Contacts of the helix formed by residues 765 - 777 (chain C) in PDB entry 3HZJ
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 ALA 765 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711C CYS* 3.8 2.0 - - - -
763C TYR* 3.2 4.4 - - - +
764C ARG* 1.3 81.5 - - - +
766C GLU* 1.3 65.5 + - - +
767C GLU* 3.3 7.0 - - + +
768C ASN* 3.2 25.4 + - - +
769C ALA 3.1 18.5 + - - -
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Residues in contact with GLU 766 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C SER 5.4 0.2 - - - +
544C ARG* 5.4 5.7 + - - -
711C CYS* 4.0 23.3 - - + +
715C HIS* 2.8 33.7 + - - -
764C ARG 3.9 1.6 + - - -
765C ALA* 1.3 71.5 - - - +
767C GLU* 1.3 57.7 + - - +
769C ALA* 3.5 0.7 + - - +
770C ARG* 2.9 30.7 + - + +
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Residues in contact with GLU 767 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765C ALA* 3.3 4.8 - - + +
766C GLU* 1.3 80.3 - - - +
768C ASN* 1.3 63.5 + - - +
770C ARG* 3.9 5.6 - - - +
771C ARG* 3.0 28.6 + - - +
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Residues in contact with ASN 768 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762C ARG 3.3 28.0 - - - +
763C TYR* 3.7 11.2 - - + -
765C ALA* 3.2 26.4 + - - +
767C GLU* 1.3 80.9 + - - +
769C ALA* 1.3 61.0 + - - +
771C ARG* 3.4 6.3 + - - +
772C LEU* 2.9 30.0 + - - +
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Residues in contact with ALA 769 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711C CYS* 3.9 10.3 - - - -
712C MSE 3.7 36.3 - - + -
715C HIS* 4.2 9.0 - - + -
763C TYR* 4.1 8.6 - - - +
765C ALA 3.1 15.5 + - - +
766C GLU* 3.9 3.4 - - - +
768C ASN* 1.3 73.8 - - - +
770C ARG* 1.3 64.9 + - - +
772C LEU* 3.2 7.7 + - - +
773C MSE 3.0 28.9 + - - +
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Residues in contact with ARG 770 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C LYS 5.1 3.8 - - - +
537C SER* 5.2 7.4 - - - +
715C HIS* 4.2 17.5 + - + +
766C GLU* 2.9 26.7 + - + +
767C GLU* 3.9 6.1 - - - +
769C ALA* 1.3 73.6 - - - +
771C ARG* 1.3 63.9 + - - +
773C MSE 3.1 6.7 + - - +
774C GLU* 3.0 22.0 + - - +
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Residues in contact with ARG 771 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767C GLU 3.0 20.1 + - - +
768C ASN* 3.5 9.6 - - - +
770C ARG* 1.3 75.8 - - - +
772C LEU* 1.3 61.7 + - - +
774C GLU* 3.2 9.3 + - - +
775C GLN* 3.1 32.7 + - - +
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Residues in contact with LEU 772 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712C MSE 3.8 23.6 - - + -
731C VAL* 4.4 7.4 - - + +
734C ALA* 4.0 20.8 - - + +
735C LEU* 3.8 24.5 - - + +
738C THR* 5.1 0.4 - - - +
763C TYR* 3.8 32.1 - - + +
768C ASN 2.9 16.8 + - - +
769C ALA 3.2 2.9 + - - +
771C ARG* 1.3 75.5 - - - +
773C MSE 1.3 80.9 + - + +
775C GLN* 3.3 19.3 + - - +
776C ALA* 2.9 25.8 + - - +
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Residues in contact with MSE 773 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C LYS* 4.4 8.3 - - - +
712C MSE 3.4 32.5 - - + +
715C HIS* 3.5 30.3 - - + +
716C ILE* 4.0 18.2 - - + -
719C LEU* 3.8 23.8 - - + -
731C VAL* 4.1 18.8 - - + -
769C ALA 3.0 16.5 + - - +
770C ARG 3.1 7.6 + - - +
772C LEU* 1.3 98.3 - - + +
774C GLU* 1.3 59.8 + - - +
776C ALA* 3.3 3.4 + - - +
777C CYS* 3.0 34.9 + - - -
911C UNX 4.1 10.3 - - - -
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Residues in contact with GLU 774 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C LYS* 5.4 8.0 + - + -
770C ARG 3.0 11.8 + - - +
771C ARG* 3.2 12.3 + - - +
773C MSE 1.3 76.0 - - - +
775C GLN* 1.3 61.4 + - + +
777C CYS* 3.4 5.4 + - - +
778C ASN* 3.2 33.5 + - - +
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Residues in contact with GLN 775 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734C ALA* 4.2 10.5 + - + +
738C THR* 2.9 30.6 + - - +
763C TYR* 5.8 0.2 + - - -
771C ARG* 3.1 20.6 + - - +
772C LEU* 3.5 23.2 - - - +
774C GLU* 1.3 73.4 - - + +
776C ALA* 1.3 65.9 + - - +
778C ASN* 3.3 7.6 + - - +
779C ILE* 3.2 26.4 + - + +
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Residues in contact with ALA 776 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719C LEU* 6.0 0.4 - - + -
727C ILE* 6.1 0.4 - - + -
730C HIS* 3.0 58.6 + - + +
731C VAL* 3.8 19.1 - - + +
734C ALA* 3.8 4.2 - - + +
772C LEU 2.9 16.2 + - - +
773C MSE 3.3 9.6 + - - +
775C GLN* 1.3 76.5 - - - +
777C CYS* 1.3 59.0 + - - +
778C ASN 3.2 0.2 - - - -
779C ILE* 3.3 11.8 + - - +
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Residues in contact with CYS 777 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C SER* 5.6 6.7 - - - +
536C LYS* 4.8 15.7 - - + -
719C LEU* 4.0 34.5 - - - -
723C GLU* 4.9 9.9 - - - -
727C ILE* 5.5 3.8 - - - -
730C HIS* 4.6 6.5 - - - -
773C MSE 3.0 20.2 + - - +
774C GLU* 4.1 5.2 - - - +
775C GLN 3.3 0.2 - - - -
776C ALA* 1.3 76.6 - - - +
778C ASN* 1.3 64.3 + - - +
779C ILE 3.5 3.1 - - - +
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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