Contacts of the helix formed by residues 698 - 717 (chain 3) in PDB entry 5U8T
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 THR 698 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5413 SER* 5.5 10.7 + - - -
6833 TYR* 3.3 18.7 - - - -
6873 ARG* 4.5 2.5 - - - +
6963 PRO* 5.1 8.1 - - + -
6973 ILE* 1.3 82.8 - - - +
6993 ALA* 1.3 61.9 + - - +
7003 ARG* 3.1 21.3 + - - +
7013 THR* 2.7 38.6 + - + +
4627 PRO* 4.1 27.4 - - + -
6027 ASP* 5.7 2.0 - - - -
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Residues in contact with ALA 699 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6833 TYR* 3.5 13.8 + - - +
6873 ARG* 5.3 0.2 - - - +
6983 THR* 1.3 73.6 - - - +
7003 ARG* 1.3 57.9 + - - +
7023 LEU* 3.0 11.3 + - - +
7033 GLU* 2.9 35.4 + - + +
6027 ASP* 5.6 2.0 + - - -
6127 LEU* 5.4 7.4 - - + -
6167 VAL* 5.0 15.9 - - + -
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Residues in contact with ARG 700 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4003 ARG* 3.7 28.0 - - - +
4913 GLU* 2.4 50.7 + - - +
5413 SER* 3.2 39.7 - - - +
5423 ARG* 4.0 16.7 - - - +
5443 ASP* 5.8 0.2 - - - +
6983 THR* 3.1 11.8 + - - +
6993 ALA* 1.3 78.7 - - - +
7013 THR* 1.3 57.3 + - + +
7033 GLU* 2.8 45.8 + - + +
7043 THR* 2.9 17.0 + - + +
7073 ARG* 5.4 1.5 - - - +
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Residues in contact with THR 701 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5413 SER* 5.4 6.7 - - - +
5433 PHE 5.7 3.8 - - - +
5443 ASP 6.1 1.1 - - - +
6833 TYR* 4.2 6.1 - - - -
6863 LEU* 5.6 2.5 - - - +
6963 PRO* 5.1 9.9 - - + +
6973 ILE* 4.4 14.3 - - - +
6983 THR* 2.7 43.6 + - + +
7003 ARG* 1.3 77.7 - - + +
7023 LEU* 1.3 55.5 + - - +
7043 THR* 2.1 36.3 + - - -
7053 LEU* 3.7 4.7 + - - +
7333 LEU* 4.3 16.4 - - - +
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Residues in contact with LEU 702 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6793 ILE* 4.7 6.7 - - + +
6803 VAL* 5.2 2.9 - - + -
6833 TYR* 3.4 53.8 - - + -
6863 LEU* 6.4 0.4 - - - -
6993 ALA* 3.0 11.7 + - - +
7013 THR* 1.3 78.2 + - - +
7033 GLU* 1.3 61.5 + - - +
7043 THR 2.9 1.6 - - - -
7053 LEU* 2.4 51.0 + - + +
7063 ILE* 3.4 9.0 + - + -
6137 ALA* 4.2 16.8 - - + +
6167 VAL* 3.5 33.4 - - + -
6177 THR* 5.4 7.9 - - + -
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Residues in contact with GLU 703 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6993 ALA* 2.9 21.2 + - - +
7003 ARG* 2.8 41.0 + - - +
7023 LEU* 1.3 71.5 - - - +
7043 THR* 1.3 61.1 + - - +
7063 ILE* 3.1 26.3 - - + +
7073 ARG* 3.1 40.0 + - - +
6167 VAL* 4.6 16.3 - - + +
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Residues in contact with THR 704 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5433 PHE 5.4 0.7 - - - +
5443 ASP* 3.2 43.6 + - - +
7003 ARG* 2.9 17.5 + - + +
7013 THR* 2.1 34.5 + - - +
7033 GLU* 1.3 75.8 - - - +
7053 LEU* 1.3 59.8 + - - +
7073 ARG* 3.0 10.8 + - - +
7083 LEU* 2.7 52.5 + - - +
7333 LEU* 4.5 9.9 - - - +
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Residues in contact with LEU 705 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6793 ILE* 3.6 51.7 - - + +
6823 ASN* 5.3 5.4 - - + +
6833 TYR* 4.5 7.4 - - + +
6863 LEU* 5.4 7.0 - - + -
7013 THR 4.2 4.0 - - - +
7023 LEU* 2.4 54.2 + - + +
7043 THR* 1.3 74.4 + - - +
7063 ILE* 1.3 61.9 + - + +
7083 LEU* 4.0 7.1 - - + +
7093 ALA* 3.0 28.8 + - - +
7293 ALA* 4.3 24.6 - - + +
7303 ALA* 5.1 2.9 - - - +
7333 LEU* 4.8 16.4 - - + -
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Residues in contact with ILE 706 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6713 LEU* 5.4 10.3 - - + -
6763 ILE* 6.5 0.4 - - + -
6793 ILE* 5.2 8.2 - - + +
7023 LEU* 4.3 12.6 - - + +
7033 GLU* 3.1 29.4 - - + +
7053 LEU* 1.3 77.3 - - + +
7073 ARG* 1.3 57.6 + - + +
7093 ALA* 3.7 3.1 - - - +
7103 THR* 2.1 44.1 + - - +
6167 VAL* 4.9 11.7 - - + +
6177 THR* 6.3 3.6 - - + -
6197 VAL 5.0 1.8 - - - +
6207 HIS* 3.2 46.4 - - + +
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Residues in contact with ARG 707 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3883 GLY* 4.3 6.1 - - - +
4003 ARG* 2.4 73.5 + - - +
4013 GLY* 3.2 30.3 - - - +
4023 ASP 3.5 11.2 + - - -
4033 ILE* 4.4 11.5 - - + +
5443 ASP* 3.3 24.9 + - - +
7003 ARG* 5.0 1.8 + - - +
7033 GLU* 3.1 24.9 + - - +
7043 THR* 3.0 26.5 + - - +
7063 ILE* 1.3 83.1 - - + +
7083 LEU* 1.3 55.0 - - + +
7103 THR* 3.3 7.6 + - - -
7113 ALA* 2.8 34.0 + - - +
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Residues in contact with LEU 708 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3833 LEU* 4.3 21.9 - - + +
4033 ILE* 5.1 9.9 - - + -
5443 ASP* 4.9 11.7 - - + -
5453 LEU* 5.0 14.8 - - + -
7043 THR* 2.7 50.7 + - + +
7053 LEU* 4.0 8.3 - - + +
7073 ARG* 1.3 72.6 - - + +
7093 ALA* 1.3 67.1 + - - +
7113 ALA* 3.1 8.4 + - - +
7123 HIS* 3.0 22.2 + - - +
7283 VAL* 6.0 0.5 - - - +
7293 ALA* 4.0 24.0 - - + +
7323 LEU* 4.2 26.5 - - + -
7333 LEU* 4.9 7.6 - - + +
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Residues in contact with ALA 709 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6753 ALA* 5.2 3.1 - - + -
6793 ILE* 5.9 2.7 - - + -
7053 LEU 3.0 19.8 + - - +
7063 ILE* 3.7 3.1 - - - +
7083 LEU* 1.3 78.2 - - - +
7103 THR* 1.3 57.3 + - - +
7123 HIS* 3.3 2.4 + - - -
7133 ALA* 2.8 28.7 + - - +
7213 VAL* 5.1 13.0 - - + -
7253 ASP* 3.8 18.6 - - + +
7263 ALA* 4.2 26.0 - - + +
7293 ALA* 4.2 2.5 - - + +
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Residues in contact with THR 710 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3883 GLY* 4.0 10.5 - - - +
3893 VAL* 3.4 32.7 - - + +
6693 PRO* 3.5 14.4 - - + +
6703 GLN 4.5 10.2 + - - +
7063 ILE* 2.1 39.6 + - + +
7073 ARG* 3.5 8.1 - - - -
7083 LEU 3.1 0.2 - - - -
7093 ALA* 1.3 73.7 - - - +
7113 ALA* 1.3 61.5 + - - +
7133 ALA* 3.1 8.3 - - - +
7143 LYS* 2.9 28.1 + - - +
7213 VAL* 4.6 5.9 - - + +
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Residues in contact with ALA 711 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3833 LEU* 3.3 44.4 - - + +
3863 MET* 3.8 8.5 - - + +
3883 GLY* 4.4 9.8 - - - -
4033 ILE* 5.0 0.7 - - + -
7073 ARG 2.8 13.9 + - - +
7083 LEU* 3.1 10.1 + - - +
7103 THR* 1.3 73.4 - - - +
7123 HIS* 1.3 67.7 + - - +
7143 LYS* 3.0 8.0 + - - +
7153 VAL* 3.0 23.1 + - - +
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Residues in contact with HIS 712 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3603 PHE* 3.4 46.3 - + + +
3833 LEU* 3.8 6.6 - - + +
7083 LEU 3.0 11.2 + - - +
7093 ALA 3.9 6.5 - - - +
7113 ALA* 1.3 77.3 - - - +
7133 ALA* 1.3 56.6 + - - +
7153 VAL* 2.9 10.2 + - + -
7163 ARG* 2.9 46.7 + - + -
7243 VAL* 6.0 0.2 - - + -
7253 ASP* 2.4 31.6 + - + +
7283 VAL* 3.4 38.0 - - + +
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Residues in contact with ALA 713 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6693 PRO* 3.6 26.5 - - + -
7093 ALA 2.8 14.5 + - - +
7103 THR* 3.1 16.2 - - - +
7113 ALA 3.0 0.4 - - - -
7123 HIS* 1.3 78.7 - - - +
7143 LYS* 1.3 59.5 + - - +
7163 ARG* 3.5 2.2 + - - +
7173 LEU 3.4 13.9 + - - -
7183 SER* 3.5 15.8 + - - +
7203 THR 4.8 1.8 - - - +
7213 VAL* 4.0 12.6 - - + -
7253 ASP* 4.0 17.0 - - - +
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Residues in contact with LYS 714 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3863 MET* 3.2 53.1 + - + +
3873 GLY* 4.4 0.6 - - - -
3883 GLY 4.9 0.2 - - - +
3893 VAL* 3.4 42.4 - - - +
6633 ALA* 3.3 19.3 - - - +
6643 LYS* 3.8 23.1 + - - +
6673 VAL 3.8 17.7 - - - +
6683 ILE* 4.8 3.5 - - - +
6693 PRO* 4.0 5.8 - - + -
7103 THR 2.9 13.1 + - - +
7113 ALA 3.4 8.7 - - - +
7133 ALA* 1.3 77.0 - - - +
7153 VAL* 1.3 61.9 + - - +
7173 LEU* 3.1 26.9 + - - +
7183 SER 5.6 0.4 - - - -
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Residues in contact with VAL 715 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3593 ILE* 4.0 9.2 - - + +
3603 PHE* 3.4 46.7 - - + +
3633 LEU* 4.0 21.1 - - + -
3823 LEU* 4.4 9.0 - - + -
3833 LEU* 4.5 3.1 - - + -
3863 MET* 3.7 19.5 - - + -
6593 TYR* 2.7 22.4 + - - -
7113 ALA 3.0 15.7 + - - +
7123 HIS* 2.9 19.1 + - + +
7143 LYS* 1.3 77.7 - - - +
7163 ARG* 1.3 58.0 + - - +
7173 LEU 3.1 0.2 - - - -
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Residues in contact with ARG 716 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3543 SER* 4.1 18.2 - - - +
3573 LYS* 5.4 19.7 - - + +
3593 ILE* 5.3 3.1 - - - -
7123 HIS* 2.9 29.3 + - + +
7133 ALA 4.0 2.9 - - - +
7143 LYS 3.3 0.4 - - - -
7153 VAL* 1.3 75.4 - - - +
7173 LEU* 1.3 67.0 - - - +
7183 SER* 3.0 22.1 + - - +
7223 ASN* 3.1 27.5 - - - +
7243 VAL* 3.4 34.3 - - - +
7253 ASP* 2.9 40.1 + - - +
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Residues in contact with LEU 717 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3503 ILE* 4.4 6.1 - - + -
3513 ASN* 3.8 22.0 - - - +
3543 SER* 4.0 20.4 - - - +
6593 TYR* 3.2 28.0 - - + +
6623 TYR* 3.9 20.4 - - + -
6633 ALA* 3.6 16.8 - - + -
6663 ARG 4.6 10.1 - - - +
6673 VAL* 5.5 7.8 + - - +
7133 ALA 3.4 2.6 + - - -
7143 LYS* 3.1 30.0 + - - +
7153 VAL 3.1 4.0 - - - -
7163 ARG* 1.3 80.2 - - - +
7183 SER* 1.3 64.7 + - - +
7193 LYS* 3.6 1.7 + - - -
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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
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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