Contacts of the helix formed by residues 737 - 749 (chain B) in PDB entry 4K6J
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 737 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701B ALA* 3.8 27.9 - - + +
705B LYS* 6.0 1.4 - - - +
735B ASP 3.7 1.0 + - - +
736B LEU* 1.3 74.9 - - - +
738B ARG* 1.3 68.3 + - - +
739B ALA* 3.7 17.7 + - - +
740B SER* 2.8 37.8 + - - -
741B LEU* 3.3 13.3 + - - +
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Residues in contact with ARG 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946A TRP* 3.7 37.0 - - + -
949A THR* 4.1 3.8 - - - +
950A LYS* 3.6 23.4 - - - +
953A GLU* 2.8 40.4 + - - -
997A ARG* 3.9 19.8 - - - +
737B ASP* 1.3 75.4 - - - +
739B ALA* 1.3 62.0 + - - +
741B LEU* 3.3 11.6 + - + +
742B ASP* 3.0 33.0 + - - +
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Residues in contact with ALA 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705B LYS* 6.0 10.8 - - + -
708B ASP* 5.8 4.0 - - + +
737B ASP* 3.2 16.4 - - - +
738B ARG* 1.3 79.3 - - - +
740B SER* 1.3 56.4 - - - +
742B ASP* 3.4 12.7 - - - +
743B LEU* 3.0 25.5 + - - +
746B ARG* 3.7 6.3 + - - +
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Residues in contact with SER 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701B ALA* 5.3 1.3 - - - -
704B PHE* 3.9 25.8 - - - -
724B MET* 3.5 14.3 - - - +
736B LEU* 3.3 26.1 - - - +
737B ASP* 2.8 41.6 + - - -
739B ALA* 1.3 76.8 - - - +
741B LEU* 1.3 60.6 + - - +
743B LEU* 3.3 9.1 - - - +
744B MET* 3.1 20.1 + - - +
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Residues in contact with LEU 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724B MET* 5.5 2.7 - - - -
736B LEU* 4.4 24.0 - - + -
737B ASP 3.3 12.3 + - - +
738B ARG* 3.3 14.0 + - + +
739B ALA 3.3 0.2 - - - -
740B SER* 1.3 77.1 + - - +
742B ASP* 1.3 66.9 + - - +
744B MET* 3.0 9.1 + - + +
745B ILE* 2.9 36.2 + - + +
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Residues in contact with ASP 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738B ARG* 3.0 26.5 + - - +
739B ALA* 3.4 12.0 - - - +
741B LEU* 1.3 75.8 - - - +
743B LEU* 1.3 62.0 + - - +
745B ILE* 3.4 11.9 + - - +
746B ARG* 3.0 41.3 + - - +
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Residues in contact with LEU 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B PHE* 3.7 47.6 - - + +
707B LEU 3.9 20.2 - - - +
708B ASP* 3.9 8.7 - - + +
710B SER* 4.4 6.7 - - - -
711B GLN 4.7 2.5 - - - +
720B THR* 4.1 8.5 - - + -
724B MET* 4.9 2.7 - - + -
739B ALA 3.0 14.5 + - - +
740B SER* 3.3 10.5 - - - +
741B LEU 3.1 0.2 - - - -
742B ASP* 1.3 77.4 - - - +
744B MET* 1.3 64.8 + - - +
746B ARG* 3.1 34.4 + - + +
747B LEU* 3.0 37.0 + - + +
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Residues in contact with MET 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720B THR* 4.2 5.8 - - + +
721B ALA* 4.0 17.3 - - - +
724B MET* 3.4 51.8 - - + -
740B SER 3.1 8.3 + - - +
741B LEU* 3.0 12.1 + - + +
743B LEU* 1.3 80.6 - - + +
745B ILE* 1.3 58.3 + - + +
747B LEU* 3.2 31.0 + - + +
748B LEU* 2.9 26.6 + - - +
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Residues in contact with ILE 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741B LEU* 2.9 27.2 + - + +
742B ASP* 3.7 11.9 - - - +
744B MET* 1.3 75.2 - - + +
746B ARG* 1.3 66.2 + - + +
748B LEU* 3.1 17.5 + - + +
749B GLU* 3.0 40.2 + - - +
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Residues in contact with ARG 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B ASP* 3.1 26.5 + - - +
711B GLN* 2.8 53.0 + - + +
739B ALA* 3.7 7.3 + - - +
742B ASP* 3.0 27.5 + - - +
743B LEU* 3.2 46.7 - - - +
745B ILE* 1.3 77.6 - - + +
747B LEU* 1.3 62.1 + - - +
749B GLU* 3.3 19.5 + - + +
750B LEU* 3.0 23.8 + - - +
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Residues in contact with LEU 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B SER* 4.3 4.3 - - - -
711B GLN* 3.8 34.3 - - + +
717B SER* 3.9 20.6 - - - +
720B THR* 4.3 11.9 - - + -
721B ALA* 4.0 25.6 - - + +
743B LEU* 3.0 22.6 + - + +
744B MET* 3.5 37.7 - - + +
746B ARG* 1.3 76.5 - - - +
748B LEU* 1.3 61.3 + - - +
750B LEU* 3.5 21.5 + - + +
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Residues in contact with LEU 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744B MET 2.9 12.8 + - - +
745B ILE* 3.1 22.2 + - + +
747B LEU* 1.3 80.5 - - - +
749B GLU* 1.3 59.9 + - + +
750B LEU 3.3 4.2 + - - +
751B GLU* 5.2 1.9 - - - +
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Residues in contact with GLU 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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745B ILE* 3.0 28.5 + - - +
746B ARG* 3.4 23.7 - - + +
748B LEU* 1.3 77.9 - - + +
750B LEU* 1.3 63.0 + - - +
751B GLU* 3.6 13.8 + - - +
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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