Contacts of the helix formed by residues 762 - 773 (chain A) in PDB entry 5XA0
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 762 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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759A LEU 5.3 2.5 - - - +
760A ASP 3.4 4.4 + - - +
761A VAL* 1.4 84.0 - - - +
763A LEU* 1.3 63.8 + - - +
764A ILE* 3.1 3.4 - - - +
765A LEU* 3.0 25.3 + - + +
766A ARG* 3.1 13.0 + - - +
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Residues in contact with LEU 763 (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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761A VAL 3.5 4.3 + - - +
762A ASP* 1.3 78.4 - - - +
764A ILE* 1.3 51.9 + - - +
766A ARG* 3.6 6.1 + - - +
767A CYS* 2.7 37.6 + - - +
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Residues in contact with ILE 764 (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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761A VAL* 5.6 4.5 - - + +
762A ASP* 3.1 3.9 - - - +
763A LEU* 1.3 77.2 - - - +
765A LEU* 1.3 59.4 + - - +
767A CYS* 2.7 25.1 + - - +
768A MET* 2.9 18.0 + - - +
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Residues in contact with LEU 765 (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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762A ASP* 3.0 19.0 + - + +
764A ILE* 1.3 78.9 - - - +
766A ARG* 1.3 61.2 + - - +
768A MET* 4.0 7.1 + - - +
769A SER 4.5 2.6 + - - -
782A CYS* 3.7 24.3 - - + +
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Residues in contact with ARG 766 (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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762A ASP 3.1 11.5 + - - +
763A LEU* 3.9 8.1 - - - +
765A LEU* 1.3 77.2 - - - +
767A CYS* 1.3 62.3 + - - +
768A MET 3.3 1.6 + - - -
769A SER* 3.8 4.4 + - - -
770A ASP* 3.3 23.8 + - - +
782A CYS* 5.6 1.3 - - - -
978A LEU* 6.3 3.4 - - + -
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Residues in contact with CYS 767 (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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763A LEU 2.7 21.0 + - - +
764A ILE* 2.7 17.2 + - - +
766A ARG* 1.3 73.2 - - - +
768A MET* 1.3 50.5 + - - +
770A ASP* 4.6 5.4 - - - -
771A GLU* 2.6 41.7 + - + +
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Residues in contact with MET 768 (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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764A ILE 2.9 12.9 + - - +
765A LEU* 4.5 4.9 - - - +
766A ARG 3.3 0.6 + - - -
767A CYS* 1.3 73.3 - - - +
769A SER* 1.3 69.7 + - - +
771A GLU* 4.7 1.3 - - - -
772A ASN* 2.8 28.4 + - + +
773A LEU 3.2 2.9 + - - -
778A ARG* 5.3 2.9 - - - +
782A CYS* 6.4 0.2 - - + -
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Residues in contact with SER 769 (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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765A LEU 4.5 2.0 + - - -
766A ARG* 3.8 6.9 + - - -
768A MET* 1.3 74.1 - - - +
770A ASP* 1.3 56.0 + - - +
773A LEU* 2.3 45.4 + - - +
778A ARG 4.3 5.2 + - - -
779A ALA* 3.0 48.9 - - - +
782A CYS* 4.6 10.0 - - - +
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Residues in contact with ASP 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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766A ARG 3.3 15.4 + - - +
767A CYS* 4.3 4.9 - - - +
768A MET 3.3 0.4 - - - -
769A SER* 1.3 84.7 - - - +
771A GLU* 1.3 66.9 + - + +
773A LEU* 3.4 7.7 + - - +
975A ILE* 6.2 2.5 - - - +
978A LEU* 4.9 17.7 - - + -
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Residues in contact with GLU 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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767A CYS* 2.6 27.1 + - + +
768A MET* 4.1 0.9 - - - +
770A ASP* 1.3 79.3 - - + +
772A ASN* 1.3 59.5 + - + +
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Residues in contact with ASN 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* 2.8 14.6 + - - +
771A GLU* 1.3 74.8 - - + +
773A LEU* 1.3 69.9 + - - +
774A PRO* 2.7 14.7 - - - +
778A ARG* 4.3 5.6 - - + +
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Residues in contact with LEU 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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768A MET 3.2 0.8 + - - -
769A SER* 2.3 44.2 + - - +
770A ASP* 3.4 7.8 + - - +
772A ASN* 1.3 71.1 - - - +
774A PRO* 1.3 66.2 - - - +
775A TYR* 2.5 24.8 + - - +
776A ASP* 5.9 0.4 - - - -
778A ARG* 3.3 19.1 - - - +
779A ALA* 4.3 10.8 - - + -
971A LYS* 6.5 1.1 - - + -
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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