Contacts of the helix formed by residues 749 - 759 (chain A) in PDB entry 5LUQ
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 VAL 749 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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748A TYR* 1.3 72.6 - - - +
750A PRO* 1.3 69.5 - - + +
751A ALA 2.9 6.1 + - - -
752A LEU* 3.8 25.2 + - + -
753A GLN* 3.3 27.9 + - + +
792A ILE* 4.6 16.8 - - + +
795A CYS* 4.0 33.7 - - + -
796A LEU* 4.4 4.7 - - + -
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Residues in contact with PRO 750 (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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715A ALA* 5.5 11.7 - - + -
718A MSE 5.1 1.4 - - - +
719A LYS* 3.9 31.9 - - - +
748A TYR* 3.1 22.7 - - + -
749A VAL* 1.3 94.4 - - + +
751A ALA* 1.3 69.1 + - + +
753A GLN* 4.2 7.9 - - + +
754A MSE 3.8 16.3 + - - +
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Residues in contact with ALA 751 (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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715A ALA* 5.8 7.2 - - + -
718A MSE 4.0 13.2 - - - +
734A LEU 5.6 2.5 - - - +
738A HIS* 5.0 24.0 - - + +
745A VAL* 6.0 2.9 - - + -
748A TYR* 4.6 8.7 - - + +
749A VAL 2.9 1.8 + - - -
750A PRO* 1.3 82.2 - - + +
752A LEU* 1.3 67.6 + - + +
753A GLN 2.9 2.8 + - - -
754A MSE 3.0 7.4 + - - +
755A ALA* 2.9 19.7 + - - +
776A TRP* 6.2 2.0 - - + +
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Residues in contact with LEU 752 (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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748A TYR 4.6 4.7 - - - +
749A VAL* 3.9 24.7 - - + +
751A ALA* 1.3 79.5 - - - +
753A GLN* 1.3 63.6 + - + +
755A ALA* 3.4 11.9 - - - -
756A PHE* 2.8 51.8 + - + +
776A TRP* 3.2 44.0 - - + +
785A MSE 4.9 7.2 - - + -
792A ILE* 5.9 0.9 - - + -
796A LEU* 3.4 18.2 - - + -
799A TYR* 3.2 34.1 - - + +
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Residues in contact with GLN 753 (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 VAL* 3.3 25.5 + - + +
750A PRO* 4.4 6.1 - - + +
751A ALA 2.9 1.8 + - - -
752A LEU* 1.3 87.5 - - + +
754A MSE 1.3 52.1 + - - +
756A PHE* 4.7 0.2 - - - +
757A LYS* 2.5 49.5 + - + +
795A CYS* 4.3 28.7 + - + +
799A TYR* 4.4 12.8 - - + +
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Residues in contact with MSE 754 (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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718A MSE 3.5 37.2 - - + +
719A LYS* 5.4 17.0 - - + +
722A LYS 6.1 0.2 - - - +
724A GLU* 6.6 0.4 - - + -
727A ALA* 5.1 15.5 - - + -
731A THR* 5.1 5.1 - - + +
750A PRO 3.8 9.2 + - - +
751A ALA 3.0 4.1 + - - +
753A GLN* 1.3 75.8 - - - +
755A ALA* 1.3 70.8 + - - +
757A LYS* 4.2 4.0 - - - -
758A LEU* 3.0 32.1 + - + +
1020A PRO* 4.9 17.9 - - + -
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Residues in contact with ALA 755 (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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718A MSE 4.1 8.0 - - + +
731A THR* 5.2 10.8 - - - +
735A SER* 4.9 13.7 - - - -
751A ALA 2.9 9.1 + - - +
752A LEU* 3.1 22.2 + - - +
754A MSE 1.3 83.8 - - - +
756A PHE* 1.3 70.2 + - + +
758A LEU* 2.8 10.0 + - - +
759A GLY* 2.8 8.2 + - - -
773A LEU* 4.2 15.9 - - + -
776A TRP* 6.3 1.3 - - + -
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Residues in contact with PHE 756 (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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752A LEU* 2.8 47.7 + - + +
755A ALA* 1.3 77.7 - - + +
757A LYS* 1.3 56.2 + - - +
759A GLY 2.4 38.1 + - - +
760A LEU* 2.9 8.4 - - + +
773A LEU* 3.3 55.5 - - + +
774A GLU* 5.3 0.2 - - - -
776A TRP* 3.6 31.4 - + + -
777A SER* 3.8 12.3 - - - -
799A TYR* 3.2 50.0 - + + -
800A LEU* 5.0 4.9 - - + -
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Residues in contact with LYS 757 (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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753A GLN* 2.5 32.6 + - + +
754A MSE 3.9 6.1 - - - +
755A ALA 2.9 0.6 + - - -
756A PHE* 1.3 76.7 - - - +
758A LEU* 1.3 62.0 + - - +
760A LEU* 3.2 23.2 - - + +
762A TYR* 3.8 17.3 - - + -
798A GLY 3.6 17.4 + - - -
799A TYR* 3.9 11.7 - - + +
801A LYS* 3.7 14.5 - - - +
802A THR* 3.4 23.1 + - - +
877A ASP* 4.9 3.4 + - - -
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Residues in contact with LEU 758 (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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724A GLU* 4.3 15.7 - - + +
727A ALA* 5.3 1.1 - - + -
728A SER* 3.7 35.4 - - - +
731A THR* 5.0 6.7 - - + +
754A MSE 3.0 25.2 + - + +
755A ALA* 2.8 8.8 + - - +
757A LYS* 1.3 75.1 - - - +
759A GLY* 1.3 52.2 + - - +
760A LEU 2.6 18.6 + - - -
762A TYR* 3.4 48.8 + - + +
763A THR* 3.0 22.1 + - + -
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Residues in contact with GLY 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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755A ALA 2.8 7.3 + - - -
756A PHE* 2.4 23.4 + - - +
758A LEU* 1.3 68.6 - - - +
760A LEU* 1.3 64.4 + - - +
763A THR* 2.9 15.0 - - - -
769A GLY* 4.3 3.1 - - - -
770A LEU* 3.3 10.4 - - - +
773A LEU* 3.3 30.3 - - - +
803A SER* 4.6 1.7 - - - -
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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