Contacts of the helix formed by residues 629 - 653 (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 PHE 629 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A ILE* 3.9 27.8 - - + -
612A TYR* 3.6 27.2 - + + -
615A SER* 3.4 38.4 - - - -
622A MET* 4.1 10.7 - - + +
627A VAL* 4.3 2.5 - - + -
628A SER* 1.3 74.7 + - - +
630A ASP* 1.3 66.8 + - - +
631A SER 3.3 3.1 - - - -
632A LEU* 3.0 29.6 + - + -
633A PHE* 3.1 33.6 + + + -
708A ILE* 4.2 15.0 - - + -
712A LEU* 4.7 1.6 - - + -
728A VAL* 4.8 1.1 - - + -
732A ILE* 3.6 36.3 - - + -
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Residues in contact with ASP 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A SER* 3.0 20.0 + - - +
629A PHE* 1.3 79.9 + - - +
631A SER* 1.3 57.4 + - - +
633A PHE* 3.4 7.6 + - - +
634A SER* 2.9 30.4 + - - -
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Residues in contact with SER 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A SER* 4.7 2.2 + - - -
630A ASP* 1.3 77.5 - - - +
632A LEU* 1.3 60.7 + - - +
634A SER* 3.4 5.5 + - - -
635A ALA* 3.0 25.1 + - - +
732A ILE* 3.7 17.3 + - - +
733A TYR* 4.9 3.2 - - - -
736A ALA* 3.5 18.1 - - - +
1E NAG 3.4 16.4 - - - +
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Residues in contact with LEU 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608A ALA* 4.3 13.5 - - + -
611A ILE* 4.2 7.4 - - + -
629A PHE* 3.0 24.0 + - + +
631A SER* 1.3 79.7 + - - +
633A PHE* 1.3 65.7 + - + +
635A ALA* 3.3 2.9 + - - +
636A VAL* 3.0 29.4 + - + +
705A PHE* 3.8 33.4 - - + -
708A ILE* 4.0 24.9 - - + -
732A ILE* 4.5 9.9 - - + -
735A ALA* 4.0 7.0 - - + +
736A ALA* 3.8 29.8 - - + +
739A VAL* 4.3 6.3 - - + -
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Residues in contact with PHE 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A ARG* 3.7 24.5 - - - -
608A ALA* 3.7 35.2 - - + -
609A ASP* 3.3 27.4 - - - -
612A TYR* 4.0 21.5 - + + -
629A PHE* 3.1 43.0 + + + -
630A ASP* 4.0 8.7 - - - +
632A LEU* 1.3 76.8 - - + +
634A SER* 1.3 56.6 + - - +
636A VAL* 3.2 4.9 + - + +
637A LYS* 2.9 30.4 + - - +
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Residues in contact with SER 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A ASP 2.9 18.4 + - - -
631A SER* 3.5 7.6 - - - -
632A LEU 3.3 0.2 - - - -
633A PHE* 1.3 76.6 - - - +
635A ALA* 1.4 56.8 + - - +
637A LYS* 3.3 8.6 + - - +
638A ASN* 2.9 34.8 + - - +
1E NAG 2.9 33.2 + - - -
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Residues in contact with ALA 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A SER 3.0 17.2 + - - +
632A LEU 3.3 4.7 + - - +
634A SER* 1.4 76.4 - - - +
636A VAL* 1.3 57.7 - - - +
638A ASN* 3.3 3.1 + - - +
639A PHE* 2.9 29.6 + - - +
736A ALA* 3.3 29.8 - - - +
739A VAL* 3.6 11.8 - - + +
740A GLN* 3.8 22.1 + - + +
1E NAG 3.8 7.6 - - + +
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Residues in contact with VAL 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ALA 4.3 1.6 - - - +
604A LEU* 4.0 28.3 - - + +
605A ARG* 3.7 41.5 - - + +
608A ALA* 4.4 9.6 - - + -
632A LEU* 3.0 30.6 + - + +
633A PHE* 3.7 7.0 - - - +
634A SER 3.2 0.2 - - - -
635A ALA* 1.3 73.5 - - - +
637A LYS* 1.3 63.3 + - - +
639A PHE* 3.2 4.5 + - + +
640A THR* 2.8 35.1 + - - +
705A PHE* 5.0 1.1 - - + -
739A VAL* 4.2 14.4 - - + -
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Residues in contact with LYS 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A PHE 2.9 16.6 + - - +
634A SER* 3.3 8.7 + - - +
636A VAL* 1.3 76.2 - - - +
638A ASN* 1.4 62.7 + - - +
640A THR* 3.2 8.2 + - - -
641A GLU* 2.7 68.1 + - + +
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Residues in contact with ASN 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A SER* 2.9 13.8 + - - +
635A ALA 3.5 1.3 - - - +
637A LYS* 1.4 81.1 + - - +
639A PHE* 1.4 59.9 + - - +
641A GLU* 3.3 13.8 + - - +
642A ILE* 2.8 44.0 + - + +
740A GLN* 2.8 27.3 + - - +
743A ALA* 5.1 0.4 - - + -
1E NAG 1.5 64.2 + - - +
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Residues in contact with PHE 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A CYS 3.7 21.5 - - - -
600A TYR* 3.9 14.1 - - + -
601A ALA* 3.7 25.4 - - + -
604A LEU* 4.0 11.7 - - + -
635A ALA 2.9 16.7 + - - +
636A VAL* 3.5 9.2 - - - +
638A ASN* 1.4 71.6 - - - +
640A THR* 1.3 58.5 + - - +
642A ILE* 3.9 0.5 - - - +
643A ALA* 2.8 41.9 + - + +
671A LEU* 3.9 27.1 - - + -
675A PHE* 3.8 21.3 - + - -
739A VAL* 3.7 14.6 - - + -
742A ALA* 4.1 0.2 - - + -
743A ALA* 3.6 40.7 - - + +
746A LEU* 4.4 3.8 - - + +
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Residues in contact with THR 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ARG* 5.8 0.3 - - - +
601A ALA* 3.7 29.7 + - + +
605A ARG* 5.7 0.9 - - - +
636A VAL* 2.8 26.8 + - - +
637A LYS* 3.4 11.1 - - - -
638A ASN 3.1 0.2 - - - -
639A PHE* 1.3 76.7 - - - +
641A GLU* 1.3 59.0 + - + +
643A ALA* 3.9 1.4 - - - +
644A SER* 3.0 30.6 + - - -
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Residues in contact with GLU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A LYS* 2.7 60.5 + - + +
638A ASN* 3.8 11.3 - - - +
640A THR* 1.3 78.2 - - + +
642A ILE* 1.4 64.4 + - + +
644A SER* 3.3 7.1 + - - -
645A LYS* 3.1 42.3 + - - +
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Residues in contact with ILE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A ASN* 2.8 31.6 + - + +
639A PHE 4.1 1.6 - - - +
641A GLU* 1.4 74.9 - - + +
643A ALA* 1.3 58.1 - - - +
645A LYS* 3.3 9.0 + - + +
646A PHE* 2.9 27.2 + - - +
649A ARG* 5.2 0.7 + - - +
740A GLN* 4.7 9.2 - - - +
743A ALA* 3.3 41.3 - - + +
744A GLU* 4.6 3.1 - - + +
746A LEU* 3.8 7.4 - - + +
747A SER* 3.6 33.9 - - - +
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Residues in contact with ALA 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A CYS* 3.6 37.5 - - + +
598A ARG* 4.3 7.6 - - + +
601A ALA* 4.7 0.7 - - + -
639A PHE* 2.8 31.3 + - + +
640A THR* 4.0 4.0 - - - +
642A ILE* 1.3 73.7 - - - +
644A SER* 1.3 65.3 + - - +
646A PHE* 3.6 4.1 - - - +
647A SER* 2.8 30.6 + - - -
746A LEU* 4.3 5.8 - - + +
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Residues in contact with SER 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ARG* 4.5 11.2 - - - +
640A THR* 3.0 20.6 + - - -
641A GLU* 3.6 7.2 - - - -
642A ILE 3.2 0.2 - - - -
643A ALA* 1.3 77.8 - - - +
645A LYS* 1.3 63.2 + - - +
647A SER* 3.3 6.1 + - - -
648A GLU* 3.1 36.5 + - - +
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Residues in contact with LYS 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A GLU* 3.1 32.8 + - - +
642A ILE* 3.9 7.4 - - + +
644A SER* 1.3 76.3 - - - +
646A PHE* 1.3 65.3 + - - +
648A GLU* 3.2 19.7 + - - +
649A ARG* 3.0 36.1 + - + +
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Residues in contact with PHE 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597A CYS* 3.7 17.3 - - - -
642A ILE 2.9 21.0 + - - +
643A ALA* 3.6 4.7 - - - +
645A LYS* 1.3 72.1 - - - +
647A SER* 1.3 61.1 + - - +
649A ARG* 3.2 22.5 + - - +
650A LEU* 2.8 47.5 + - + +
664A MET* 3.8 31.0 - - + -
667A GLN* 3.4 34.3 - - + -
668A LEU* 3.6 27.8 - - + -
746A LEU* 3.4 37.9 - - + +
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Residues in contact with SER 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A ASP* 4.3 1.7 + - - -
597A CYS* 3.7 8.7 - - - -
598A ARG* 3.3 42.2 + - - +
643A ALA 2.8 20.5 + - - -
644A SER 3.5 5.6 - - - -
646A PHE* 1.3 75.7 - - - +
648A GLU* 1.3 67.5 + - - +
650A LEU* 3.2 12.4 + - - +
651A GLN* 3.0 33.1 + - - +
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Residues in contact with GLU 648 (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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644A SER* 3.1 26.3 + - - +
645A LYS* 3.4 18.5 - - - +
647A SER* 1.3 78.8 - - - +
649A ARG* 1.4 60.4 + - + +
651A GLN* 3.0 8.3 + - - +
652A ASP* 2.8 42.5 + - - +
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Residues in contact with ARG 649 (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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642A ILE* 5.2 0.6 + - - +
645A LYS* 3.0 34.4 + - - +
646A PHE* 3.6 22.1 - - - +
648A GLU* 1.4 76.5 - - + +
650A LEU* 1.3 55.5 - - - +
652A ASP* 4.2 8.3 - - - +
653A PHE* 2.8 37.5 + - + +
663A MET* 6.1 1.8 - - - +
664A MET* 4.1 16.0 - - + +
667A GLN* 4.5 3.4 + - - +
746A LEU 2.8 28.7 + - - -
747A SER* 3.7 3.2 + - - +
748A GLU* 3.6 50.5 + - - +
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Residues in contact with LEU 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A VAL* 3.8 34.2 - - + +
595A PHE 4.9 7.0 - - - +
646A PHE* 2.8 30.9 + - + +
647A SER* 3.2 13.0 + - - +
649A ARG* 1.3 75.4 - - - +
651A GLN* 1.3 63.5 + - + +
653A PHE* 3.4 25.6 - - + -
664A MET* 3.8 34.5 - - + +
668A LEU* 4.2 15.5 - - + -
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Residues in contact with GLN 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ARG* 4.3 24.9 - - - +
647A SER* 3.0 21.4 + - - +
648A GLU* 3.7 8.4 - - - +
650A LEU* 1.3 82.4 - - + +
652A ASP* 1.3 61.7 + - - +
653A PHE 3.8 1.2 + - - +
2D NAG 3.6 52.0 + - - +
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Residues in contact with ASP 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A GLU* 2.8 33.0 + - - +
649A ARG* 3.8 7.7 + - - +
651A GLN* 1.3 78.9 - - - +
653A PHE* 1.3 67.4 + - - +
654A ASP* 3.5 1.9 + - - -
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Residues in contact with PHE 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A VAL* 4.3 6.5 - - + -
649A ARG* 2.8 20.3 + - + +
650A LEU* 3.4 35.9 - - + -
651A GLN 3.5 3.6 - - - +
652A ASP* 1.3 77.2 - - - +
654A ASP* 1.3 95.0 + - - +
655A LYS* 2.7 28.5 + - + +
657A ASN 3.7 2.9 - - - -
660A VAL* 3.5 25.8 - - + -
661A LEU* 3.3 56.8 - - + -
664A MET* 4.1 18.4 - - + -
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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