Contacts of the helix formed by residues 909 - 916 (chain A) in PDB entry 6PUO
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 ARG 909 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806A TYR* 3.3 21.5 - - + +
843A GLU* 5.9 1.4 + - - -
868A TRP* 4.2 30.2 + - - +
871A LEU* 5.9 3.6 - - - -
872A ASP* 5.0 13.2 - - - +
905A LEU 3.7 6.4 + - - +
906A PHE* 3.2 21.0 + - + +
907A CYS 3.1 0.6 - - - -
908A LEU* 1.3 78.0 - - - +
910A LEU* 1.3 60.5 + - - +
911A MET 3.1 0.2 - - - -
912A HIS* 3.1 65.7 + - - +
913A ILE* 5.7 0.2 - - - +
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Residues in contact with LEU 910 (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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803A ILE* 3.9 11.4 - - + +
806A TYR* 3.6 33.0 - - + -
807A PHE* 4.4 23.1 - - + +
810A LEU* 3.9 20.9 - - + -
906A PHE 4.3 0.2 + - - -
907A CYS* 3.4 11.5 + - + +
908A LEU 3.2 1.2 - - - -
909A ARG* 1.3 73.3 - - - +
911A MET* 1.3 58.7 + - - +
912A HIS 3.1 6.5 + - - -
913A ILE* 3.4 46.7 + - + +
914A PHE* 5.0 4.2 - - - -
939D PHE* 6.3 3.6 - - + -
943D VAL* 4.6 25.1 - - + -
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Residues in contact with MET 911 (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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868A TRP* 3.9 15.0 - - + -
907A CYS 4.8 0.4 + - - -
908A LEU* 3.4 19.3 + - + +
909A ARG 3.1 2.0 + - - -
910A LEU* 1.3 75.7 - - - +
912A HIS* 1.3 59.6 + - - +
913A ILE 3.1 4.7 + - - -
914A PHE* 3.7 25.8 + - + +
915A THR* 4.7 4.2 - - - +
924A ILE* 4.9 11.4 - - + +
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Residues in contact with HIS 912 (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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799A PHE* 5.9 6.1 - + - -
868A TRP* 3.4 54.9 - + + +
909A ARG* 3.1 41.3 + - - +
910A LEU 3.1 1.0 - - - -
911A MET* 1.3 74.5 - - - +
913A ILE* 1.3 59.1 + - + +
914A PHE 3.4 0.2 - - - -
915A THR* 3.0 36.7 + - + +
1070A LEU* 4.5 24.3 - - + +
1073A GLU* 6.1 0.2 - - - -
1074A TYR* 6.2 1.1 - + - -
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Residues in contact with ILE 913 (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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799A PHE* 4.8 19.1 - - + -
803A ILE* 3.8 38.8 - - + -
910A LEU* 3.4 32.3 - - + +
911A MET 3.1 0.6 - - - -
912A HIS* 1.3 78.9 - - + +
914A PHE* 1.3 75.9 + - + +
915A THR 3.0 6.9 + - - -
916A ILE* 3.1 27.7 + - + +
939D PHE* 5.5 11.9 - - + -
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Residues in contact with PHE 914 (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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910A LEU 5.0 7.6 - - - -
911A MET* 3.7 18.8 + - + +
912A HIS 3.4 0.6 - - - -
913A ILE* 1.3 89.5 - - + +
915A THR* 1.3 64.2 + - - +
916A ILE 3.2 0.4 - - - -
917A SER* 3.2 22.8 + - - +
920A LEU* 3.6 31.4 - - + -
921A GLY* 3.4 14.5 + - - -
924A ILE* 4.6 15.5 - - + -
936D PHE* 4.6 12.8 - + + -
939D PHE* 3.5 36.1 - + - -
940D LEU* 3.9 34.5 - - + -
943D VAL* 6.5 0.2 - - + -
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Residues in contact with THR 915 (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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868A TRP* 4.8 9.9 - - + +
911A MET 4.7 3.6 - - - +
912A HIS* 3.0 34.5 + - + +
913A ILE 4.0 0.2 + - - -
914A PHE* 1.3 76.9 - - - +
916A ILE* 1.3 60.3 + - - +
917A SER 3.4 1.6 + - - +
921A GLY* 4.3 10.3 - - - -
924A ILE* 4.8 19.1 - - + -
1063A TRP* 2.8 33.0 + - - -
1070A LEU* 3.8 19.3 - - - +
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Residues in contact with ILE 916 (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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743A TRP* 4.1 28.7 - - + +
799A PHE* 4.0 25.1 - - + -
913A ILE* 3.1 19.9 + - + +
915A THR* 1.3 79.2 + - - +
917A SER* 1.3 66.5 + - - +
918A LYS 3.8 0.3 + - - -
1063A TRP* 4.5 5.5 - - + -
1067A ARG* 5.2 11.2 - - + +
1070A LEU* 3.7 30.5 - - + -
1071A ILE* 4.5 19.5 - - + -
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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