Contacts of the helix formed by residues 769 - 779 (chain A) in PDB entry 1WUG
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 ASP 769 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748A PHE* 3.2 15.7 - - + +
749A MET 3.7 0.7 - - - +
751A PRO* 3.0 40.8 - - + +
760A TYR* 5.7 3.4 - - - +
767A PRO 5.4 0.6 - - - +
768A MET* 1.3 78.9 - - - +
770A LEU* 1.3 62.7 + - - +
771A LYS* 3.0 26.3 + - - +
772A THR* 3.1 27.3 + - - +
773A MET* 3.7 11.1 + - - +
795A VAL* 3.8 13.7 - - + -
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Residues in contact with LEU 770 (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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736A LEU* 3.0 43.4 - - + +
739A VAL* 4.0 26.0 - - + -
740A LYS* 4.4 5.6 - - + -
745A ALA* 4.1 7.9 - - + -
748A PHE* 3.2 28.1 + - + +
749A MET* 3.6 34.9 - - + +
769A ASP* 1.3 73.2 - - - +
771A LYS* 1.3 61.4 + - - +
772A THR 3.0 7.1 + - - -
773A MET* 3.5 15.0 + - + +
774A SER* 4.0 10.2 + - - -
775A GLU* 5.3 0.2 - - - +
792A LEU* 5.0 7.4 - - + -
795A VAL* 5.2 5.2 - - + -
816A LEU* 4.9 1.1 - - + -
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Residues in contact with LYS 771 (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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749A MET 3.3 14.5 + - - +
750A GLU* 5.2 0.4 - - - -
751A PRO* 3.3 32.4 - - + +
769A ASP* 3.0 20.0 + - - +
770A LEU* 1.3 79.6 - - - +
772A THR* 1.3 67.5 + - + +
775A GLU* 3.1 26.6 - - + +
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Residues in contact with THR 772 (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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768A MET* 3.8 24.5 - - + +
769A ASP* 3.1 23.5 + - - +
771A LYS* 1.3 93.3 - - + +
773A MET* 1.3 70.8 + - - +
775A GLU* 3.9 3.4 - - - -
776A ARG* 2.8 55.6 + - - +
782A TYR* 4.7 1.3 - - - -
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Residues in contact with MET 773 (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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736A LEU* 3.3 20.4 - - + -
768A MET* 5.4 2.9 - - + -
769A ASP 3.7 13.0 + - - +
770A LEU* 3.5 10.1 + - + +
772A THR* 1.3 85.8 + - - +
774A SER* 1.3 68.0 + - - +
776A ARG* 2.9 2.6 + - - +
777A LEU* 2.8 21.1 + - - +
782A TYR* 3.7 14.8 - - + -
788A PHE* 3.1 55.0 - - + +
791A ASP* 3.5 18.4 - - + -
792A LEU* 3.3 40.8 - - + +
795A VAL* 5.6 1.1 - - + -
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Residues in contact with SER 774 (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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736A LEU* 3.8 25.4 - - - +
740A LYS* 4.6 13.1 + - - -
770A LEU 4.0 6.8 + - - -
773A MET* 1.3 79.6 - - - +
775A GLU* 1.3 69.7 + - - +
777A LEU* 2.9 10.8 + - - +
778A LYS* 2.7 29.2 + - - +
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Residues in contact with GLU 775 (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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770A LEU 5.3 0.2 - - - +
771A LYS* 3.1 28.1 - - + +
772A THR* 3.4 9.8 + - - +
773A MET 3.2 0.2 - - - -
774A SER* 1.3 81.5 + - - +
776A ARG* 1.3 69.5 + - - +
778A LYS* 3.2 23.9 - - - +
779A ASN* 3.9 4.9 + - - +
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Residues in contact with ARG 776 (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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772A THR* 2.8 55.4 + - - +
775A GLU* 1.3 77.6 - - - +
777A LEU* 1.3 63.7 + - - +
779A ASN* 3.1 8.7 + - - +
781A TYR* 2.8 59.3 + - + +
782A TYR* 3.1 35.9 - - + +
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Residues in contact with LEU 777 (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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729A TYR* 3.1 39.3 - - + +
732A LEU* 3.4 29.6 - - + -
733A LYS* 3.3 39.5 - - + +
736A LEU* 5.4 2.7 - - + -
773A MET 2.8 10.4 + - - +
774A SER* 3.3 13.7 - - - +
776A ARG* 1.3 73.7 - - - +
778A LYS* 1.3 68.1 + - - +
780A ARG* 2.7 14.7 + - - +
781A TYR 4.3 3.1 - - - +
782A TYR* 4.1 15.8 - - + +
788A PHE* 3.5 23.8 - - + -
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Residues in contact with LYS 778 (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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729A TYR* 3.5 17.2 + - - -
774A SER* 2.7 19.3 + - - +
775A GLU* 3.2 23.1 - - - +
777A LEU* 1.3 74.3 - - - +
779A ASN* 1.3 69.3 + - - +
780A ARG 3.5 1.0 + - - -
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Residues in contact with ASN 779 (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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775A GLU 4.8 3.9 + - - +
776A ARG* 3.1 6.9 + - - +
777A LEU 3.0 0.6 - - - -
778A LYS* 1.3 93.0 + - - +
780A ARG* 1.3 68.5 + - - +
781A TYR* 2.5 30.7 + - + +
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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
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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