Contacts of the helix formed by residues 780 - 790 (chain A) in PDB entry 3W3K
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 780 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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750A THR* 4.2 11.0 - - - +
751A ILE 5.7 0.7 - - - +
774A PHE* 4.3 17.5 - - + -
775A GLU 3.5 22.9 - - - +
776A CYS* 4.4 13.5 - - + +
777A THR 3.2 13.4 + - - +
778A CYS 3.1 1.0 - - - -
779A ASP* 1.3 79.0 + - - +
781A GLY* 1.3 69.1 + - - +
782A ASP 3.2 1.6 - - - -
783A PHE* 3.1 24.5 + - + +
784A ARG* 3.2 19.7 + - + +
814A ILE* 3.7 44.2 - - + +
817A LEU* 5.7 4.9 - - + -
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Residues in contact with GLY 781 (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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778A CYS 2.9 14.4 + - - -
780A ILE* 1.3 84.1 - - - +
782A ASP* 1.3 61.7 + - - +
784A ARG* 3.1 10.9 + - - +
785A ARG* 3.1 39.0 + - - +
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Residues in contact with ASP 782 (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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751A ILE 5.1 2.0 - - - +
752A ASN* 5.3 0.7 - - - -
753A LYS* 4.2 30.6 - - - +
756A LEU* 4.2 12.3 - - + +
778A CYS 4.5 0.8 + - - -
779A ASP* 4.1 11.9 + - - +
781A GLY* 1.3 78.0 - - - +
783A PHE* 1.3 59.8 + - - +
785A ARG* 3.3 30.7 + - - +
786A TRP* 3.3 18.2 + - - +
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Residues in contact with PHE 783 (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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732A LEU* 4.7 2.0 - - + -
751A ILE* 3.6 50.7 + - + +
756A LEU* 4.3 7.2 - - + -
767A LEU* 4.5 8.5 - - + -
769A LEU* 3.2 31.9 - - + -
774A PHE* 5.4 3.1 - + - -
780A ILE* 3.1 18.0 + - + +
782A ASP* 1.3 76.6 - - - +
784A ARG* 1.3 60.5 + - - +
786A TRP* 3.3 30.8 + + + -
787A MET* 3.1 59.1 + - + +
795A ILE* 4.9 1.1 - - + -
814A ILE* 4.0 15.5 - - + -
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Residues in contact with ARG 784 (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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780A ILE* 3.2 21.9 + - + +
781A GLY* 3.1 13.8 + - - +
783A PHE* 1.3 79.7 - - + +
785A ARG* 1.3 57.4 + - + +
787A MET* 3.3 25.0 - - - +
788A ASP* 3.1 43.0 + - - +
814A ILE* 2.7 44.1 + - + +
815A VAL* 3.6 28.5 + - - +
817A LEU* 3.3 28.3 + - - +
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Residues in contact with ARG 785 (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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778A CYS 5.8 0.8 + - - -
781A GLY* 3.1 19.2 + - - +
782A ASP* 3.3 47.2 + - - +
783A PHE 3.2 0.2 - - - -
784A ARG* 1.3 75.6 - - + +
786A TRP* 1.3 59.7 + - - +
788A ASP* 3.2 11.1 + - - +
789A GLU* 2.8 43.2 + - - +
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Residues in contact with TRP 786 (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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32A ARG* 5.3 0.7 - - - -
732A LEU* 4.3 18.3 - - + +
733A SER* 5.1 5.5 + - - -
756A LEU* 3.5 45.5 + - + +
762A THR* 3.5 27.8 - - - -
764A LEU* 4.9 2.5 - - + -
767A LEU* 4.3 16.2 - - + -
782A ASP 3.3 9.6 + - - +
783A PHE* 3.3 24.4 + + + +
785A ARG* 1.3 77.4 - - - +
787A MET* 1.3 69.3 + - + +
789A GLU* 3.3 8.9 + - - -
790A HIS* 3.0 54.3 + + + -
793A VAL* 3.8 40.2 - - + -
795A ILE* 5.1 3.8 - - + -
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Residues in contact with MET 787 (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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32A ARG* 3.4 32.5 + - - +
769A LEU* 4.8 1.1 - - + -
783A PHE* 3.1 48.2 + - + +
784A ARG* 3.3 30.5 - - - +
785A ARG 3.1 0.2 - - - -
786A TRP* 1.3 81.0 - - + +
788A ASP* 1.3 64.4 + - - +
790A HIS 2.8 24.8 - - - +
791A LEU* 3.8 1.2 + - - +
795A ILE* 3.9 31.6 - - + -
798A LEU* 4.4 12.6 - - + -
801A VAL* 5.7 0.4 - - + -
814A ILE* 4.1 12.3 - - + -
815A VAL* 5.1 9.9 - - + -
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Residues in contact with ASP 788 (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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31A SER* 4.9 13.9 + - - +
32A ARG* 5.6 2.8 + - - -
784A ARG* 3.1 28.0 + - - +
785A ARG* 3.2 11.4 + - - +
787A MET* 1.3 78.6 - - - +
789A GLU* 1.3 63.4 + - - +
791A LEU* 3.9 22.4 - - - +
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Residues in contact with GLU 789 (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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785A ARG* 2.8 30.7 + - - +
786A TRP* 3.4 10.2 - - - +
787A MET 3.1 0.2 - - - -
788A ASP* 1.3 80.9 - - - +
790A HIS* 1.3 84.0 + - + +
791A LEU* 3.8 2.4 + - - +
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Residues in contact with HIS 790 (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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32A ARG* 2.7 30.5 + - - -
761A THR* 4.8 14.9 - - - -
762A THR* 5.0 12.9 + - - -
786A TRP* 3.0 59.4 + + + +
787A MET* 2.8 6.0 - - - +
789A GLU* 1.3 97.9 - - + +
791A LEU* 1.3 54.4 + - - +
792A ASN* 4.0 14.6 - - - +
793A VAL* 3.7 26.1 + - + +
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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