Contacts of the helix formed by residues 866 - 877 (chain A) in PDB entry 5LUQ
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 ILE 866 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797A ASP* 2.6 38.5 - - - +
800A LEU* 5.3 0.2 - - + -
859A LEU* 4.3 34.3 - - + +
862A LEU* 4.5 9.2 - - + -
863A GLY* 3.1 48.9 - - - +
864A GLY 3.8 0.4 + - - -
865A GLN* 1.3 71.3 - - - +
867A ASN* 1.3 62.1 + - - +
870A LEU* 3.3 22.4 - - + +
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Residues in contact with ASN 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A GLY 4.6 6.7 + - - -
864A GLY 4.1 12.4 + - - +
865A GLN* 3.2 11.2 - - - -
866A ILE* 1.3 81.1 - - + +
868A LYS* 1.3 78.1 + - - +
869A ASN 2.6 16.3 + - - -
870A LEU* 3.0 20.3 + - - +
871A LEU* 3.0 15.7 + - + +
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Residues in contact with LYS 868 (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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789A TYR* 5.5 1.8 - - - -
790A LYS* 3.0 46.0 - - + +
794A PRO* 5.3 0.7 - - - +
864A GLY 5.5 1.8 + - - -
865A GLN* 4.5 15.2 - - + +
867A ASN* 1.3 89.8 + - - +
869A ASN* 1.3 75.7 + - - +
871A LEU* 3.7 23.8 - - + +
872A THR* 3.5 17.7 + - - -
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Residues in contact with ASN 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789A TYR 4.8 1.4 + - - -
790A LYS* 4.1 7.1 + - - +
793A LEU* 3.0 40.5 - - - +
794A PRO* 3.4 28.1 - - + +
797A ASP* 3.2 16.8 - - + +
865A GLN* 2.7 25.3 + - - +
867A ASN 2.6 5.3 + - - -
868A LYS* 1.3 85.7 + - - +
870A LEU* 1.3 60.2 + - - +
871A LEU 2.9 9.4 + - - -
872A THR* 3.2 6.2 + - - -
873A VAL* 3.0 26.4 + - - +
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Residues in contact with LEU 870 (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 ASP* 3.8 19.0 - - + +
801A LYS* 5.6 5.8 - - + -
805A LEU* 5.4 12.8 - - + -
866A ILE* 3.3 27.4 - - + +
867A ASN* 3.0 12.2 + - - +
869A ASN* 1.3 75.8 - - - +
871A LEU* 1.3 52.5 + - + +
873A VAL* 3.4 15.5 - - + -
874A THR* 2.7 47.4 + - + +
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Residues in contact with LEU 871 (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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867A ASN* 3.0 12.7 + - + +
868A LYS* 3.7 28.5 - - + +
869A ASN 2.9 0.2 + - - -
870A LEU* 1.3 73.7 - - + +
872A THR* 1.3 66.9 + - - +
873A VAL 2.9 4.4 + - - -
874A THR* 2.9 23.0 + - - +
875A SER* 3.0 12.3 + - - -
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Residues in contact with THR 872 (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 PRO* 5.7 5.8 - - - -
868A LYS 3.5 12.6 + - - -
869A ASN* 3.2 5.6 + - - -
871A LEU* 1.3 75.2 - - - +
873A VAL* 1.3 56.8 + - - +
875A SER* 4.5 7.0 - - - -
876A SER* 2.9 46.5 + - - +
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Residues in contact with VAL 873 (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 PRO* 3.1 30.7 - - + +
798A GLY* 3.3 17.9 - - - +
801A LYS* 3.2 39.3 - - + +
869A ASN 3.0 23.9 + - - +
870A LEU* 3.4 11.0 - - + +
871A LEU 2.9 0.8 + - - -
872A THR* 1.3 74.1 - - - +
874A THR* 1.3 62.0 + - - +
876A SER* 3.9 1.8 - - - -
877A ASP* 2.9 33.3 + - - +
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Residues in contact with THR 874 (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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801A LYS* 4.7 9.9 - - + +
805A LEU* 5.0 13.0 - - + -
870A LEU* 2.7 32.9 + - + +
871A LEU* 2.9 12.7 + - - +
873A VAL* 1.3 79.5 - - + +
875A SER* 1.3 56.6 + - - +
877A ASP* 3.5 6.2 + - - +
878A GLU* 3.0 28.6 + - - +
879A MSE 4.5 20.6 - - + +
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Residues in contact with SER 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A LEU* 3.0 18.5 + - - -
872A THR* 4.3 6.5 - - - -
874A THR* 1.3 76.0 + - - +
876A SER* 1.3 61.0 + - - +
878A GLU* 2.8 25.8 + - - +
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Residues in contact with SER 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A THR* 2.9 33.9 + - - +
873A VAL* 3.9 1.8 - - - -
875A SER* 1.3 74.9 - - - +
877A ASP* 1.3 59.8 + - - +
878A GLU* 2.9 25.1 - - - +
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Residues in contact with ASP 877 (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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757A LYS* 4.9 3.5 + - - -
801A LYS* 2.3 35.6 + - - +
873A VAL* 2.9 16.1 + - - +
874A THR* 3.9 4.7 - - - +
876A SER* 1.3 73.3 - - - +
878A GLU* 1.3 65.4 + - - +
879A MSE 2.4 34.0 + - - +
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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
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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