Contacts of the helix formed by residues 739 - 750 (chain A) in PDB entry 2LNX
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 SER 739 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A ILE* 4.5 13.8 - - - +
668A TYR* 3.9 9.2 - - - -
729A ILE* 3.3 11.7 - - - +
737A PHE* 3.8 1.0 - - - +
738A ASP* 1.3 82.8 - - - +
740A LEU* 1.3 66.8 + - - +
741A LEU* 3.2 9.0 + - - -
742A GLU* 3.2 33.5 + - - +
743A LEU 3.3 8.0 + - - -
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Residues in contact with LEU 740 (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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668A TYR* 2.9 40.1 + - + +
673A TRP* 6.3 1.8 - - + -
674A PHE* 5.8 2.0 - - + -
697A ILE* 5.1 12.1 - - + -
707A PHE* 3.3 45.5 - - + -
709A ILE* 6.1 1.3 - - + -
722A VAL* 4.9 10.1 - - + -
724A GLU* 4.1 4.8 - - - +
729A ILE* 3.6 34.0 - - + +
739A SER* 1.3 70.8 - - - +
741A LEU* 1.3 61.4 + - - +
743A LEU* 3.2 6.8 + - + +
744A VAL* 3.0 44.9 + - + +
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Residues in contact with LEU 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A ILE* 3.7 27.6 - - + -
668A TYR* 3.2 33.6 - - + +
671A TYR* 3.6 33.2 - - + +
673A TRP* 5.0 5.6 - - + -
739A SER* 3.1 5.8 - - - -
740A LEU* 1.3 76.7 - - - +
742A GLU* 1.3 61.9 + - - +
743A LEU 3.1 0.3 + - - -
744A VAL* 3.2 3.3 + - - -
745A GLU* 2.6 56.3 + - + +
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Residues in contact with GLU 742 (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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737A PHE* 3.2 21.0 - - + -
738A ASP* 4.8 8.6 - - - +
739A SER* 3.2 37.0 + - - +
741A LEU* 1.3 84.7 - - - +
743A LEU* 1.3 61.3 + - - +
745A GLU* 4.3 5.1 - - - +
746A TYR* 3.1 28.3 + - + +
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Residues in contact with LEU 743 (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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709A ILE* 5.3 4.0 - - + -
722A VAL* 4.1 9.4 - - + -
729A ILE* 3.5 22.9 - - + -
730A HIS* 3.5 29.4 - - - +
731A ILE* 3.8 29.2 - - + +
737A PHE* 3.3 33.8 - - + -
739A SER 3.3 7.8 + - - +
740A LEU* 3.2 12.7 + - + +
741A LEU 3.1 0.4 - - - -
742A GLU* 1.3 81.3 - - - +
744A VAL* 1.3 70.6 + - + +
746A TYR* 3.6 5.5 + - - +
747A TYR* 3.6 21.6 + - + +
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Residues in contact with VAL 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A TRP* 5.1 19.3 - - + -
697A ILE* 4.6 23.8 - - + -
709A ILE* 5.3 6.1 - - + -
740A LEU* 3.0 36.1 + - + +
741A LEU* 4.1 2.7 - - - +
743A LEU* 1.3 79.0 - - + +
745A GLU* 1.3 65.5 + - + +
747A TYR* 3.0 31.8 - - + +
748A GLN* 3.1 16.3 - - + +
763A LEU* 3.3 26.0 - - + -
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Residues in contact with GLU 745 (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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671A TYR* 5.4 7.7 + - - -
673A TRP* 6.2 4.7 - - + -
741A LEU* 2.6 46.7 + - + +
742A GLU* 4.3 4.7 - - - +
744A VAL* 1.3 74.3 - - + +
746A TYR* 1.3 58.9 + - - +
748A GLN* 3.0 38.8 + - - +
749A CYS* 4.2 4.7 + - - +
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Residues in contact with TYR 746 (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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735A LYS* 3.7 31.5 + - + -
737A PHE* 3.5 27.6 - + + -
742A GLU* 3.1 19.2 + - + +
743A LEU 3.9 0.7 - - - +
744A VAL 3.2 0.4 - - - -
745A GLU* 1.3 78.9 - - - +
747A TYR* 1.3 62.8 + - + +
748A GLN 3.2 1.9 + - - -
749A CYS* 3.8 1.6 + - - +
750A HIS* 3.4 44.8 + + + +
754A GLU* 5.8 4.3 - - - -
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Residues in contact with TYR 747 (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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695A TYR* 5.5 0.2 - - - -
697A ILE* 5.6 1.6 - - - +
709A ILE* 3.9 33.4 - - + +
711A ILE* 5.5 1.0 - - + +
720A ILE* 6.2 4.0 - - + -
731A ILE* 5.3 13.9 - - + -
737A PHE* 6.2 1.1 - - + -
743A LEU* 3.6 16.3 + - + +
744A VAL* 3.0 43.9 - - + +
746A TYR* 1.3 79.3 - - + +
748A GLN* 1.3 60.0 + - - +
749A CYS 3.3 0.2 - - - -
750A HIS* 2.7 27.4 - - - +
751A SER 5.5 0.7 - - - +
752A LEU* 3.7 40.9 + - + -
761A THR 5.2 0.2 - - - +
762A THR* 3.7 9.7 - - - +
763A LEU* 3.3 36.5 + - + +
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Residues in contact with GLN 748 (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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673A TRP* 5.7 4.9 - - - +
695A TYR* 5.5 4.9 + - - -
744A VAL* 3.1 17.6 + - - +
745A GLU* 3.0 47.1 + - - +
747A TYR* 1.3 79.2 - - - +
749A CYS* 1.3 66.2 + - + +
762A THR* 3.3 18.5 + - - -
763A LEU* 3.6 40.5 + - + +
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Residues in contact with CYS 749 (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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745A GLU 4.7 3.6 - - - +
746A TYR 3.8 3.4 + - - +
748A GLN* 1.3 93.9 - - + +
750A HIS* 1.3 79.3 + - + +
762A THR* 4.1 6.4 + - - +
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Residues in contact with HIS 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746A TYR* 3.4 43.3 + + + +
747A TYR* 2.7 31.4 - - - +
749A CYS* 1.3 92.6 - - + +
751A SER* 1.3 69.0 + - - +
754A GLU* 6.2 2.2 - - - +
762A THR* 3.1 5.3 - - - +
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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