Contacts of the helix formed by residues 724 - 732 (chain B) in PDB entry 1ED8
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 THR 724 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711B PHE 3.7 7.4 - - - -
712B ALA* 3.7 16.1 - - - +
713B GLU 3.0 10.5 - - - -
714B THR* 3.9 11.2 - - + +
723B LYS* 1.3 78.5 - - - +
725B LEU* 1.3 60.4 + - - +
726B ARG* 3.3 9.7 + - - +
727B GLU* 3.2 40.5 + - - +
728B GLN* 3.0 27.5 + - - +
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Residues in contact with LEU 725 (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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671B PRO* 4.1 20.6 - - + -
692B THR* 3.6 32.3 - - + -
693B GLU* 4.3 17.3 - - + +
696B LEU* 3.7 9.8 - - + +
710B THR* 4.0 11.7 - - + +
711B PHE* 3.3 22.5 + - + +
713B GLU* 2.6 26.4 + - + +
714B THR 4.5 0.9 - - - -
715B ALA* 4.2 16.4 - - + +
723B LYS 4.6 0.2 - - - +
724B THR* 1.3 74.2 - - - +
726B ARG* 1.3 58.1 + - - +
728B GLN* 3.5 22.6 + - - +
729B ALA* 3.0 26.5 + - - +
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Residues in contact with ARG 726 (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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711B PHE* 3.1 26.5 + - + +
724B THR* 3.2 7.8 - - - +
725B LEU* 1.3 73.5 - - - +
727B GLU* 1.3 60.4 + - + +
729B ALA* 3.1 7.8 + - - +
730B GLN* 2.9 44.4 + - - +
736B LEU* 3.4 44.2 - - + +
737B VAL 5.1 2.2 + - - -
738B SER* 4.9 15.0 - - - -
758B LEU* 4.8 14.4 - - + +
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Residues in contact with GLU 727 (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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723B LYS* 3.4 36.1 - - + +
724B THR* 3.2 36.6 + - - +
726B ARG* 1.3 73.1 - - + +
728B GLN* 1.3 56.9 + - - +
729B ALA 3.0 0.2 + - - -
730B GLN* 3.2 14.3 + - - +
731B ALA* 2.6 39.7 + - - +
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Residues in contact with GLN 728 (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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693B GLU* 4.8 12.4 + - - +
696B LEU* 3.4 22.5 - - + +
697B ASN* 4.7 0.3 - - - +
715B ALA* 4.9 6.7 - - - +
720B TRP* 3.9 41.5 - - + +
723B LYS* 4.8 2.0 + - - +
724B THR 3.0 12.6 + - - +
725B LEU* 3.6 22.7 - - - +
727B GLU* 1.3 75.5 - - - +
729B ALA* 1.3 53.5 + - - +
731B ALA* 3.1 7.8 - - - +
732B ARG* 2.7 77.1 + - - +
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Residues in contact with ALA 729 (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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696B LEU* 3.8 20.4 - - + -
711B PHE* 5.2 0.4 - - + -
725B LEU 3.0 14.6 + - - +
726B ARG* 3.1 13.2 - - - +
727B GLU 3.0 0.4 - - - -
728B GLN* 1.3 75.2 - - - +
730B GLN* 1.3 69.3 + - - +
732B ARG* 2.8 11.1 + - - -
734B TYR* 3.1 31.5 + - + +
736B LEU* 4.2 18.6 - - + -
756B LEU* 4.6 5.4 - - + -
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Residues in contact with GLN 730 (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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726B ARG* 2.9 39.8 + - - +
727B GLU* 3.8 14.9 - - - +
729B ALA* 1.3 72.7 - - - +
731B ALA* 1.3 64.1 + - - +
733B GLY* 3.0 15.6 + - - -
734B TYR 4.0 11.9 + - - +
736B LEU* 3.9 27.1 - - + +
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Residues in contact with ALA 731 (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 TRP* 4.1 18.3 + - + +
723B LYS* 5.6 7.2 - - - +
727B GLU 2.6 24.9 + - - +
728B GLN* 3.1 13.0 - - - +
730B GLN* 1.3 73.9 - - - +
732B ARG* 1.3 58.0 + - - +
733B GLY 3.3 0.7 + - - -
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Residues in contact with ARG 732 (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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696B LEU* 4.1 10.6 + - - -
697B ASN* 2.6 47.3 + - - +
699B ARG* 2.9 36.5 + - - +
720B TRP* 3.6 42.5 - - + -
728B GLN* 2.7 52.4 + - - +
729B ALA* 2.8 5.4 + - - +
731B ALA* 1.3 73.9 - - - +
733B GLY* 1.3 57.5 + - - +
734B TYR* 3.3 17.3 - - + -
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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