Contacts of the helix formed by residues 758 - 772 (chain A) in PDB entry 4RG7
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 GLN 758 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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753A TYR* 3.3 16.4 + - + +
754A LYS* 5.1 0.4 - - - -
756A LEU* 3.5 6.7 + - + -
757A GLY* 1.3 70.8 - - - +
759A THR* 1.3 63.5 + - - +
760A HIS 3.4 2.2 - - - +
761A LEU* 4.1 17.7 - - + -
762A ALA* 3.2 22.5 + - - +
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Residues in contact with THR 759 (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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754A LYS* 5.6 3.1 - - - +
757A GLY 2.6 13.7 + - - -
758A GLN* 1.3 69.8 - - - +
760A HIS* 1.3 64.4 + - - +
762A ALA* 3.8 4.9 - - - +
763A LEU* 3.3 24.9 + - - +
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Residues in contact with HIS 760 (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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758A GLN* 3.4 0.4 - - - +
759A THR* 1.3 78.8 - - - +
761A LEU* 1.3 60.9 + - + +
763A LEU* 4.1 4.7 + - - +
764A MET* 3.5 20.3 + - - +
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Residues in contact with LEU 761 (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 ILE 5.5 0.2 - - - +
753A TYR* 4.3 5.9 - - + +
758A GLN* 3.6 20.6 + - + +
759A THR 3.3 0.2 - - - -
760A HIS* 1.3 78.0 - - + +
762A ALA* 1.3 65.6 + - - +
764A MET* 3.4 17.7 - - - +
765A ASN* 3.4 11.3 + - - +
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Residues in contact with ALA 762 (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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750A GLY* 3.3 30.1 - - - +
753A TYR* 3.6 11.8 - - + +
754A LYS* 3.7 13.2 - - + +
758A GLN 3.2 17.5 + - - +
759A THR* 3.8 5.6 - - - +
761A LEU* 1.3 74.0 - - - +
763A LEU* 1.3 67.9 + - - +
764A MET 3.0 1.8 + - - -
765A ASN* 3.2 11.8 + - - -
766A PHE* 3.2 14.0 + - - +
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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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759A THR 3.3 14.2 + - - +
760A HIS* 4.2 5.2 - - - +
762A ALA* 1.3 78.7 - - - +
764A MET* 1.3 64.7 + - - +
766A PHE* 3.5 6.1 + - - +
767A SER* 3.3 21.0 + - - -
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Residues in contact with MET 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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760A HIS 3.5 14.4 + - - +
761A LEU* 3.4 15.5 - - - +
762A ALA 3.0 0.2 - - - -
763A LEU* 1.3 77.1 - - - +
765A ASN* 1.3 61.9 + - + +
767A SER* 3.0 21.6 + - - -
768A TRP* 3.5 8.9 + - - +
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Residues in contact with ASN 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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746A TYR* 3.6 23.1 - - + +
749A ILE* 4.3 10.5 - - + -
750A GLY 4.3 7.6 - - - +
761A LEU 3.4 10.2 + - - +
762A ALA 3.2 4.6 + - - +
764A MET* 1.3 79.3 - - - +
766A PHE* 1.3 57.3 + - - +
768A TRP* 3.6 7.9 - - - +
769A ALA* 2.8 28.8 + - - +
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Residues in contact with PHE 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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746A TYR 4.8 1.8 - - - -
747A PHE* 5.4 2.9 - - - +
750A GLY* 4.8 7.8 - - - -
762A ALA 3.2 15.7 + - - +
763A LEU* 3.8 7.9 - - - +
764A MET 3.2 0.4 - - - -
765A ASN* 1.3 78.9 - - - +
767A SER* 1.3 52.5 + - - +
769A ALA* 3.2 8.1 + - - +
770A MET* 2.8 39.8 + - + +
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Residues in contact with SER 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 3.3 10.1 + - - -
764A MET* 3.0 17.7 + - - -
766A PHE* 1.3 74.5 - - - +
768A TRP* 1.3 57.6 + - - +
770A MET* 3.6 9.7 + - - +
771A ASP* 3.0 27.4 + - - +
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Residues in contact with TRP 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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746A TYR* 5.0 4.3 - - + -
764A MET 3.5 8.6 + - - +
765A ASN* 3.6 12.1 - - - +
766A PHE 3.3 0.2 - - - -
767A SER* 1.3 74.7 + - - +
769A ALA* 1.3 69.1 - - - +
771A ASP* 2.8 19.2 + - - +
772A LEU* 2.9 15.3 + - - +
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Residues in contact with ALA 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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743A SER* 3.2 35.3 + - - +
746A TYR* 3.4 23.9 - - + +
747A PHE* 3.5 22.4 - - + +
765A ASN 2.8 19.6 + - - +
766A PHE* 3.3 7.6 - - - +
768A TRP* 1.3 76.7 - - - +
770A MET* 1.3 59.6 + - + +
772A LEU* 3.4 3.3 + - - +
773A ASP* 3.3 5.2 + - - +
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Residues in contact with MET 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 PHE* 2.8 22.4 + - + +
767A SER* 3.6 10.8 - - - +
768A TRP 3.0 0.2 - - - -
769A ALA* 1.3 72.6 - - + +
771A ASP* 1.3 64.1 + - - +
772A LEU 3.2 1.6 - - - -
773A ASP* 3.1 26.3 + - - +
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Residues in contact with ASP 771 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767A SER 3.0 17.4 + - - +
768A TRP* 2.8 12.0 + - - +
770A MET* 1.3 73.1 - - - +
772A LEU* 1.3 58.8 + - - +
773A ASP 3.1 4.2 + - - +
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Residues in contact with LEU 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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741A LYS 4.2 17.4 - - - +
742A GLU 5.5 0.2 - - - -
743A SER* 3.4 12.2 + - - +
746A TYR* 6.5 0.2 - - + -
768A TRP 2.9 14.0 + - - +
769A ALA* 3.9 7.6 - - - +
770A MET 3.2 0.4 - - - -
771A ASP* 1.3 76.7 - - - +
773A ASP* 1.3 59.2 + - - +
774A PRO* 3.9 2.9 - - - +
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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