32.8 - - + +
672A ARG* 4.5 8.7 - - + -
676A ILE* 4.0 22.0 - - + -
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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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560A ASP* 3.1 26.9 + - - -
612A LEU* 2.7 28.0 + - - +
613A SER 3.8 4.5 - - - -
614A ASP 3.3 0.2 - - - -
615A ILE* 1.3 77.5 - - - +
617A SER* 1.3 61.6 + - - +
619A MET* 3.4 12.6 + - - +
620A ALA* 3.0 24.0 + - - +
672A ARG* 3.1 21.5 + - - +
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Residues in contact with SER 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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613A SER 3.0 14.1 + - - -
614A ASP* 3.2 12.3 + - - -
616A SER* 1.3 77.9 - - - +
618A ALA* 1.3 61.7 + - - +
620A ALA* 3.2 11.9 + - - +
621A ASN* 2.8 28.2 + - - +
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Residues in contact with ALA 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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614A ASP 3.0 11.6 + - - +
615A ILE* 3.4 9.9 - - - +
617A SER* 1.3 75.6 - - - +
619A MET* 1.3 63.7 + - - +
621A ASN* 3.0 15.6 + - - +
623A ASN* 3.1 31.1 + - - +
626A GLU* 4.1 17.7 - - - +
627A ALA* 3.8 25.4 - - + +
630A LEU* 4.5 2.9 - - + -
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Residues in contact with MET 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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615A ILE* 3.0 14.1 + - + +
616A SER* 3.4 25.8 - - - +
618A ALA* 1.3 76.2 - - - +
620A ALA* 1.3 63.1 + - - +
622A GLY 3.1 10.1 + - - +
623A ASN 4.9 0.4 - - - +
624A TRP* 3.6 47.1 - - + -
627A ALA* 3.9 8.0 - - + +
672A ARG* 3.3 59.2 - - + +
675A GLU* 5.0 6.1 - - - +
676A ILE* 3.7 27.8 - - + -
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Residues in contact with ALA 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A SER 3.0 16.9 + - - +
617A SER* 3.5 8.7 - - - +
618A ALA 3.2 0.4 - - - -
619A MET* 1.3 77.4 - - - +
621A ASN* 1.3 63.5 + - - +
622A GLY 3.3 0.7 + - - -
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Residues in contact with ASN 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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617A SER* 2.8 24.0 + - - +
618A ALA* 3.0 5.1 + - - +
620A ALA* 1.3 81.9 + - - +
622A GLY* 1.3 61.7 + - - +
623A ASN* 3.2 24.3 + - - +
328B C 4.5 25.7 + - - +
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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
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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