Contacts of the helix formed by residues 596 - 616 (chain A) in PDB entry 2OR4
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 596 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A PRO 4.2 1.0 - - - +
469A LEU* 3.3 18.1 + - - +
472A SER* 3.9 20.2 + - - +
594A PRO 4.4 0.2 + - - -
595A PHE* 1.3 73.2 - - - +
597A CYS* 1.4 63.6 + - - +
598A ARG* 2.9 56.5 + - - +
599A ASP* 3.1 36.5 + - - +
600A TYR 3.9 0.2 + - - -
647A SER* 4.3 2.8 + - - -
1D NAG 5.5 2.0 - - - +
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Residues in contact with CYS 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 3.8 13.0 - - - +
595A PHE 3.9 2.6 + - - -
596A ASP* 1.4 72.0 + - - +
598A ARG* 1.4 64.2 + - - +
600A TYR* 3.0 14.8 + - - +
601A ALA 3.2 8.1 + - - -
639A PHE* 3.7 6.0 - - + -
643A ALA* 3.6 33.4 - - + +
646A PHE* 3.7 22.4 - - - -
647A SER* 3.7 9.4 - - - -
650A LEU* 6.5 0.2 - - - -
668A LEU* 4.7 7.5 - - + +
671A LEU* 3.5 26.0 - - + -
746A LEU* 3.9 9.2 - - + -
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Residues in contact with ARG 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A ASP* 2.9 35.7 + - - +
597A CYS* 1.4 77.5 - - - +
599A ASP* 1.3 63.6 + - - +
601A ALA* 3.1 19.3 + - + +
602A VAL* 3.1 19.1 + - + +
640A THR 5.8 0.2 - - - +
643A ALA* 4.1 14.4 - - + +
644A SER* 4.5 11.0 - - - +
647A SER* 3.3 32.4 + - - +
651A GLN* 4.3 20.2 - - - +
1D NAG 6.3 0.8 - - - -
2D NAG 4.8 16.4 - - - +
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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
----------------------------------------------------------
468A PRO* 3.4 22.6 - - - +
471A TYR* 3.9 17.9 - - + +
472A SER* 2.8 35.5 + - - -
596A ASP* 3.1 19.4 + - - +
598A ARG* 1.3 76.5 - - - +
600A TYR* 1.3 66.1 + - - +
602A VAL* 3.5 10.8 + - - +
603A VAL* 3.3 27.4 + - - +
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Residues in contact with TYR 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A THR* 3.5 14.0 + - - -
468A PRO* 3.8 27.6 - - + +
469A LEU* 3.6 26.5 - - + -
596A ASP 3.9 1.4 + - - -
597A CYS 3.0 13.0 + - - +
599A ASP* 1.3 79.7 - - - +
601A ALA* 1.3 63.4 + - - +
603A VAL* 3.2 3.8 + - + +
604A LEU* 2.9 38.8 + - + +
639A PHE* 3.9 11.7 - - + -
671A LEU* 4.9 2.9 - - + -
672A GLU* 2.5 33.8 + - - -
675A PHE* 3.6 29.8 - + - -
689A HIS* 3.4 7.3 - - - -
691A ILE* 4.3 13.0 - - + -
692A TYR* 3.2 26.0 - + - -
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Residues in contact with ALA 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A CYS 3.2 3.9 + - - +
598A ARG* 3.1 16.2 + - + +
600A TYR* 1.3 78.8 - - - +
602A VAL* 1.3 62.7 + - + +
604A LEU* 3.4 4.8 + - - +
605A ARG* 3.2 22.2 + - - +
636A VAL* 4.3 1.7 - - - +
639A PHE* 3.7 18.3 - - + -
640A THR* 3.7 45.2 + - + +
643A ALA* 4.7 2.0 - - + -
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Residues in contact with VAL 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A PHE* 4.4 25.4 - - + -
598A ARG* 3.1 15.5 + - + +
599A ASP* 3.7 13.7 - - - +
600A TYR 3.3 0.2 - - - -
601A ALA* 1.3 78.3 - - + +
603A VAL* 1.3 71.0 + - + +
605A ARG* 3.3 11.4 + - - +
606A LYS* 3.3 13.2 + - + +
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Residues in contact with VAL 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PRO* 3.4 26.2 - - + -
471A TYR* 3.7 31.6 - - + +
506A PHE* 6.5 0.7 - - + -
599A ASP 3.3 8.9 + - - +
600A TYR* 3.2 14.7 + - + +
602A VAL* 1.3 81.1 - - + +
604A LEU* 1.3 69.0 + - - +
606A LYS* 3.1 21.5 + - - +
607A TYR* 2.8 51.3 + - + +
692A TYR* 4.0 0.2 - - - +
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Residues in contact with LEU 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A TYR* 2.9 34.6 + - + +
601A ALA* 3.8 4.5 - - - +
602A VAL 3.3 0.4 - - - -
603A VAL* 1.3 77.4 - - - +
605A ARG* 1.4 57.6 + - - +
607A TYR* 3.4 4.8 + - + +
608A ALA* 2.9 30.3 + - - +
636A VAL* 4.0 14.7 - - + +
639A PHE* 4.0 39.0 - - + -
675A PHE* 4.3 3.1 - - + -
691A ILE* 3.7 45.3 - - + -
705A PHE* 4.1 14.0 - - + -
739A VAL* 4.2 13.7 - - + -
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Residues in contact with ARG 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ALA 3.2 10.8 + - - +
602A VAL* 3.7 9.0 - - - +
603A VAL 3.2 0.6 - - - -
604A LEU* 1.4 74.1 - - - +
606A LYS* 1.3 65.9 + - - +
608A ALA* 3.3 1.3 + - - -
609A ASP* 2.9 51.6 + - - +
633A PHE* 3.7 24.2 - - - -
636A VAL* 3.7 19.4 - - + +
640A THR* 5.7 1.1 - - - +
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Residues in contact with LYS 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A TYR* 5.2 3.0 + - - -
505A GLU* 3.1 47.1 + - + +
506A PHE* 5.8 3.4 - - + -
514A LYS* 6.3 0.4 - - - +
602A VAL* 3.3 11.1 + - + +
603A VAL* 3.1 23.3 + - - +
605A ARG* 1.3 79.9 - - - +
607A TYR* 1.3 86.6 + - + +
609A ASP* 3.3 9.6 + - - +
610A LYS* 3.0 31.9 + - + +
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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
----------------------------------------------------------
471A TYR* 4.3 7.1 + - - -
514A LYS* 3.7 20.5 - - + +
603A VAL* 2.8 40.4 + - + +
604A LEU* 3.8 3.6 - - + +
606A LYS* 1.3 100.7 + - + +
608A ALA* 1.3 58.8 + - - +
610A LYS* 3.3 10.6 + - + +
611A ILE* 2.9 31.0 + - - +
691A ILE* 3.7 18.4 - - + -
692A TYR* 2.7 47.9 + + - -
704A SER* 3.5 27.1 + - - -
705A PHE* 3.6 21.1 - - + -
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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
----------------------------------------------------------
604A LEU 2.9 18.3 + - - +
605A ARG* 3.7 3.1 - - - +
607A TYR* 1.3 72.8 - - - +
609A ASP* 1.3 66.1 + - - +
611A ILE* 3.3 11.3 - - - +
612A TYR* 2.9 26.3 + - - +
629A PHE* 5.2 0.2 - - - -
632A LEU* 4.3 19.7 - - + -
633A PHE* 3.7 27.3 - - + -
636A VAL* 4.4 7.6 - - + -
705A PHE* 3.6 5.5 - - + -
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Residues in contact with ASP 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ARG* 2.9 51.0 + - - +
606A LYS* 3.6 11.5 - - - +
608A ALA* 1.3 74.7 - - - +
610A LYS* 1.3 57.3 + - - +
612A TYR* 3.6 4.6 - - - +
613A SER* 2.9 34.8 + - - +
633A PHE* 3.3 14.7 - - - -
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Residues in contact with LYS 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LYS* 4.5 13.3 - - - +
606A LYS* 3.0 18.7 + - + +
607A TYR* 3.6 9.2 - - + +
608A ALA 3.2 0.2 - - - -
609A ASP* 1.3 77.4 - - - +
611A ILE* 1.3 63.1 + - - +
613A SER* 3.2 6.8 + - - -
614A ILE* 3.0 38.7 + - + +
703A GLU* 4.0 18.0 + - - -
704A SER* 4.4 16.0 + - - +
709A TYR* 6.0 1.7 - - - -
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Residues in contact with ILE 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 TYR 2.9 17.0 + - - +
608A ALA* 3.3 16.8 - - - +
610A LYS* 1.3 74.0 - - - +
612A TYR* 1.3 69.6 + - - +
614A ILE* 3.2 17.9 + - + +
615A SER* 3.0 21.1 + - - -
629A PHE* 3.9 14.6 - - + -
632A LEU* 4.2 7.0 - - + -
704A SER 5.1 2.0 - - - +
705A PHE* 4.1 18.6 - - + +
708A ILE* 3.5 25.4 - - + -
709A TYR* 3.6 39.5 - - + +
712A LEU* 3.9 13.1 - - + +
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Residues in contact with TYR 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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608A ALA 2.9 19.5 + - - +
609A ASP* 3.6 4.5 - - - +
611A ILE* 1.3 79.8 - - - +
613A SER* 1.3 64.8 + - - +
615A SER* 3.1 4.7 + - - -
616A MET* 2.9 71.2 + - + +
622A MET* 4.3 9.0 - - + -
629A PHE* 3.6 38.1 - + + -
633A PHE* 4.0 21.5 - + + -
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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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609A ASP* 2.9 23.8 + - - +
610A LYS* 3.6 6.7 - - - -
612A TYR* 1.3 82.4 - - - +
614A ILE* 1.3 64.5 + - - +
616A MET* 3.4 13.4 + - - +
617A LYS* 3.6 15.0 + - - +
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Residues in contact with ILE 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 LYS* 3.0 32.0 + - + +
611A ILE* 3.2 16.4 + - + +
613A SER* 1.3 76.5 - - - +
615A SER* 1.3 62.5 + - - +
617A LYS* 3.3 43.9 + - + +
618A HIS* 3.7 7.7 + - + -
709A TYR* 3.8 35.2 - - + -
712A LEU* 4.0 27.1 - - + +
713A PHE* 6.4 0.2 - - - -
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Residues in contact with SER 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ILE 3.0 6.8 + - - -
612A TYR 3.4 5.6 - - - -
614A ILE* 1.3 76.7 - - - +
616A MET* 1.3 57.7 + - - +
617A LYS 3.1 0.2 - - - -
618A HIS* 2.9 28.1 + - - +
622A MET* 3.2 23.9 - - - +
627A VAL* 4.4 0.7 - - - +
629A PHE* 3.4 36.3 - - - -
712A LEU* 4.0 16.2 - - - +
725A TRP* 3.5 18.2 - - - -
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Residues in contact with MET 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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612A TYR* 2.9 59.0 + - + +
613A SER* 3.9 8.7 - - - +
614A ILE 3.2 0.6 - - - -
615A SER* 1.3 74.3 - - - +
617A LYS* 1.3 58.1 + - - +
618A HIS 3.0 6.3 + - - +
619A PRO* 3.4 29.7 - - + +
622A MET* 3.4 25.4 - - - +
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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
------------------------------------------------------------
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