Contacts of the helix formed by residues 839 - 850 (chain A) in PDB entry 3OPY
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 839 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830A HIS* 3.5 11.7 - - - -
835A SER 3.6 16.6 - - - +
836A LYS* 3.9 11.9 - - - +
837A VAL 2.9 14.3 + - - +
838A TYR* 1.3 72.1 - - - +
840A THR* 1.4 56.6 + - - +
841A ASP* 3.6 9.7 + - - +
842A LEU* 3.0 17.3 + - - +
843A ILE* 2.8 32.1 + - - +
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Residues in contact with THR 840 (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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768A VAL* 3.6 34.7 - - + +
770A GLU* 3.2 40.5 + - + +
830A HIS* 3.2 30.8 + - - +
839A THR* 1.4 71.1 - - - +
841A ASP* 1.4 59.8 + - - +
843A ILE 3.6 0.2 + - - -
844A ALA* 3.0 31.7 + - - +
859A THR* 3.7 16.8 - - + -
860A ALA 4.8 1.1 - - - +
861A VAL* 5.3 2.9 - - + -
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Residues in contact with ASP 841 (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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839A THR* 3.1 8.0 + - - +
840A THR* 1.4 79.1 - - - +
842A LEU* 1.4 58.7 + - - +
844A ALA* 3.6 2.1 + - - +
845A ALA* 3.0 28.1 + - - +
859A THR* 3.4 25.4 + - - +
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Residues in contact with LEU 842 (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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837A VAL* 3.5 36.1 - - + +
838A TYR* 3.8 25.4 - - + -
839A THR* 3.0 14.5 + - - +
841A ASP* 1.4 72.9 - - - +
843A ILE* 1.4 66.4 - - - +
845A ALA* 3.1 12.3 + - + +
846A ILE* 2.9 42.1 + - + +
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Residues in contact with ILE 843 (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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768A VAL* 4.3 8.3 - - + -
793A TYR* 3.7 45.3 - - + +
804A VAL* 3.9 22.2 - - + -
830A HIS* 3.8 18.8 - - + -
838A TYR* 3.7 29.6 - - + +
839A THR 2.8 23.8 + - - +
840A THR 4.1 2.9 - - - +
842A LEU* 1.4 69.6 - - - +
844A ALA* 1.4 62.2 + - - +
846A ILE* 3.1 8.0 + - + +
847A ILE* 3.1 43.2 + - + +
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Residues in contact with ALA 844 (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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768A VAL* 3.8 18.6 - - + +
840A THR 3.0 19.3 + - - +
841A ASP 3.8 3.1 - - - +
843A ILE* 1.4 74.7 - - - +
845A ALA* 1.3 61.1 + - - +
847A ILE* 3.4 1.1 + - - -
848A GLY 3.1 8.3 + - - -
857A SER* 2.4 35.2 + - - +
858A ARG 4.6 5.2 - - - -
859A THR* 3.4 23.6 - - + -
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Residues in contact with ALA 845 (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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841A ASP 3.0 19.0 + - - +
842A LEU* 3.1 16.5 + - + +
844A ALA* 1.3 76.5 - - - +
846A ILE* 1.3 60.4 + - + +
847A ILE 3.5 0.2 - - - -
848A GLY* 3.7 1.7 + - - -
849A GLU* 3.5 21.3 + - - +
857A SER* 4.7 0.9 - - - -
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Residues in contact with ILE 846 (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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801A LEU* 5.8 4.7 - - + -
804A VAL* 3.6 34.1 - - + -
808A ILE* 3.9 12.6 - - + -
838A TYR* 4.6 11.4 - - + -
842A LEU* 2.9 48.8 + - + +
843A ILE* 3.1 6.3 + - - +
845A ALA* 1.3 74.4 - - - +
847A ILE* 1.3 64.6 + - - +
849A GLU* 3.5 5.4 + - - +
850A ALA* 3.1 21.5 + - - +
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Residues in contact with ILE 847 (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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766A THR* 4.0 11.0 - - + -
768A VAL* 3.8 20.2 - - + -
808A ILE* 3.7 23.3 - - + -
811A LEU* 3.6 24.5 - - + -
828A PHE* 4.0 24.9 - - + -
843A ILE* 3.1 33.5 + - + +
844A ALA 3.4 6.0 + - - +
846A ILE* 1.3 73.5 - - - +
848A GLY* 1.3 62.7 + - - +
850A ALA* 3.1 16.5 + - - +
855A PHE* 3.3 22.1 - - + -
857A SER* 3.6 16.2 - - - -
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Residues in contact with GLY 848 (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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844A ALA 3.1 11.0 + - - -
845A ALA 3.7 2.9 + - - -
846A ILE 3.3 0.4 - - - -
847A ILE* 1.3 77.0 - - - +
849A GLU* 1.4 59.1 + - - +
850A ALA 3.3 1.7 + - - +
853A GLY* 3.5 19.6 - - - -
855A PHE 3.7 17.7 - - - +
857A SER* 3.3 16.2 + - - -
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Residues in contact with GLU 849 (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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845A ALA 3.5 16.3 + - - +
846A ILE* 3.9 4.5 - - - +
847A ILE 3.5 0.2 - - - -
848A GLY* 1.4 70.8 - - - +
850A ALA* 1.4 62.3 + - - +
852A LYS* 3.5 15.2 + - - -
853A GLY* 3.5 6.1 + - - +
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Residues in contact with ALA 850 (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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808A ILE* 3.6 31.4 - - + -
846A ILE 3.1 13.5 + - - +
847A ILE* 3.1 21.5 + - - +
848A GLY 3.7 0.5 - - - +
849A GLU* 1.4 75.6 - - - +
851A GLY* 1.3 59.0 + - - +
854A ARG* 3.1 24.4 + - - +
855A PHE* 3.7 12.2 - - + -
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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