Contacts of the helix formed by residues 596 - 619 (chain A) in PDB entry 2P8Q
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 GLN 596 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A TYR* 2.9 35.0 + - + +
548A GLN* 5.0 3.6 + - - +
595A VAL* 1.3 71.3 - - - +
597A HIS* 1.3 54.1 + - - +
598A GLN* 4.0 20.3 - - + +
599A ASP* 2.8 46.0 + - + +
600A ALA* 2.8 15.1 + - - +
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Residues in contact with HIS 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL 3.5 4.0 + - - -
596A GLN* 1.3 72.2 - - - +
598A GLN* 1.3 65.6 + - + +
600A ALA* 3.3 9.1 + - + +
601A LEU* 3.0 52.4 + - + +
637A GLU 5.5 0.4 + - - -
638A VAL* 3.3 28.4 + - + -
642A GLU* 5.7 2.9 - - - -
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Residues in contact with GLN 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A GLN* 3.0 19.6 - - + +
597A HIS* 1.3 81.7 - - + +
599A ASP* 1.3 59.9 + - - +
601A LEU* 3.4 12.8 - - - +
602A GLN* 2.6 36.7 + - - +
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Residues in contact with ASP 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A TYR* 4.9 2.0 - - - -
548A GLN* 4.4 12.0 - - - +
595A VAL* 4.5 13.2 - - + +
596A GLN* 2.8 40.2 + - + +
598A GLN* 1.3 73.7 - - - +
600A ALA* 1.3 61.8 + - - +
601A LEU 3.0 2.8 + - - -
602A GLN* 3.1 12.0 + - - +
603A ILE* 2.7 41.0 + - + +
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Residues in contact with ALA 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LEU* 3.8 23.2 - - + +
595A VAL* 3.9 19.9 - - + +
596A GLN 2.8 15.4 + - - +
597A HIS* 3.5 14.6 - - + +
599A ASP* 1.3 72.6 - - - +
601A LEU* 1.3 52.6 + - - +
603A ILE* 3.5 3.3 + - - +
604A SER* 2.5 38.0 + - - -
638A VAL* 3.7 17.0 - - + -
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Residues in contact with LEU 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A HIS* 3.0 46.0 + - + +
598A GLN* 3.4 13.2 - - - +
599A ASP 3.0 0.8 - - - -
600A ALA* 1.3 75.1 - - - +
602A GLN* 1.3 74.1 + - - +
604A SER* 2.9 15.3 + - - -
605A ASP* 3.1 21.0 + - - +
638A VAL* 3.6 19.5 - - + +
639A LEU* 4.1 11.0 - - + -
642A GLU* 3.8 28.0 - - - +
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Residues in contact with GLN 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A GLN* 2.6 36.4 + - - +
599A ASP* 3.1 16.3 + - - +
601A LEU* 1.3 87.2 - - - +
603A ILE* 1.3 67.0 + - + +
605A ASP* 4.0 6.0 + - - +
606A VAL* 3.0 31.2 + - - +
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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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551A THR* 4.9 10.8 - - + -
555A MET* 3.3 46.9 - - + -
588A LEU* 4.8 4.5 - - + -
591A VAL* 6.2 0.2 - - + -
592A LEU* 3.5 25.4 - - + -
595A VAL* 6.0 2.7 - - + -
599A ASP* 2.7 38.8 - - + +
600A ALA* 3.7 4.7 - - - +
601A LEU 3.1 0.6 - - - -
602A GLN* 1.3 85.9 - - + +
604A SER* 1.3 58.2 + - - +
606A VAL* 3.3 3.8 + - - +
607A VAL* 2.9 43.2 + - + +
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Residues in contact with SER 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A LEU* 4.1 6.1 - - - +
600A ALA 2.5 22.8 + - - -
601A LEU* 2.9 5.3 + - - -
603A ILE* 1.3 73.6 - - - +
605A ASP* 1.3 61.4 + - - +
608A MET* 2.9 33.4 + - - +
635A LEU* 3.8 23.1 - - - +
638A VAL* 3.3 19.6 - - - +
639A LEU* 3.8 26.7 - - - -
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Residues in contact with ASP 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A LEU* 3.1 17.4 + - - +
602A GLN* 4.3 5.8 - - - +
604A SER* 1.3 77.8 - - - +
606A VAL* 1.3 65.2 + - + +
608A MET* 4.0 0.2 - - - +
609A ALA* 3.0 24.9 + - - +
639A LEU* 3.2 24.0 - - - +
642A GLU 5.5 0.3 - - - +
645A LYS* 5.7 2.1 - - - +
646A TYR* 3.1 31.8 + - - +
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Residues in contact with VAL 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A MET* 5.1 9.2 - - - -
559A GLN* 3.6 25.4 - - + +
602A GLN 3.0 17.7 - - - +
603A ILE* 3.3 8.7 + - - +
604A SER 3.2 0.8 - - - -
605A ASP* 1.3 79.5 - - + +
607A VAL* 1.3 61.0 + - + +
609A ALA* 3.5 6.6 + - - +
610A SER* 3.2 21.0 + - - -
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Residues in contact with VAL 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A MET* 4.5 7.6 - - + -
558A LEU* 4.0 17.5 - - + -
559A GLN* 4.0 17.0 - - - +
562A LEU* 5.0 2.5 - - + -
585A CYS* 6.5 0.2 - - - -
588A LEU* 3.9 29.4 - - + -
603A ILE* 2.9 37.5 + - + +
604A SER* 3.9 2.7 - - - +
606A VAL* 1.3 72.8 - - - +
608A MET* 1.3 67.4 + - - +
610A SER* 2.9 5.5 + - - -
611A LEU* 2.9 40.3 + - + +
635A LEU* 4.1 9.0 - - + -
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Residues in contact with MET 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A SER 2.9 18.6 + - - +
605A ASP 4.0 2.7 - - - +
607A VAL* 1.3 75.7 - - - +
609A ALA* 1.3 63.6 + - - +
611A LEU* 3.2 9.5 + - - +
612A LEU* 2.9 36.8 + - + +
615A PHE* 5.7 1.1 - - - -
632A VAL* 3.7 29.4 - - + -
635A LEU* 3.2 40.2 - - + +
639A LEU* 5.1 1.1 - - + -
643A PHE* 3.3 28.5 - - + -
646A TYR* 3.9 38.6 - - + -
650A PHE* 5.5 3.8 - - - -
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Residues in contact with ALA 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ASP 3.0 19.0 + - - +
606A VAL* 3.6 7.4 - - - +
608A MET* 1.3 76.1 - - - +
610A SER* 1.3 61.7 + - - +
612A LEU* 3.6 9.8 + - - +
613A ARG* 3.3 36.5 + - - +
646A TYR* 4.8 7.5 - - + +
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Residues in contact with SER 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A GLN* 2.6 30.8 + - - -
562A LEU* 3.5 28.4 - - - +
606A VAL* 3.2 8.6 + - - +
607A VAL 2.9 9.2 + - - -
609A ALA* 1.3 76.4 - - - +
611A LEU* 1.3 64.5 + - - +
613A ARG* 3.3 25.7 + - - +
614A MET* 3.0 21.5 + - - +
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Residues in contact with LEU 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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558A LEU* 5.9 0.2 - - + -
562A LEU* 3.8 26.7 - - + -
581A GLN* 5.3 0.4 - - - -
585A CYS* 4.9 14.4 - - - -
607A VAL* 2.9 34.9 + - + +
608A MET* 3.7 13.0 - - - +
610A SER* 1.3 74.9 - - - +
612A LEU* 1.3 53.6 + - - +
614A MET* 3.0 20.7 + - + +
615A PHE* 2.7 50.7 + - + -
628A ALA* 4.7 12.8 - - + -
631A ALA* 4.6 14.6 - - + -
632A VAL* 4.7 7.2 - - + -
635A LEU* 4.0 16.2 - - + -
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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
----------------------------------------------------------
608A MET* 2.9 28.9 + - + +
609A ALA* 3.8 7.2 - - - +
611A LEU* 1.3 76.4 - - - +
613A ARG* 1.3 58.1 - - - +
615A PHE* 3.4 11.0 + - + +
616A GLN* 2.9 30.0 + - - +
646A TYR* 3.8 31.6 - - + -
649A ALA* 3.8 37.9 - - + +
650A PHE* 3.9 19.5 - - + -
653A PHE* 4.2 15.8 - - + -
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Residues in contact with ARG 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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559A GLN* 4.8 2.6 + - - -
563A GLN* 6.1 5.3 - - - +
566A SER* 5.7 5.2 - - - +
609A ALA* 3.3 32.9 + - - +
610A SER* 3.4 30.7 + - - +
611A LEU 3.1 0.6 - - - -
612A LEU* 1.3 78.5 - - - +
614A MET* 1.3 62.8 - - - +
616A GLN* 3.2 9.2 + - + +
617A SER* 3.1 28.9 + - - +
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Residues in contact with MET 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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562A LEU* 3.7 26.0 + - + +
565A GLU* 4.0 25.5 - - + +
566A SER* 5.5 3.1 - - - +
581A GLN* 3.5 22.4 - - - +
610A SER 3.0 12.7 + - - +
611A LEU* 3.0 28.4 + - + +
613A ARG* 1.3 77.0 - - - +
615A PHE* 1.3 74.8 + - + +
617A SER* 4.9 2.9 - - - -
618A THR* 2.5 61.7 + - - +
625A GLN* 3.9 16.4 - - - +
628A ALA* 4.3 1.8 - - + -
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Residues in contact with PHE 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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608A MET* 5.7 0.9 - - - -
611A LEU* 2.7 40.1 + - + +
612A LEU* 3.5 11.7 - - + +
613A ARG 3.2 0.2 - - - -
614A MET* 1.3 96.0 - - + +
616A GLN* 1.3 61.5 + - - +
617A SER 3.3 0.5 + - - -
618A THR* 3.3 15.9 - - + +
619A ALA* 3.4 11.1 + - + +
624A VAL* 3.2 33.9 - - + -
625A GLN* 5.5 0.7 - - - -
628A ALA* 3.8 28.0 - - + -
629A LEU* 5.1 1.6 - - + -
632A VAL* 4.5 7.9 - - + -
650A PHE* 4.3 20.4 - + - -
653A PHE* 3.3 49.1 - + + -
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Residues in contact with GLN 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LEU 2.9 13.9 + - - +
613A ARG* 3.2 12.8 + - + +
615A PHE* 1.3 77.0 - - - +
617A SER* 1.3 60.8 + - - +
619A ALA 5.0 2.8 - - - +
653A PHE* 3.5 14.0 - - + -
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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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565A GLU 5.1 0.2 - - - -
566A SER* 3.3 40.0 - - - -
613A ARG* 3.1 14.7 + - - +
614A MET 4.0 1.1 - - - -
616A GLN* 1.3 81.2 - - - +
618A THR* 1.3 71.1 - - - +
619A ALA* 3.3 2.5 + - - -
620A GLY 4.6 1.6 + - - -
621A SER* 4.8 0.7 - - - -
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Residues in contact with THR 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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565A GLU* 4.4 14.9 + - - -
568A ILE* 5.8 5.2 - - - +
614A MET* 2.5 51.9 + - - +
615A PHE* 3.3 20.6 - - + +
617A SER* 1.3 75.6 - - - +
619A ALA* 1.3 72.6 + - + +
621A SER* 2.6 41.2 + - - -
623A GLY* 4.7 2.2 - - - -
624A VAL* 6.1 0.7 - - + -
625A GLN* 4.3 14.7 + - - +
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Residues in contact with ALA 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A PHE* 3.4 13.5 + - + +
616A GLN 5.0 2.3 - - - +
617A SER 3.3 1.7 + - - -
618A THR* 1.3 88.9 - - + +
620A GLY* 1.3 54.1 + - - +
621A SER 3.0 5.6 - - - +
623A GLY* 2.9 50.4 - - - +
624A VAL* 4.8 3.6 - - + -
653A PHE* 4.2 12.6 - - + -
656A ILE* 6.2 0.3 - - - +
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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) + - + + + + + -
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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