Contacts of the helix formed by residues 714 - 736 (chain A) in PDB entry 5XJY
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 714 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712A TYR 4.7 4.2 - - - +
713A SER* 1.3 78.5 + - - +
715A PRO* 1.4 67.2 - - + +
716A SER* 2.8 20.3 + - - +
717A VAL* 3.2 24.5 + - + +
718A VAL* 3.9 3.5 + - - +
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Residues in contact with PRO 715 (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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701A VAL* 3.4 20.6 - - + +
705A LYS* 3.7 48.2 - - + +
713A SER 3.8 4.3 - - - +
714A ASP* 1.4 82.2 - - + +
716A SER* 1.3 61.0 + - - +
718A VAL* 3.3 22.2 - - + +
719A PHE* 4.0 2.4 + - - +
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Residues in contact with SER 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A ASP* 2.8 11.2 + - - +
715A PRO* 1.3 79.1 - - - +
717A VAL* 1.3 78.9 + - - +
719A PHE* 2.9 23.6 + - - +
720A VAL* 3.0 18.2 + - - +
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Residues in contact with VAL 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A SER* 4.3 15.5 - - - +
714A ASP* 3.3 20.6 - - + +
716A SER* 1.3 86.8 + - - +
718A VAL* 1.3 63.0 + - + +
719A PHE 3.2 0.2 - - - -
720A VAL* 3.8 13.0 - - + +
721A PHE* 2.9 29.5 + - - +
794A PHE* 4.5 9.3 - - + -
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Residues in contact with VAL 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A VAL* 3.9 18.6 - - + -
704A LEU* 4.1 27.1 - - + -
705A LYS* 6.5 0.2 - - + -
710A LEU* 5.2 4.9 - - + -
713A SER* 5.0 11.0 - - - +
714A ASP 4.8 3.8 - - - +
715A PRO* 3.3 29.2 - - + +
717A VAL* 1.3 81.0 - - + +
719A PHE* 1.3 59.5 + - - +
721A PHE* 4.0 3.7 - - - +
722A LEU* 2.9 36.7 + - + +
794A PHE* 3.9 27.8 - - + -
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Residues in contact with PHE 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A LEU* 3.8 36.8 - - + -
697A ALA* 4.2 4.7 - - + -
698A GLY* 3.5 39.5 - - - -
701A VAL* 3.6 17.5 - - + -
715A PRO 4.2 5.6 - - - +
716A SER* 2.9 11.6 + - - +
718A VAL* 1.3 79.4 - - - +
720A VAL* 1.3 67.4 + - + +
722A LEU* 3.9 1.7 - - - +
723A SER* 3.0 29.8 + - - -
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Residues in contact with VAL 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A SER* 3.0 20.4 + - - +
717A VAL* 4.0 12.6 - - + +
719A PHE* 1.3 82.3 - - + +
721A PHE* 1.3 58.3 + - - +
723A SER* 2.3 29.1 + - - +
724A VAL* 3.0 19.4 + - + +
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Residues in contact with PHE 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A VAL 2.9 19.5 + - - +
718A VAL 4.0 2.0 - - - +
720A VAL* 1.3 79.3 - - - +
722A LEU* 1.3 59.2 + - + +
724A VAL* 3.1 15.7 + - + +
725A PHE* 3.0 26.3 + - + +
786A ALA 4.4 0.4 - - - -
787A PHE* 3.4 54.5 - + - -
790A GLY* 4.3 9.9 - - - -
791A CYS* 4.5 1.1 - - - -
794A PHE* 3.7 33.4 - + + -
821A LEU* 5.6 3.4 - - + -
824A SER* 4.3 25.1 - - - -
825A VAL* 4.8 13.7 - - + -
828A MET* 5.7 2.7 - - + -
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Residues in contact with LEU 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A MET* 3.7 27.8 - - + -
648A TRP* 3.7 9.2 - - + -
697A ALA* 3.9 34.2 - - + +
700A LEU* 3.6 30.7 - - + -
701A VAL* 4.8 2.9 - - + -
718A VAL* 2.9 22.7 + - + +
719A PHE* 4.2 2.5 - - - +
721A PHE* 1.3 76.2 - - + +
723A SER* 1.3 61.0 + - - +
725A PHE* 4.3 2.7 - - + +
726A ALA* 2.9 28.6 + - - +
787A PHE* 3.8 27.4 - - + -
794A PHE* 6.4 0.9 - - + -
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Residues in contact with SER 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A LEU* 3.9 24.0 - - - -
697A ALA* 5.0 0.6 - - - +
719A PHE* 3.0 20.6 + - - -
720A VAL* 2.3 31.6 + - - +
722A LEU* 1.3 76.2 - - - +
724A VAL* 1.3 65.8 + - - +
726A ALA* 3.3 7.8 + - - +
727A VAL* 3.0 27.6 + - - +
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Residues in contact with VAL 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A VAL* 3.0 21.9 + - + +
721A PHE* 3.1 17.2 + - + +
723A SER* 1.3 84.7 + - - +
725A PHE* 1.3 57.3 + - - +
727A VAL* 3.0 10.0 + - + +
728A VAL* 3.0 31.1 + - + +
825A VAL* 5.1 13.9 - - + +
828A MET* 3.8 28.7 - - + -
829A LEU* 5.2 2.9 - - + +
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Residues in contact with PHE 725 (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 MET* 5.2 6.3 - - + -
645A THR* 4.9 10.3 - - - -
648A TRP* 3.4 35.0 - + - -
721A PHE* 3.0 13.9 + - + +
722A LEU* 4.1 4.0 - - + +
724A VAL* 1.3 77.3 - - - +
726A ALA* 1.3 57.3 + - - +
728A VAL* 4.4 4.0 - - + +
729A THR* 2.9 32.6 + - - +
754A TYR* 4.3 16.2 - + - -
783A SER* 3.9 21.8 - - - -
784A PRO* 4.1 19.5 - - + -
787A PHE* 3.5 66.0 - + + -
828A MET* 6.1 1.3 - - - -
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Residues in contact with ALA 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A TRP* 3.8 19.5 - - + -
690A LEU* 5.4 6.1 - - + -
693A LEU* 4.5 22.2 - - + +
694A LEU* 5.3 5.8 - - + +
697A ALA* 5.6 0.7 - - + -
722A LEU 2.9 19.1 + - - +
723A SER* 3.4 9.2 - - - +
725A PHE* 1.3 75.6 - - - +
727A VAL* 1.3 64.8 + - + +
729A THR* 3.2 7.7 - - - +
730A ILE* 3.0 28.1 + - - +
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Residues in contact with VAL 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A PHE* 3.7 23.1 - - + -
690A LEU* 3.7 24.2 - - + -
723A SER* 3.0 15.5 + - - +
724A VAL* 3.0 12.3 + - + +
726A ALA* 1.3 76.2 - - - +
728A VAL* 1.3 64.6 + - + +
730A ILE* 3.0 11.2 + - - +
731A LEU* 3.0 34.1 + - + +
832A THR* 5.0 3.8 - - - -
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Residues in contact with VAL 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A VAL* 3.0 19.7 + - + +
725A PHE* 4.4 5.4 - - + +
727A VAL* 1.3 79.8 - - + +
729A THR* 1.3 58.0 + - - +
731A LEU* 3.4 1.6 + - + +
732A GLN* 2.9 30.2 + - + +
783A SER* 3.3 31.9 - - - +
828A MET* 3.4 43.3 - - + +
829A LEU* 5.2 0.7 - - - -
831A ASP* 4.5 4.9 - - + -
832A THR* 3.9 24.7 - - - +
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Residues in contact with THR 729 (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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648A TRP* 3.9 17.7 - - + -
652A VAL* 3.8 10.5 - - + +
693A LEU* 4.8 7.4 - - + -
725A PHE* 2.9 26.5 + - - +
726A ALA* 3.2 20.0 - - - +
728A VAL* 1.3 75.1 - - - +
730A ILE* 1.3 63.0 + - + +
732A GLN* 3.8 5.4 - - - +
733A CYS* 3.0 27.0 + - - +
754A TYR* 2.5 38.3 + - - +
783A SER* 4.8 2.6 + - - -
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Residues in contact with ILE 730 (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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652A VAL* 5.9 0.7 - - + -
655A ILE* 5.8 2.0 - - + -
686A PHE* 3.7 25.1 - - + +
689A SER* 3.4 27.1 - - - +
690A LEU* 3.6 38.8 - - + +
693A LEU* 3.8 16.8 - - + -
726A ALA 3.0 18.9 + - - +
727A VAL* 3.0 9.9 + - - +
729A THR* 1.3 77.7 - - - +
731A LEU* 1.3 59.5 + - - +
733A CYS* 2.8 22.3 + - + +
734A PHE* 2.9 32.5 + - + -
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Residues in contact with LEU 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A PHE* 4.4 18.2 - - + -
727A VAL* 3.0 19.3 + - + +
728A VAL* 4.1 3.8 - - - +
730A ILE* 1.3 75.3 - - - +
732A GLN* 1.3 59.9 + - - +
734A PHE* 3.4 29.1 + - + +
735A LEU* 3.0 26.0 + - - +
832A THR* 3.4 39.5 - - - +
835A TYR* 4.0 19.1 - - + +
836A GLY* 4.9 13.5 - - - +
839A THR* 5.8 2.5 - - - -
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Residues in contact with GLN 732 (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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728A VAL* 2.9 21.5 + - + +
729A THR* 4.1 6.1 - - - +
731A LEU* 1.3 76.8 - - - +
733A CYS* 1.3 58.2 + - - +
735A LEU* 3.6 27.4 - - - +
736A ILE* 3.0 34.2 + - - +
754A TYR* 5.7 0.7 - - + -
757A LEU* 3.9 36.6 - - + +
781A LEU 5.1 8.3 + - - +
783A SER* 4.0 28.6 - - - +
831A ASP* 4.2 9.3 + - - +
835A TYR* 3.6 23.4 - - - +
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Residues in contact with CYS 733 (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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652A VAL* 3.6 43.5 - - + -
655A ILE* 3.6 18.8 - - + -
656A ILE* 3.7 17.0 - - - -
659A ILE* 6.4 0.2 - - - -
729A THR 3.0 13.4 + - - +
730A ILE* 2.8 14.8 + - - +
732A GLN* 1.3 77.6 - - - +
734A PHE* 1.3 63.1 + - + +
736A ILE* 3.5 6.7 - - - +
737A SER* 2.7 29.6 + - - -
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Residues in contact with PHE 734 (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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655A ILE* 4.9 10.1 - - + -
659A ILE* 4.1 27.6 - - + -
682A TRP* 3.8 47.6 - + + -
685A TRP* 3.8 31.6 - - + -
686A PHE* 4.0 6.1 - - + -
730A ILE* 2.9 29.8 + - + -
731A LEU* 3.4 29.1 + - + +
733A CYS* 1.3 79.7 - - + +
735A LEU* 1.3 61.6 + - - +
737A SER* 2.9 16.7 + - - -
738A THR* 3.0 19.4 + - - +
839A THR* 5.0 13.7 - - - -
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Residues in contact with LEU 735 (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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731A LEU 3.0 15.2 + - - +
732A GLN* 3.6 37.7 - - - +
733A CYS 3.3 0.2 - - - -
734A PHE* 1.3 77.4 - - - +
736A ILE* 1.3 68.0 + - + +
737A SER 3.4 0.3 + - - -
738A THR* 3.9 15.2 - - - +
739A LEU* 4.0 14.2 - - + +
835A TYR* 3.8 26.2 + - + +
838A MET* 3.9 21.5 - - + -
839A THR* 5.6 4.2 - - - +
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Residues in contact with ILE 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A VAL* 4.4 14.4 - - + -
656A ILE* 3.6 22.6 - - + +
732A GLN* 3.0 24.8 + - + +
733A CYS* 3.5 8.1 - - - +
735A LEU* 1.3 84.3 - - + +
737A SER* 1.3 61.0 + - - +
738A THR 3.6 0.2 - - - -
739A LEU* 4.3 9.9 + - - +
740A PHE* 4.0 17.8 - - - -
750A GLY* 3.7 29.6 - - - +
753A ILE* 4.3 32.8 - - + +
754A TYR* 5.2 4.0 - - + +
757A LEU* 5.6 8.7 - - + -
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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
------------------------------------------------------------
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