Contacts of the helix formed by residues 711 - 719 (chain B) in PDB entry 3T9K
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 711 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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661B LYS* 5.7 0.4 - - - +
708B GLY* 4.2 6.9 + - - -
710B GLU* 1.3 76.7 - - - +
712B TYR* 1.3 53.8 + - - +
713B LEU 3.3 1.6 - - - -
714B ASP* 3.7 16.6 - - - +
715B ILE* 2.6 36.3 + - - +
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Residues in contact with TYR 712 (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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694B LEU* 5.1 17.8 - - + +
697B MET* 6.6 0.4 - - + -
708B GLY 3.3 21.6 + - - +
709B ASP* 3.3 16.6 - - - +
710B GLU 3.1 1.0 - - - -
711B THR* 1.3 76.0 - - - +
713B LEU* 1.3 61.1 + - - +
715B ILE* 3.9 6.6 - - - +
716B PHE* 2.9 33.3 + - - +
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Residues in contact with LEU 713 (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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657B CYS* 3.5 23.7 - - - +
660B LEU* 6.0 4.3 - - + -
661B LYS* 4.3 13.2 - - + +
691B LEU* 4.0 16.5 - - + +
694B LEU* 6.3 1.1 - - - -
709B ASP 4.6 0.6 + - - -
710B GLU 3.9 10.6 + - - +
711B THR 3.3 0.2 - - - -
712B TYR* 1.3 80.0 - - - +
714B ASP* 1.3 51.6 + - - +
716B PHE 3.7 0.3 - - - -
717B ARG* 2.8 34.5 + - - +
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Residues in contact with ASP 714 (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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466B GLU* 5.6 2.5 - - - +
657B CYS* 4.7 0.2 - - - -
661B LYS* 3.6 20.5 - - - +
711B THR* 3.5 19.5 + - - +
712B TYR 3.4 0.2 - - - -
713B LEU* 1.3 77.6 - - - +
715B ILE* 1.3 59.8 + - - +
717B ARG* 3.4 8.0 - - - +
718B ASP* 2.8 32.4 + - - +
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Residues in contact with ILE 715 (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 THR* 2.6 23.7 + - - +
712B TYR* 3.9 7.0 - - - +
714B ASP* 1.3 72.0 - - - +
716B PHE* 1.3 57.9 + - - +
718B ASP* 3.6 4.5 + - - +
719B PHE* 3.0 29.9 + - - +
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Residues in contact with PHE 716 (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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690B THR* 5.5 6.3 - - + -
691B LEU* 4.5 14.1 - - + -
694B LEU* 4.9 12.8 - - + -
712B TYR 2.9 18.7 + - - +
713B LEU 4.0 2.0 - - - +
715B ILE* 1.3 76.4 - - - +
717B ARG* 1.3 58.3 + - - +
719B PHE* 3.4 7.0 - - - -
720B SER* 2.8 29.1 + - - -
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Residues in contact with ARG 717 (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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653B THR* 4.9 8.9 - - + +
654B GLY* 5.6 3.8 - - - -
657B CYS* 3.9 20.2 - - + -
691B LEU* 5.4 1.6 - - + -
713B LEU 2.8 20.3 + - - +
714B ASP* 3.1 11.2 + - - +
716B PHE* 1.3 74.7 - - - +
718B ASP* 1.3 65.2 + - - +
720B SER* 3.2 19.7 + - - -
721B LEU 3.8 3.3 + - - -
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Residues in contact with ASP 718 (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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714B ASP 2.8 18.9 + - - +
715B ILE* 4.0 4.7 - - - +
717B ARG* 1.3 72.6 - - - +
719B PHE* 1.3 57.4 + - - +
720B SER 3.1 4.1 + - - -
721B LEU* 3.6 16.1 + - - +
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Residues in contact with PHE 719 (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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715B ILE 3.0 19.9 + - - +
716B PHE* 3.4 8.7 - - - +
717B ARG 3.3 0.2 - - - -
718B ASP* 1.3 74.0 - - - +
720B SER* 1.3 61.3 + - - +
721B LEU* 4.8 2.7 - - - +
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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