Contacts of the helix formed by residues 854 - 875 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D GLU* 3.7 20.4 - - - +
351D GLU* 4.3 17.6 + - - +
853D ARG* 1.3 76.6 - - - +
855D TYR* 1.3 61.1 + - - +
857D LYS* 3.3 27.6 + - - +
858D ILE* 3.0 45.0 + - + +
861D ARG* 4.9 5.2 + - - +
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Residues in contact with TYR 855 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291D GLU 6.1 0.4 - - - -
292D ASP* 2.9 38.9 + - + -
344D ALA* 3.6 37.0 + - + -
348D GLY 3.9 15.3 - - - -
349D ASP* 3.3 45.8 - - + +
350D VAL 5.4 0.7 - - - +
351D GLU* 4.7 4.0 + - - +
365D ARG* 3.5 11.4 + - - -
853D ARG* 3.5 13.3 - - - +
854D GLN* 1.3 78.8 - - - +
856D GLN* 1.3 64.8 + - - +
858D ILE* 3.9 5.0 - - - +
859D MET* 2.9 50.4 + - + +
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Residues in contact with GLN 856 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D GLU* 3.5 35.4 + - - +
853D ARG* 3.1 61.2 + - + +
854D GLN 3.3 0.2 - - - -
855D TYR* 1.3 84.0 - - - +
857D LYS* 1.3 59.2 + - + +
859D MET* 3.6 5.3 + - - +
860D LYS* 2.9 31.8 + - - +
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Residues in contact with LYS 857 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ASP* 3.9 31.4 + - - +
853D ARG 3.4 16.2 + - - +
854D GLN* 3.3 30.6 + - - +
855D TYR 3.3 0.4 - - - -
856D GLN* 1.3 78.4 - - + +
858D ILE* 1.3 57.0 + - + +
860D LYS* 3.3 7.1 + - - +
861D ARG* 3.0 40.0 + - - +
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Residues in contact with ILE 858 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340D GLU* 3.6 43.5 - - + +
341D GLU* 4.0 15.7 - - + -
344D ALA* 3.7 26.2 - - + -
854D GLN* 3.0 36.5 + - + +
855D TYR* 4.0 4.3 - - - +
857D LYS* 1.3 74.5 - - - +
859D MET* 1.3 58.9 + - - +
861D ARG* 3.4 21.9 + - - +
862D LEU* 3.0 43.2 + - + +
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Residues in contact with MET 859 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D GLU 4.9 10.3 - - - +
292D ASP* 3.9 9.2 - - - +
293D PRO* 3.8 33.4 - - + -
294D VAL* 4.2 13.2 - - + -
332D LEU* 4.7 4.0 - - + -
344D ALA* 4.4 5.4 - - - +
345D ILE* 4.0 23.6 - - + -
855D TYR* 2.9 54.0 + - + +
856D GLN* 4.1 6.3 - - - +
858D ILE* 1.3 77.2 - - - +
860D LYS* 1.3 56.6 + - - +
862D LEU* 3.8 9.1 - - + +
863D ILE* 2.9 38.7 + - + +
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Residues in contact with LYS 860 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TYR* 5.3 11.0 - - - +
88A PHE* 3.7 20.8 - - + -
89A SER 3.2 26.9 + - - +
90A ASP* 4.2 16.8 + - - +
91A ARG 5.8 0.4 - - - -
92A SER* 5.4 5.3 - - - -
856D GLN 2.9 19.8 + - - +
857D LYS* 3.7 7.0 - - - +
858D ILE 3.3 0.2 - - - -
859D MET* 1.3 78.4 - - - +
861D ARG* 1.3 57.0 + - - +
863D ILE* 3.4 5.7 + - - -
864D LYS* 3.0 27.9 + - - +
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Residues in contact with ARG 861 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 5.5 0.2 + - - -
210A ASP* 5.6 4.3 - - - +
212A ASP* 3.0 49.8 + - - +
213A GLY* 5.4 7.3 - - - -
338D ASN* 4.0 5.9 - - - +
340D GLU* 3.9 19.6 + - - -
341D GLU* 3.6 17.5 + - - +
854D GLN* 4.9 4.4 + - - +
857D LYS* 3.0 24.6 + - - +
858D ILE* 3.4 28.1 + - - +
860D LYS* 1.3 76.0 - - - +
862D LEU* 1.3 63.7 + - + +
864D LYS* 3.4 6.8 + - - +
865D ARG* 3.0 58.2 + - + +
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Residues in contact with LEU 862 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D LEU* 3.9 15.9 - - + +
335D LEU* 4.3 15.0 - - + +
336D CYS* 4.2 14.4 - - - -
341D GLU* 3.6 15.0 - - + +
344D ALA* 5.2 0.2 - - + -
345D ILE* 3.8 31.4 - - + -
858D ILE* 3.0 39.1 + - + +
859D MET* 3.9 9.9 - - + +
861D ARG* 1.3 77.4 - - + +
863D ILE* 1.3 60.6 + - - +
865D ARG* 3.4 30.5 + - - +
866D TYR* 2.9 27.9 + - - +
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Residues in contact with ILE 863 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TYR* 6.0 3.1 - - + -
88A PHE* 3.8 28.3 - - + -
287D SER* 3.4 34.8 - - - +
290D SER 4.9 4.5 - - - +
291D GLU 4.6 6.7 - - - +
293D PRO* 3.8 37.2 - - + -
328D PHE* 6.1 0.4 - - + -
332D LEU* 5.1 4.9 - - + -
859D MET* 2.9 29.5 + - + +
860D LYS* 3.9 4.7 - - - +
862D LEU* 1.3 75.0 - - + +
864D LYS* 1.3 58.5 + - - +
866D TYR* 3.2 6.5 + - - +
867D VAL* 3.0 32.0 + - + +
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Residues in contact with LYS 864 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.7 24.0 - - + -
90A ASP* 4.8 3.4 - - + +
132A MET* 2.7 37.1 + - - +
133A GLY* 4.0 6.7 + - - -
134A GLN* 4.3 4.8 - - - +
209A TYR* 3.6 35.5 - - - +
210A ASP* 2.5 44.4 + - - +
860D LYS 3.0 17.8 + - - +
861D ARG* 3.8 6.1 - - - +
863D ILE* 1.3 78.0 - - - +
865D ARG* 1.3 61.8 + - - +
867D VAL* 3.4 4.3 + - - +
868D LEU* 3.0 32.1 + - + +
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Residues in contact with ARG 865 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A TYR* 4.7 11.2 - - - +
214A THR 5.1 2.1 + - - +
215A ARG 5.7 2.0 - - - +
335D LEU* 3.0 39.3 + - + -
337D ARG* 3.7 44.0 - - - +
341D GLU* 2.4 46.7 + - - -
861D ARG* 3.0 40.8 + - - +
862D LEU* 3.5 16.8 - - - +
863D ILE 3.4 0.2 - - - -
864D LYS* 1.3 76.3 - - - +
866D TYR* 1.3 57.7 + - - +
868D LEU* 4.0 4.5 - - - +
869D GLN* 2.9 33.3 + - - +
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Residues in contact with TYR 866 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D TYR* 4.0 12.7 + + - -
283D PRO* 3.7 23.3 - - + +
287D SER* 4.3 13.2 - - - -
327D ASP 5.1 0.9 + - - -
328D PHE* 3.5 46.8 - + - -
331D GLY* 4.1 20.9 - - - -
332D LEU* 3.8 18.4 - - + -
335D LEU* 3.7 20.6 - - + +
862D LEU 2.9 17.4 + - - +
863D ILE* 3.2 6.7 + - + +
865D ARG* 1.3 76.5 - - - +
867D VAL* 1.3 59.8 + - - +
869D GLN* 4.1 2.1 - - + +
870D ALA* 2.9 37.2 + - + +
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Residues in contact with VAL 867 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 5.1 1.3 - - + -
132A MET* 3.8 26.0 - - + -
232D TYR* 4.0 29.3 - - + -
287D SER* 4.4 9.6 - - - +
288D LEU* 4.3 19.1 - - + -
863D ILE* 3.0 26.3 + - + +
864D LYS* 3.9 4.5 - - - +
866D TYR* 1.3 76.6 - - - +
868D LEU* 1.3 58.3 + - + +
870D ALA* 3.4 4.8 + - - +
871D GLN* 3.0 50.6 + - - +
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Residues in contact with LEU 868 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A MET* 3.8 27.1 - - + -
134A GLN* 4.5 8.5 - - - +
209A TYR* 3.8 36.6 - - + +
215A ARG* 4.1 20.2 - - + +
864D LYS* 3.0 27.3 + - + +
865D ARG* 4.1 4.5 - - - +
867D VAL* 1.3 77.1 - - + +
869D GLN* 1.3 56.6 + - - +
871D GLN* 3.4 17.5 + - - +
872D ILE* 3.0 38.0 + - + +
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Residues in contact with GLN 869 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D LEU* 4.2 23.2 - - + +
865D ARG 2.9 19.3 + - - +
866D TYR* 4.1 3.1 - - + +
868D LEU* 1.3 76.7 - - - +
870D ALA* 1.3 57.2 + - - +
872D ILE* 3.6 22.7 - - - +
873D ASP* 2.9 60.4 + - - +
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Residues in contact with ALA 870 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D TYR* 3.3 35.0 - - + +
866D TYR* 2.9 29.2 + - + +
867D VAL 3.7 2.0 - - - +
869D GLN* 1.3 74.8 - - - +
871D GLN* 1.3 59.8 + - - +
873D ASP* 3.4 7.2 + - - +
874D LYS* 2.9 29.6 + - - +
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Residues in contact with GLN 871 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A TYR* 4.1 17.0 + - - -
132A MET* 5.2 2.1 - - - +
232D TYR* 3.8 27.4 - - + +
233D GLU* 5.0 2.0 - - - +
867D VAL* 3.0 40.0 + - - +
868D LEU* 3.8 17.8 - - - +
869D GLN 3.3 0.2 - - - -
870D ALA* 1.3 73.1 - - - +
872D ILE* 1.3 61.7 + - + +
874D LYS* 3.3 13.4 + - - +
875D GLU* 3.0 36.5 + - - +
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Residues in contact with ILE 872 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 6.5 0.4 - - + -
171A LYS* 6.4 1.3 - - - +
215A ARG* 6.1 4.0 - - - +
216A PHE* 6.4 2.2 - - + -
868D LEU* 3.0 26.4 + - + +
869D GLN* 3.6 22.7 - - - +
870D ALA 3.3 0.2 - - - -
871D GLN* 1.3 76.7 - - + +
873D ASP* 1.3 70.0 + - - +
875D GLU* 3.2 21.3 + - - +
876D SER* 3.5 15.6 + - - +
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Residues in contact with ASP 873 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869D GLN* 2.9 46.9 + - - +
870D ALA* 3.9 7.1 - - - +
871D GLN 3.3 0.2 - - - -
872D ILE* 1.3 79.2 - - - +
874D LYS* 1.3 61.6 + - - +
876D SER* 3.4 18.3 + - - -
877D ASP* 4.0 11.4 - - - +
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Residues in contact with LYS 874 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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881A GLU* 3.1 30.1 - - - +
229D CYS 5.6 1.3 - - - +
230D GLN* 2.6 38.5 + - + +
231D GLU* 4.6 5.3 + - - +
232D TYR* 3.3 28.8 - - - +
870D ALA 2.9 16.7 + - - +
871D GLN* 3.7 13.6 - - - +
872D ILE 3.3 0.2 - - - -
873D ASP* 1.3 75.3 - - - +
875D GLU* 1.3 59.5 + - + +
876D SER 3.1 6.2 + - - -
877D ASP* 3.7 16.3 + - - +
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Residues in contact with GLU 875 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LYS* 4.3 15.8 + - - -
880A ASN* 3.6 8.0 + - - -
881A GLU* 4.4 12.6 - - + +
882A GLY* 3.4 34.8 + - - +
885A LYS* 3.3 30.6 + - - +
871D GLN* 3.0 20.3 + - - +
872D ILE* 3.2 13.0 + - - +
874D LYS* 1.3 78.4 - - + +
876D SER* 1.3 56.3 + - - -
877D ASP 3.7 0.7 - - - -
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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