Contacts of the helix formed by residues 854 - 875 (chain B) in PDB entry 6UZA
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 GLN 854 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B GLU* 3.7 19.0 - - - +
351B GLU* 4.3 17.8 + - - +
853B ARG* 1.3 77.9 - - - +
855B TYR* 1.3 59.6 + - - +
857B LYS* 3.3 25.8 + - - +
858B ILE* 3.0 45.3 + - + +
861B ARG* 4.9 5.8 + - - +
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Residues in contact with TYR 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B GLU 6.1 0.4 - - - -
292B ASP* 2.9 38.6 + - + -
344B ALA* 3.6 37.2 + - + -
348B GLY 3.9 16.4 - - - -
349B ASP* 3.3 44.9 - - + +
350B VAL 5.4 0.9 - - - +
351B GLU* 4.7 3.9 + - - +
365B ARG* 3.5 11.8 + - - -
853B ARG* 3.5 13.5 - - - +
854B GLN* 1.3 79.0 - - - +
856B GLN* 1.3 64.0 + - - +
858B ILE* 3.9 3.9 - - - -
859B MET* 2.9 49.9 + - + +
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Residues in contact with GLN 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU* 3.5 33.7 + - - +
853B ARG* 3.1 61.7 + - + +
854B GLN 3.3 0.4 - - - -
855B TYR* 1.3 83.5 - - - +
857B LYS* 1.3 57.7 + - + +
859B MET* 3.9 4.7 - - - +
860B LYS* 2.9 31.6 + - - +
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Residues in contact with LYS 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853B ARG 3.4 16.5 + - - +
854B GLN* 3.3 30.6 + - - +
855B TYR 3.3 0.4 - - - -
856B GLN* 1.3 78.7 - - + +
858B ILE* 1.3 58.5 + - + +
860B LYS* 3.3 7.4 + - - +
861B ARG* 3.0 39.2 + - - +
212C ASP* 3.9 31.5 + - - +
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Residues in contact with ILE 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLU* 3.6 42.6 - - + +
341B GLU* 4.0 15.7 - - + -
344B ALA* 3.7 26.2 - - + -
854B GLN* 3.0 35.4 + - + +
855B TYR* 4.0 4.5 - - - +
857B LYS* 1.3 75.6 - - - +
859B MET* 1.3 58.5 + - - +
861B ARG* 3.4 21.4 + - + +
862B LEU* 3.0 43.0 + - + +
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Residues in contact with MET 859 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLU 4.9 10.3 - - - +
292B ASP* 3.9 9.0 - - - +
293B PRO* 3.8 32.8 - - + -
294B VAL* 4.2 14.1 - - + -
332B LEU* 4.7 4.5 - - + -
344B ALA* 4.4 4.3 - - - +
345B ILE* 4.0 22.9 - - + -
855B TYR* 2.9 55.0 + - + +
856B GLN* 4.1 5.6 - - - +
858B ILE* 1.3 76.5 - - - +
860B LYS* 1.3 57.4 + - - +
862B LEU* 3.8 8.8 - - + +
863B ILE* 2.9 38.8 + - + +
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Residues in contact with LYS 860 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856B GLN 2.9 19.8 + - - +
857B LYS* 3.7 7.2 - - - +
858B ILE 3.3 0.4 - - - -
859B MET* 1.3 76.4 - - - +
861B ARG* 1.3 56.3 + - - +
863B ILE* 3.4 5.7 + - - -
864B LYS* 3.0 27.7 + - - +
86C TYR* 5.3 9.9 - - - +
88C PHE* 3.7 19.6 - - + -
89C SER 3.2 27.7 + - - -
90C ASP* 4.2 16.5 + - - +
91C ARG* 5.7 0.4 - - - +
92C SER* 5.4 5.3 - - - -
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Residues in contact with ARG 861 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B ASN* 4.0 6.3 - - - +
340B GLU* 3.9 18.2 + - - -
341B GLU* 3.6 16.9 + - - -
854B GLN* 4.9 4.4 + - - +
857B LYS* 3.0 24.8 + - - +
858B ILE* 3.4 27.1 - - - +
860B LYS* 1.3 76.5 - - - +
862B LEU* 1.3 65.9 + - + +
864B LYS* 3.4 6.0 + - - +
865B ARG* 3.0 57.5 + - - +
209C TYR* 5.5 0.5 + - - -
210C ASP* 5.6 4.9 - - - +
212C ASP* 3.0 49.1 + - - +
213C GLY* 5.4 7.5 - - - -
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Residues in contact with LEU 862 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B LEU* 3.9 16.8 - - + +
335B LEU* 4.3 14.4 - - + +
336B CYS* 4.2 14.8 - - - -
341B GLU* 3.6 15.0 - - + +
344B ALA* 5.2 0.4 - - + -
345B ILE* 3.8 30.5 - - + -
858B ILE* 3.0 38.8 + - + +
859B MET* 3.9 9.9 - - + +
860B LYS 3.3 0.2 - - - -
861B ARG* 1.3 78.8 - - + +
863B ILE* 1.3 60.0 + - + +
865B ARG* 3.4 30.5 + - - +
866B TYR* 2.9 28.1 + - - +
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Residues in contact with ILE 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B SER* 3.4 34.5 - - - +
290B SER 4.9 4.7 - - - +
291B GLU 4.6 7.2 - - - +
293B PRO* 3.8 37.5 - - + -
328B PHE* 6.1 0.4 - - + -
332B LEU* 5.1 5.2 - - + -
859B MET* 2.9 29.7 + - + +
860B LYS* 3.9 4.5 - - - +
862B LEU* 1.3 74.4 - - + +
864B LYS* 1.3 60.0 + - - +
866B TYR* 3.2 6.6 + - - +
867B VAL* 3.0 30.8 + - + +
86C TYR* 6.0 3.4 - - + -
88C PHE* 3.8 28.0 - - + -
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Residues in contact with LYS 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B LYS 3.0 18.0 + - - +
861B ARG* 3.8 7.0 - - - +
862B LEU 3.3 0.2 - - - -
863B ILE* 1.3 77.5 - - - +
865B ARG* 1.3 60.0 + - - +
867B VAL* 3.4 3.8 + - - +
868B LEU* 3.0 30.5 + - + +
88C PHE* 3.7 23.5 - - + -
90C ASP* 4.8 4.1 - - + +
132C MET* 2.7 37.2 + - - +
133C GLY* 4.0 6.5 + - - -
134C GLN* 4.3 4.7 - - - +
209C TYR* 3.6 37.3 + - - +
210C ASP* 2.5 43.5 + - - +
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Residues in contact with ARG 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 3.0 39.0 + - + +
337B ARG* 3.7 44.2 - - - +
341B GLU* 2.4 45.9 + - - -
861B ARG* 3.0 38.6 + - - +
862B LEU* 3.5 15.9 - - - +
864B LYS* 1.3 75.0 - - - +
866B TYR* 1.3 57.4 + - - +
868B LEU* 4.1 4.4 - - - +
869B GLN* 2.9 32.7 + - - +
209C TYR* 4.7 11.2 - - - +
214C THR 5.1 2.1 + - - +
215C ARG 5.7 2.0 - - - +
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Residues in contact with TYR 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TYR* 4.0 11.7 - - - -
283B PRO* 3.7 23.4 - - + +
287B SER* 4.3 13.7 - - - -
327B ASP 5.1 0.7 + - - -
328B PHE* 3.5 47.2 - + - -
331B GLY* 4.1 21.8 - - - -
332B LEU* 3.8 17.7 - - + -
335B LEU* 3.7 20.8 - - + +
862B LEU 2.9 17.2 + - - +
863B ILE* 3.2 6.9 + - + +
865B ARG* 1.3 76.2 - - - +
867B VAL* 1.3 59.3 + - - +
869B GLN* 3.9 2.6 - - + -
870B ALA* 2.9 36.9 + - + +
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Residues in contact with VAL 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TYR* 4.0 29.1 - - + -
287B SER* 4.4 9.4 - - - +
288B LEU* 4.3 19.3 - - + -
863B ILE* 3.0 25.5 + - + +
864B LYS* 3.9 4.5 - - - +
866B TYR* 1.3 77.9 - - - +
868B LEU* 1.3 57.3 + - + +
870B ALA* 3.4 5.0 + - - +
871B GLN* 3.0 50.8 + - - +
88C PHE* 5.0 1.1 - - + -
132C MET* 3.8 26.9 - - + -
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Residues in contact with LEU 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864B LYS* 3.0 27.4 + - + +
865B ARG* 4.1 4.3 - - - +
867B VAL* 1.3 76.9 - - + +
869B GLN* 1.3 56.8 + - - +
871B GLN* 3.4 17.3 + - - +
872B ILE* 3.0 37.9 + - + +
132C MET* 3.8 27.8 - - + -
134C GLN* 4.5 8.1 - - - +
209C TYR* 3.8 37.0 - - + +
215C ARG* 4.1 18.8 - - + +
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Residues in contact with GLN 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B LEU* 4.2 23.0 - - + +
865B ARG 2.9 19.8 + - - +
866B TYR* 4.1 3.1 - - + +
868B LEU* 1.3 76.3 - - - +
870B ALA* 1.3 57.4 + - - +
872B ILE* 3.3 21.8 + - - +
873B ASP* 2.9 59.6 + - - +
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Residues in contact with ALA 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TYR* 3.3 35.7 - - + +
866B TYR* 2.9 29.2 + - + +
867B VAL 3.7 1.6 - - - +
869B GLN* 1.3 75.0 - - - +
871B GLN* 1.3 60.1 + - - +
873B ASP* 3.4 7.5 + - - +
874B LYS* 2.9 30.1 + - - +
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Residues in contact with GLN 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TYR* 3.8 27.1 - - + +
233B GLU* 5.0 1.6 - - - +
867B VAL* 3.0 38.8 + - - +
868B LEU* 3.8 18.1 - - - +
870B ALA* 1.3 73.0 - - - +
872B ILE* 1.3 59.9 + - + +
874B LYS* 3.3 14.1 + - - +
875B GLU* 3.0 36.3 + - - +
131C TYR* 4.1 16.0 + - - -
132C MET* 5.2 3.0 - - - +
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Residues in contact with ILE 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868B LEU* 3.0 26.4 + - + +
869B GLN* 3.6 23.3 - - - +
871B GLN* 1.3 76.4 - - - +
873B ASP* 1.3 69.5 + - - +
875B GLU* 3.2 19.8 + - - +
876B SER* 3.5 15.6 + - - +
167C LEU* 6.5 0.4 - - + -
171C LYS* 6.4 0.9 - - - +
215C ARG* 6.1 3.8 - - - +
216C PHE* 6.4 1.8 - - + -
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Residues in contact with ASP 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869B GLN* 2.9 43.8 + - - +
870B ALA* 3.9 7.2 - - - +
871B GLN 3.3 0.2 - - - -
872B ILE* 1.3 80.2 - - - +
874B LYS* 1.3 61.4 + - - +
876B SER* 3.4 18.4 + - - -
877B ASP* 4.0 10.9 - - - +
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Residues in contact with LYS 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B CYS 5.6 2.0 - - - +
230B GLN* 2.6 37.9 + - + +
231B GLU* 4.6 5.9 + - - +
232B TYR* 3.3 30.1 - - - +
870B ALA 2.9 15.6 + - - +
871B GLN* 3.7 14.7 - - - +
872B ILE 3.3 0.4 - - - -
873B ASP* 1.3 75.7 - - - +
875B GLU* 1.3 59.6 + - + +
876B SER 3.1 4.9 + - - -
877B ASP* 3.7 17.4 + - - +
881C GLU* 3.1 29.4 - - - +
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Residues in contact with GLU 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B GLN* 3.0 20.9 + - - +
872B ILE* 3.2 14.8 + - - +
874B LYS* 1.3 76.6 - - + +
876B SER* 1.3 57.3 + - - -
877B ASP 3.7 0.9 - - - -
171C LYS* 4.3 15.2 + - - -
880C ASN* 3.6 7.8 + - - -
881C GLU* 4.4 13.2 - - + +
882C GLY* 3.4 33.9 + - - +
885C LYS* 3.3 31.5 + - - +
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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