Contacts of the helix formed by residues 798 - 815 (chain A) in PDB entry 5ZR1
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 SER 798 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A LEU* 1.3 82.5 - - - +
799A PHE* 1.3 64.1 + - - +
800A THR 3.2 5.2 - - - -
801A ALA* 3.8 11.7 - - - +
802A LYS* 3.1 24.0 + - - -
869A VAL* 5.0 1.5 - - - +
872A GLN* 5.1 2.5 + - - -
328D PHE 4.5 0.2 - - - -
329D GLU 3.6 8.7 - - - -
330D THR 3.2 20.5 + - - -
331D PHE 3.1 24.9 + - - -
332D ARG* 3.3 20.4 - - - +
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Residues in contact with PHE 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A SER* 1.3 73.7 - - - +
800A THR* 1.3 58.4 + - - +
802A LYS* 3.5 8.3 + - + +
803A LEU* 2.8 54.2 + - + +
833A ILE* 4.9 7.2 - - + -
841A PHE* 3.5 30.1 - + + -
842A VAL* 5.4 1.3 - - + -
845A ILE* 3.6 28.5 - - + -
849A LEU* 4.2 14.6 - - + -
908A ASP* 5.3 0.9 - - - -
910A THR* 3.9 17.0 - - + -
911A LEU* 3.7 32.1 - - + -
914A LEU* 5.2 7.0 - - + -
329D GLU* 3.3 29.7 + - - +
332D ARG* 4.5 5.3 - - - +
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Residues in contact with THR 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A SER 3.2 0.4 - - - -
799A PHE* 1.3 80.3 - - - +
801A ALA* 1.3 57.2 + - - +
803A LEU* 3.3 7.9 + - - +
804A PHE* 3.1 26.9 + - - +
849A LEU* 4.4 12.0 - - - +
863A ILE* 3.7 24.8 - - + +
864A ILE 3.7 6.1 + - - +
865A SER* 3.4 31.3 + - - +
869A VAL* 3.7 8.2 - - + +
329D GLU 3.3 10.7 + - - -
330D THR* 3.4 25.3 - - - +
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Residues in contact with ALA 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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797A LEU* 3.7 32.3 - - + +
798A SER* 3.6 9.7 + - - +
800A THR* 1.3 77.8 - - - +
802A LYS* 1.3 63.1 + - - +
804A PHE* 3.4 11.9 + - - +
805A ILE* 3.4 18.9 + - - +
869A VAL* 4.0 26.6 - - + +
872A GLN* 4.4 8.1 - - - +
873A LEU* 4.4 8.6 - - + +
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Residues in contact with LYS 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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794A MET 3.6 26.7 - - - +
795A THR* 3.6 18.0 + - - +
797A LEU* 3.6 19.4 + - + +
798A SER 3.1 24.5 + - - +
799A PHE* 4.0 8.1 - - - +
801A ALA* 1.3 74.3 - - - +
803A LEU* 1.3 60.4 + - - +
805A ILE 3.5 0.3 + - - -
806A TYR* 3.0 29.6 + - - +
904A ALA 5.4 0.4 - - - +
905A MET* 3.7 23.4 - - + +
908A ASP* 2.7 39.0 + - + +
911A LEU* 3.5 16.1 - - + +
332D ARG* 5.3 4.4 - - - +
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Residues in contact with LEU 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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799A PHE* 2.8 43.4 + - + +
800A THR* 3.7 5.4 - - - +
802A LYS* 1.3 73.9 - - - +
804A PHE* 1.3 60.0 + - - +
806A TYR* 4.4 4.3 - - + -
807A ALA* 3.1 27.9 + - - +
829A ILE* 3.7 31.9 - - + +
832A LEU* 3.7 34.8 - - + -
833A ILE* 4.2 13.7 - - + -
849A LEU* 4.8 7.2 - - + -
863A ILE* 4.6 9.4 - - + -
911A LEU* 4.1 17.4 - - + +
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Residues in contact with PHE 804 (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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800A THR 3.1 13.2 + - - +
801A ALA* 3.5 12.3 - - - +
802A LYS 3.2 0.4 - - - -
803A LEU* 1.3 78.2 - - - +
805A ILE* 1.3 65.0 + - + +
807A ALA* 4.0 2.6 - - - +
808A LEU* 3.1 22.3 + - + +
822A LEU* 3.8 16.2 - - + -
825A ILE* 3.7 29.5 - - + +
829A ILE* 4.1 12.3 - - + +
863A ILE* 6.1 0.4 - - + -
866A TRP* 3.6 31.6 - + - -
869A VAL* 4.7 10.3 - - + -
870A LEU* 3.6 24.5 - - + -
873A LEU* 3.8 20.4 - - + -
879A LEU* 3.6 26.7 - - + -
892A VAL* 4.8 2.0 - - + -
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Residues in contact with ILE 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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794A MET* 4.8 9.0 - - - -
797A LEU* 5.5 1.3 - - + -
801A ALA 3.4 14.1 + - - +
802A LYS 4.0 0.2 - - - +
803A LEU 3.4 0.2 - - - -
804A PHE* 1.3 80.9 - - + +
806A TYR* 1.3 59.2 + - - +
808A LEU* 3.0 6.6 + - + +
809A LEU* 2.8 48.2 + - + +
873A LEU* 3.8 26.9 - - + -
878A ILE* 4.7 9.4 - - + -
879A LEU* 4.5 5.4 - - + -
894A LEU* 4.4 21.8 - - + -
901A ALA* 4.4 13.2 - - + -
905A MET* 3.7 30.1 - - + -
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Residues in contact with TYR 806 (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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802A LYS 3.0 18.9 + - - +
803A LEU* 4.1 4.9 - - + +
804A PHE 3.4 0.2 - - - -
805A ILE* 1.3 76.8 - - - +
807A ALA* 1.3 59.7 + - - +
809A LEU* 3.7 10.9 + - + +
810A ASN* 3.0 51.9 + - - -
832A LEU* 3.6 23.3 - - + -
905A MET* 4.5 19.2 - - + +
911A LEU* 3.6 37.4 + - + -
912A ARG* 5.3 2.6 - - - -
914A LEU* 3.0 41.4 + - + -
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Residues in contact with ALA 807 (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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803A LEU 3.1 19.4 + - - +
804A PHE 4.0 2.9 - - - +
805A ILE 3.2 0.2 - - - -
806A TYR* 1.3 75.8 - - - +
808A LEU* 1.3 63.3 + - - +
810A ASN* 3.6 3.4 + - - +
811A LEU* 3.3 29.5 + - - +
825A ILE* 4.3 8.0 - - + +
828A GLU* 3.7 24.4 - - + +
829A ILE* 3.7 23.8 - - + +
832A LEU* 4.9 4.9 - - + -
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Residues in contact with LEU 808 (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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804A PHE* 3.1 19.7 + - + +
805A ILE* 3.0 13.3 + - + +
807A ALA* 1.3 77.2 - - - +
809A LEU* 1.3 60.8 + - - +
811A LEU* 3.5 3.6 + - - +
812A MET* 3.3 35.5 + - + +
820A GLN* 3.7 25.8 - - + -
825A ILE* 3.7 25.8 - - + +
879A LEU* 3.7 29.4 - - + -
892A VAL* 4.2 15.0 - - + +
893A LYS 4.7 2.0 - - - +
894A LEU* 3.8 20.9 - - + -
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Residues in contact with LEU 809 (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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805A ILE* 2.8 30.0 + - + +
806A TYR* 4.2 9.0 - - + +
807A ALA 3.3 0.2 - - - -
808A LEU* 1.3 76.4 - - + +
810A ASN* 1.3 62.9 + - - +
812A MET* 3.5 24.3 + - + +
813A LYS* 2.8 37.5 + - - +
894A LEU* 4.3 3.1 - - + -
898A VAL* 4.1 19.4 - - + +
901A ALA* 3.8 37.9 - - + +
902A LYS* 3.7 22.4 - - + -
905A MET* 4.2 10.1 - - + -
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Residues in contact with ASN 810 (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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806A TYR* 3.0 51.7 + - - +
807A ALA* 3.9 6.0 - - - +
808A LEU 3.4 0.2 - - - -
809A LEU* 1.3 78.1 - - - +
811A LEU* 1.3 56.8 + - - +
813A LYS* 3.4 22.1 + - - +
814A LYS* 3.1 35.5 + - - +
828A GLU* 4.1 17.3 + - - +
832A LEU* 3.8 13.1 - - - +
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Residues in contact with LEU 811 (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 ALA 3.3 19.6 + - - +
808A LEU* 3.8 5.4 - - - +
809A LEU 3.3 0.4 - - - -
810A ASN* 1.3 80.0 - - - +
812A MET* 1.3 57.4 + - - +
813A LYS 3.2 0.4 - - - -
814A LYS* 3.5 14.0 + - + +
815A ASN* 3.3 35.5 + - - +
820A GLN* 3.4 46.7 + - + +
824A ASP* 4.0 28.0 - - + +
825A ILE* 5.1 4.0 - - + +
828A GLU* 3.6 36.8 - - + +
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Residues in contact with MET 812 (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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808A LEU* 3.3 34.0 + - + +
809A LEU* 3.5 21.9 + - + +
810A ASN 3.3 0.2 - - - -
811A LEU* 1.3 75.6 - - - +
813A LYS* 1.3 57.4 + - - +
816A GLY* 3.3 24.8 - - - +
818A GLN* 3.8 32.5 - - - +
820A GLN* 3.8 20.6 - - + +
892A VAL 6.0 0.7 - - - +
894A LEU* 3.7 34.3 - - + -
898A VAL* 4.6 21.3 - - + +
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Residues in contact with LYS 813 (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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809A LEU* 2.8 37.0 + - - +
810A ASN* 3.4 27.0 + - - +
812A MET* 1.3 78.6 - - - +
814A LYS* 1.3 61.7 + - + +
815A ASN 3.4 0.9 - - - -
816A GLY* 4.5 1.3 - - - +
902A LYS* 4.5 22.4 - - - +
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Residues in contact with LYS 814 (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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810A ASN* 3.1 25.8 + - - +
811A LEU* 3.5 16.7 + - + +
813A LYS* 1.3 80.7 - - + +
815A ASN* 1.3 70.2 + - - +
828A GLU* 2.7 36.7 + - - +
831A LEU* 5.3 8.5 - - - +
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Residues in contact with ASN 815 (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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811A LEU* 3.3 17.7 + - - +
813A LYS 4.9 0.7 - - - -
814A LYS* 1.3 90.2 - - - +
816A GLY* 1.3 61.1 + - - +
817A SER* 3.5 20.0 + - - +
820A GLN* 3.8 18.6 - - - +
824A ASP* 5.9 0.8 + - - -
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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
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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