Contacts of the helix formed by residues 784 - 805 (chain A) in PDB entry 5MJ6
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 TYR 784 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A LEU* 3.0 20.4 + - + +
782A LEU* 3.4 44.0 - - + -
783A GLY* 1.3 72.9 - - - +
785A MET* 1.3 64.4 + - - +
786A ASP 3.4 2.2 - - - -
787A LEU* 3.3 28.8 + - + +
788A ALA* 3.0 23.1 + - - +
1018A LEU* 3.4 32.9 - - + +
1022A THR* 5.8 2.0 - - - -
1145A BR 4.4 5.4 - - - -
911B LYS* 5.3 9.2 - - - +
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Residues in contact with MET 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A GLU* 3.3 41.3 - - - +
783A GLY* 2.8 22.3 + - - +
784A TYR* 1.3 71.4 - - - +
786A ASP* 1.3 58.9 + - - +
788A ALA* 3.2 5.6 + - - +
789A SER* 2.9 30.5 + - - -
935A PHE* 3.6 36.1 - - + -
1032A VAL* 3.6 17.4 - - + +
1033A ALA 5.5 0.2 - - - +
1145A BR 3.8 2.1 - - + +
904B ARG* 4.8 14.4 - - + -
907B TYR* 4.1 9.0 - - + -
1101B BR 3.6 24.0 - - + -
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Residues in contact with ASP 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A TYR 3.4 0.2 - - - -
785A MET* 1.3 79.3 - - - +
787A LEU* 1.3 64.5 + - - +
789A SER 3.3 1.0 + - - -
790A ARG* 2.6 63.8 + - - +
1030A SER* 2.9 28.8 + - - -
1032A VAL* 3.2 16.6 - - + +
1034A PRO* 3.8 24.1 - - + +
1145A BR 3.7 17.3 - - + +
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Residues in contact with LEU 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A LEU* 4.0 21.1 - - + -
784A TYR* 3.3 24.0 + - + +
786A ASP* 1.3 81.0 + - - +
788A ALA* 1.3 57.2 + - - +
790A ARG* 3.2 10.6 + - - +
791A LEU* 3.1 26.5 + - - +
1018A LEU* 3.9 22.0 - - + -
1021A LEU* 4.1 6.5 - - + +
1022A THR* 3.8 41.7 - - + +
1025A LEU* 3.8 26.9 - - + +
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Residues in contact with ALA 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A TYR* 3.2 43.4 - - + +
779A LEU* 3.8 26.9 - - + +
780A GLU* 4.2 5.8 - - + +
784A TYR 3.0 17.1 + - - +
785A MET* 3.7 6.1 - - - +
786A ASP 3.2 0.2 - - - -
787A LEU* 1.3 75.1 - - - +
789A SER* 1.3 63.3 + - - +
791A LEU* 3.3 10.9 + - - +
792A VAL 3.3 6.8 + - - -
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Residues in contact with SER 789 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776A TYR* 4.2 4.6 - - - -
785A MET 2.9 17.1 + - - -
786A ASP 3.8 3.6 - - - -
788A ALA* 1.3 73.8 - - - +
790A ARG* 1.3 66.2 + - - +
792A VAL* 3.5 10.3 + - - +
793A THR* 3.0 25.8 + - - -
1030A SER* 3.5 3.0 - - - -
1031A GLN* 2.7 46.2 + - - +
1032A VAL* 4.1 11.2 - - - -
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Residues in contact with ARG 790 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A ASP* 2.6 43.0 + - - +
787A LEU* 3.2 13.6 + - - +
789A SER* 1.3 76.5 - - - +
791A LEU* 1.3 63.9 + - - +
793A THR 3.4 0.9 + - - -
794A ARG* 3.0 20.4 + - - +
1025A LEU* 3.3 27.6 + - + -
1026A ARG* 3.3 25.1 + - - +
1027A THR 4.6 0.2 - - - -
1028A GLU* 3.1 37.5 + - + +
1029A THR 4.0 9.0 - - - -
1030A SER* 3.6 23.7 - - - +
1034A PRO* 6.3 0.2 - - - +
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Residues in contact with LEU 791 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A PHE* 4.0 28.7 - - + -
772A THR* 3.8 25.1 - - + +
775A ILE* 3.5 30.5 - - + -
776A TYR* 3.9 13.7 - - + +
779A LEU* 4.7 5.2 - - + -
787A LEU 3.1 12.7 + - - +
788A ALA* 3.5 8.7 - - - +
789A SER 3.2 0.2 - - - -
790A ARG* 1.3 77.7 - - - +
792A VAL* 1.3 62.2 + - - +
794A ARG* 3.2 5.7 + - - +
795A VAL* 3.1 26.1 + - + +
1021A LEU* 4.7 4.7 - - + -
1024A TRP* 4.2 15.7 - - + -
1025A LEU* 4.0 16.1 - - + +
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Residues in contact with VAL 792 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A THR* 4.1 13.0 - - + -
776A TYR* 3.5 34.3 - - + -
788A ALA 3.3 6.2 + - - +
789A SER* 3.6 14.8 - - - +
791A LEU* 1.3 73.5 - - + +
793A THR* 1.3 59.7 + - - +
795A VAL* 3.9 7.2 - - - +
796A PHE* 2.7 35.6 + - - +
826A PHE* 4.0 18.5 - - + -
830A HIS* 3.9 31.0 - - + +
832A LEU* 3.8 7.9 - - + +
1031A GLN* 4.7 6.5 - - - +
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Residues in contact with THR 793 (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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789A SER 3.0 21.0 + - - -
790A ARG 3.5 4.0 - - - -
792A VAL* 1.3 75.9 - - - +
794A ARG* 1.3 64.5 + - - +
796A PHE* 3.2 6.8 + - + +
797A LYS* 3.0 39.0 + - - +
832A LEU* 3.9 16.6 - - + +
1028A GLU* 3.2 23.6 - - - +
1029A THR* 3.5 25.1 + - - +
1031A GLN* 4.1 10.7 + - - +
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Residues in contact with ARG 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A ASN* 6.1 0.7 - - - -
790A ARG 3.0 13.4 + - - +
791A LEU 3.3 9.2 - - - +
793A THR* 1.3 78.4 - - - +
795A VAL* 1.3 63.8 + - + +
797A LYS* 3.3 8.0 + - - +
798A LEU* 3.1 22.0 + - + +
1024A TRP* 3.3 71.8 + - + +
1025A LEU* 4.1 10.6 - - + +
1027A THR* 4.1 12.9 + - - -
1028A GLU* 2.4 46.2 + - - +
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Residues in contact with VAL 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A PHE* 5.2 8.1 - - + -
753A ILE* 5.4 7.0 - - + -
756A LEU* 6.3 1.3 - - + -
768A ALA* 5.8 2.0 - - + +
769A LEU* 4.3 6.1 - - + -
772A THR* 3.5 35.2 - - + +
791A LEU* 3.1 23.4 + - + +
792A VAL* 3.9 4.0 - - - +
794A ARG* 1.3 76.3 - - + +
796A PHE* 1.3 66.3 + - - +
798A LEU* 3.2 16.2 + - + +
799A LEU* 3.1 37.6 + - + +
826A PHE* 4.0 15.9 - - + -
1024A TRP* 6.0 0.4 - - + -
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Residues in contact with PHE 796 (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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792A VAL 2.7 23.2 + - - +
793A THR* 3.2 7.8 + - + +
795A VAL* 1.3 74.5 - - - +
797A LYS* 1.3 55.9 + - + +
799A LEU 3.1 2.1 + - - -
800A GLN* 2.7 69.0 + - + -
803A ILE* 3.6 41.3 - - + -
804A GLN* 5.4 0.2 - - - -
826A PHE* 4.4 6.9 - + + -
827A ALA* 4.6 2.9 - - + -
832A LEU* 3.6 39.7 - - + -
833A GLY* 3.9 25.8 - - - -
835A CYS* 5.6 0.4 - - - -
1139A BR 4.5 7.2 - - + -
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Residues in contact with LYS 797 (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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793A THR* 3.0 27.3 + - + +
794A ARG* 3.3 8.7 + - - +
796A PHE* 1.3 81.0 - - + +
798A LEU* 1.3 61.4 + - - +
800A GLN* 3.4 31.6 - - - +
1028A GLU* 3.1 31.2 - - - +
1029A THR* 4.3 8.4 + - - -
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Residues in contact with LEU 798 (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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753A ILE* 3.2 36.8 - - + +
754A ASN* 3.7 39.7 - - - +
756A LEU* 4.0 18.2 - - + -
757A GLY* 3.7 24.7 + - - +
794A ARG* 3.1 13.8 + - + +
795A VAL* 3.3 18.8 - - + +
797A LYS* 1.3 80.0 - - - +
799A LEU* 1.3 59.9 + - + +
800A GLN 3.5 0.4 + - - -
801A ASN 5.3 0.2 + - - -
802A GLN* 4.3 0.2 - - - +
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Residues in contact with LEU 799 (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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756A LEU* 3.9 30.7 - - + +
765A ILE* 4.3 20.9 - - + +
768A ALA* 6.1 0.2 - - + -
769A LEU* 3.9 28.3 - - + -
795A VAL* 3.1 22.6 + - + +
796A PHE 3.5 1.3 - - - -
798A LEU* 1.3 78.7 - - + +
800A GLN* 1.3 64.7 + - - +
801A ASN 3.0 5.0 + - - -
802A GLN* 3.0 33.0 + - + +
803A ILE* 2.9 36.9 + - + +
823A LEU* 4.5 12.8 - - + -
826A PHE* 5.8 0.9 - - + -
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Residues in contact with GLN 800 (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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796A PHE* 2.7 39.5 + - - +
797A LYS* 3.4 33.0 + - - +
798A LEU 3.5 0.8 - - - -
799A LEU* 1.3 74.7 - - - +
801A ASN* 1.3 64.4 + - - +
803A ILE* 3.9 5.7 - - - +
804A GLN* 2.8 68.1 + - - +
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Residues in contact with ASN 801 (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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757A GLY* 5.5 5.8 + - - +
798A LEU 5.3 0.6 + - - -
799A LEU 3.1 1.4 - - - -
800A GLN* 1.3 83.3 - - - +
802A GLN* 1.3 71.3 + - + +
804A GLN* 3.8 6.0 - - - +
805A GLN* 3.0 46.4 + - - +
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Residues in contact with GLN 802 (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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756A LEU 2.8 24.6 + - - +
757A GLY* 3.8 13.7 + - - +
759A GLU 2.7 29.4 + - - +
760A ASN* 5.5 2.9 - - + -
765A ILE* 4.0 8.3 - - + +
798A LEU 4.3 1.7 - - - +
799A LEU* 3.3 32.5 - - + +
801A ASN* 1.3 79.2 + - + +
803A ILE* 1.3 62.6 + - - +
805A GLN* 3.4 10.2 + - - +
806A GLN* 2.7 31.2 + - - +
819A LEU* 5.8 2.5 - - + -
823A LEU* 3.8 18.2 - - + -
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Residues in contact with ILE 803 (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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796A PHE* 3.6 42.6 - - + +
799A LEU* 2.9 31.5 + - + +
800A GLN* 3.9 3.4 - - - +
802A GLN* 1.3 75.6 - - - +
804A GLN* 1.3 63.2 + - - +
806A GLN* 3.1 27.0 + - - +
823A LEU* 3.8 31.0 - - + +
824A LEU* 4.8 6.1 - - + +
826A PHE* 4.4 18.2 - - + -
827A ALA* 4.4 4.5 - - + -
835A CYS* 4.4 12.6 - - - -
1139A BR 4.4 12.3 - - + -
1L NAG 5.8 0.7 - - - -
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Residues in contact with GLN 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
796A PHE* 5.4 0.8 - - + -
800A GLN* 2.8 58.8 + - - +
801A ASN* 4.1 6.3 - - - +
803A ILE* 1.3 76.6 - - + +
805A GLN* 1.3 60.3 + - + +
806A GLN 3.3 2.0 + - - +
1139A BR 4.0 19.3 - - + -
1L NAG 4.5 8.5 - - - -
2L NAG 3.3 63.6 - - - +
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Residues in contact with GLN 805 (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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801A ASN* 3.0 39.7 + - - +
802A GLN* 3.4 8.1 + - - +
803A ILE 3.3 0.6 + - - -
804A GLN* 1.3 74.5 - - + +
806A GLN* 1.3 66.5 + - - +
807A THR* 3.5 7.4 + - - +
2L NAG 3.9 25.8 + - - +
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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