Contacts of the helix formed by residues 843 - 863 (chain A) in PDB entry 6DMY
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 MET 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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819A LEU* 3.3 50.0 - - + +
820A TYR* 4.9 3.8 - - - -
823A HIS* 3.7 19.8 + - + +
841A PRO 3.5 3.0 + - - -
842A LYS* 1.3 77.3 - - - +
844A TRP* 1.3 68.9 + - + +
845A LEU* 3.6 27.1 - - + +
846A HIS* 2.9 36.8 + - + +
847A TYR* 3.4 6.4 + - - -
937A SER* 4.3 0.9 - - - -
974A PHE* 3.6 54.1 - - + -
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Residues in contact with TRP 844 (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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807A THR* 5.0 4.0 - - + +
812A TYR* 4.3 22.9 - + - -
819A LEU* 5.2 2.4 - - + +
843A MET* 1.3 77.6 - - + +
845A LEU* 1.3 85.8 + - + +
847A TYR* 4.5 2.2 - - - +
848A PHE* 3.0 37.3 + + + +
919A PHE* 3.8 27.6 - + - -
923A LEU* 4.1 12.3 - - + -
926A TRP* 4.1 25.8 - + + -
937A SER* 3.4 23.8 + - - +
939A ALA* 3.7 25.6 - - + -
941A ILE* 5.0 6.7 - - + -
969A ILE* 4.5 9.2 - - + -
972A ALA* 3.9 27.9 - - + +
973A GLN 3.7 11.3 + - - -
974A PHE* 4.4 11.6 - + + +
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Residues in contact with LEU 845 (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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816A GLN* 5.1 7.9 - - + -
819A LEU* 3.7 24.9 - - + -
820A TYR* 3.3 37.8 + - + +
843A MET* 3.1 20.3 - - - +
844A TRP* 1.3 113.6 - - + +
846A HIS* 1.3 58.3 + - - +
848A PHE* 4.4 2.5 - - + -
849A ARG* 2.9 33.4 + - - +
913A ILE* 5.0 2.7 - - + -
915A ASN* 4.7 9.4 - - - +
919A PHE* 4.4 21.5 - - + -
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Residues in contact with HIS 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A TYR* 3.3 40.3 - + - -
823A HIS* 3.9 28.0 - + - -
842A LYS* 3.5 44.1 - - + +
843A MET* 2.9 18.3 + - + +
845A LEU* 1.3 75.4 - - + +
847A TYR* 1.3 61.8 + - - +
849A ARG* 4.1 19.4 + - - +
850A ASP* 2.9 33.5 + - - +
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Residues in contact with TYR 847 (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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333A LYS* 4.2 14.0 + - - -
334A TYR* 3.7 41.0 - + - -
842A LYS* 4.1 46.1 + - + +
843A MET 3.4 6.9 + - - +
844A TRP* 3.6 3.6 + - - +
846A HIS* 1.3 80.6 - - - +
848A PHE* 1.3 57.0 + - - +
850A ASP* 3.9 7.7 - - + +
851A TRP* 3.0 27.9 + - - +
926A TRP* 4.2 17.5 + - + -
930A ASP* 5.0 1.0 - - - +
933A ALA* 3.9 16.4 - - + +
936A ALA* 4.7 1.6 - - + -
937A SER* 3.5 37.9 - - - -
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Residues in contact with PHE 848 (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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844A TRP* 3.0 26.4 + + + +
845A LEU* 4.0 6.3 - - + +
847A TYR* 1.3 75.6 - - - +
849A ARG* 1.3 59.5 + - - +
851A TRP* 3.1 5.2 + + - +
852A LEU* 3.0 39.1 + - + +
915A ASN* 3.4 30.3 - - - -
919A PHE* 3.5 25.1 - + - -
922A TYR* 3.2 50.7 - - + -
923A LEU* 3.7 9.9 - - + -
926A TRP* 3.5 42.6 - + + +
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Residues in contact with ARG 849 (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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820A TYR* 3.6 14.1 + - - +
845A LEU 2.9 16.8 + - - +
846A HIS* 4.1 22.8 + - - +
848A PHE* 1.3 79.4 - - - +
850A ASP* 1.3 60.2 + - - +
852A LEU* 3.4 2.2 + - - +
853A GLN* 3.0 29.8 + - + +
908A VAL* 3.6 21.9 - - + +
912A GLY 4.9 5.7 + - - -
913A ILE* 3.7 45.9 - - + +
915A ASN* 4.7 15.3 - - - +
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Residues in contact with ASP 850 (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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284A LYS* 5.9 0.6 + - - -
842A LYS* 4.1 16.7 + - - +
846A HIS 2.9 21.3 + - - +
847A TYR* 3.9 8.5 - - + +
849A ARG* 1.3 81.8 - - - +
851A TRP* 1.3 56.6 + - - +
853A GLN* 3.5 9.9 + - - +
854A GLY* 3.0 24.3 + - - -
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Residues in contact with TRP 851 (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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847A TYR 3.0 18.3 + - - +
848A PHE* 3.1 4.5 + + - +
850A ASP* 1.3 77.2 - - - +
852A LEU* 1.3 90.9 + - + +
854A GLY* 3.0 4.3 + - - -
855A LEU* 3.0 51.0 + - + +
882A LEU* 3.7 28.9 - - + -
886A LEU* 4.4 3.4 - - + -
922A TYR 4.0 3.8 - - - -
925A ALA* 3.8 18.6 - - + -
926A TRP* 3.7 35.4 - + + -
929A ASN* 4.5 11.3 + - + -
930A ASP* 3.3 32.6 + - + +
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Residues in contact with LEU 852 (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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848A PHE* 3.0 40.5 + - + +
849A ARG 4.0 3.1 - - - +
850A ASP 3.4 0.2 - - - -
851A TRP* 1.3 103.2 - - + +
853A GLN* 1.3 62.7 + - - +
855A LEU* 3.3 7.5 + - + +
856A GLN* 3.0 22.7 + - - +
886A LEU* 3.9 20.4 - - + -
907A LEU* 4.1 29.8 - - + +
908A VAL* 4.9 1.3 - - + -
915A ASN* 3.4 23.3 - - - +
922A TYR* 3.8 24.0 - - + -
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Residues in contact with GLN 853 (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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849A ARG* 3.0 18.5 + - + +
850A ASP* 3.7 11.7 - - - +
852A LEU* 1.3 75.2 - - - +
854A GLY* 1.3 59.1 + - - +
856A GLN* 3.2 8.6 + - - +
857A ASP* 2.9 50.6 + - - +
908A VAL* 3.3 36.3 - - + +
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Residues in contact with GLY 854 (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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284A LYS* 6.0 4.5 - - - -
850A ASP* 3.0 15.7 + - - -
851A TRP* 3.0 5.7 + - - -
853A GLN* 1.3 78.3 - - - +
855A LEU* 1.3 58.4 + - - +
857A ASP* 3.6 4.3 + - - +
858A ALA* 3.0 31.7 + - - +
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Residues in contact with LEU 855 (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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851A TRP* 3.0 55.1 + - + +
852A LEU* 3.3 11.0 + - + +
854A GLY* 1.3 77.0 - - - +
856A GLN* 1.3 57.0 + - - +
858A ALA* 3.6 3.2 + - - +
859A PHE* 2.9 28.6 + - - +
879A ASP* 3.3 37.2 - - + +
882A LEU* 4.0 14.8 - - + -
883A ALA* 3.5 32.0 - - + +
886A LEU* 5.4 2.2 - - + -
907A LEU* 4.5 7.6 - - + -
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Residues in contact with GLN 856 (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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852A LEU 3.0 13.4 + - - +
853A GLN* 3.2 13.7 + - - +
855A LEU* 1.3 77.7 - - - +
857A ASP* 1.3 62.0 + - - +
859A PHE* 3.0 7.9 + - + +
860A ASP* 2.9 42.5 + - - +
883A ALA* 5.3 0.2 - - - -
887A LEU* 6.5 0.9 - - + -
906A ARG* 3.3 31.3 - - + +
907A LEU* 3.4 26.1 + - + +
908A VAL* 3.4 24.2 - - - +
909A ASP* 3.5 6.0 + - - +
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Residues in contact with ASP 857 (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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853A GLN* 2.9 42.1 + - - +
854A GLY* 4.2 4.2 - - - +
856A GLN* 1.3 80.5 + - - +
858A ALA* 1.3 59.3 + - - +
860A ASP* 4.5 4.5 - - - +
861A SER* 2.9 31.7 + - - -
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Residues in contact with ALA 858 (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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280A GLU* 6.0 0.4 - - - +
854A GLY 3.0 19.8 + - - +
855A LEU* 4.0 4.0 - - - +
857A ASP* 1.3 76.9 - - - +
859A PHE* 1.3 57.9 + - - +
861A SER* 4.1 4.1 - - - -
862A ASP* 2.9 30.7 + - - +
878A ASP 4.9 2.3 - - - +
879A ASP* 4.2 28.2 - - + +
880A GLY* 4.9 0.5 + - - -
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Residues in contact with PHE 859 (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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855A LEU 2.9 18.8 + - - +
856A GLN* 3.0 7.6 + - + +
858A ALA* 1.3 77.9 - - - +
860A ASP* 1.3 76.1 + - - +
862A ASP* 4.3 2.0 - - - -
863A TRP* 2.7 57.8 + + + +
865A THR* 4.5 15.3 - - - -
867A LYS 6.1 0.7 - - - -
872A ASN* 5.5 5.8 - - - -
879A ASP 4.5 0.2 + - - -
880A GLY* 3.8 31.2 - - - -
883A ALA* 3.7 15.0 - - + -
884A TYR* 4.6 13.7 - + + -
887A LEU* 3.6 23.3 - - + -
902A LEU* 4.0 22.0 - - + -
906A ARG* 6.2 1.8 - - - -
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Residues in contact with ASP 860 (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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856A GLN* 2.9 34.8 + - - +
857A ASP* 4.5 4.2 - - - +
859A PHE* 1.3 92.9 - - - +
861A SER* 1.3 64.7 + - - +
863A TRP 3.8 14.6 - - - +
864A GLU* 4.3 11.0 + - - +
865A THR* 5.3 3.3 + - - -
906A ARG* 4.8 19.7 + - - +
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Residues in contact with SER 861 (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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857A ASP 2.9 21.6 + - - -
858A ALA* 4.1 5.4 - - - -
860A ASP* 1.3 79.3 - - - +
862A ASP* 1.3 63.7 + - - +
864A GLU* 5.0 4.3 - - - +
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Residues in contact with ASP 862 (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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858A ALA 2.9 22.3 + - - +
859A PHE* 3.1 5.4 + - - +
861A SER* 1.3 79.8 - - - +
863A TRP* 1.3 83.8 + - + +
864A GLU* 4.1 7.3 - - - +
876A GLY 3.9 7.8 - - - +
877A SER* 2.4 32.7 + - - -
878A ASP 3.5 15.0 - - - +
880A GLY* 3.7 3.6 + - - -
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Residues in contact with TRP 863 (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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859A PHE* 2.7 42.9 + + + +
860A ASP* 3.8 9.3 - - - +
862A ASP* 1.3 108.9 + - + +
864A GLU* 1.3 77.8 + - - +
865A THR* 3.5 2.5 + - - -
867A LYS* 4.4 21.3 - - + +
872A ASN* 3.9 37.7 + - - +
873A TYR* 4.8 2.2 - - + +
875A ASN* 3.7 22.9 - - + -
876A GLY 3.9 5.2 - - - -
877A SER* 3.4 24.1 + - - -
880A GLY* 5.3 5.2 - - - -
1804A NAG 5.8 3.6 - - - -
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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
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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