Contacts of the helix formed by residues 841 - 851 (chain A) in PDB entry 3DKO
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 SER 841 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801A ARG* 3.9 0.7 - - - +
839A ASP 3.5 3.6 + - - -
840A MET* 1.3 77.0 - - - +
842A ASN* 1.3 64.5 + - - +
843A GLN* 3.5 7.5 + - - +
844A ASP* 3.0 34.0 + - - +
845A VAL* 2.9 21.3 + - - +
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Residues in contact with ASN 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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800A VAL* 3.8 38.4 + - + +
801A ARG* 3.0 28.4 + - - +
835A ARG* 5.1 0.5 + - - -
841A SER* 1.3 72.7 - - - +
843A GLN* 1.3 70.2 + - - +
845A VAL* 3.2 5.3 + - - +
846A ILE* 3.1 27.8 + - + +
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Residues in contact with GLN 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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800A VAL* 6.2 0.4 - - - +
841A SER* 3.3 7.5 + - - +
842A ASN* 1.3 84.5 - - + +
844A ASP* 1.3 60.1 + - - +
846A ILE* 3.5 28.1 + - - +
847A LYS* 3.1 46.7 + - - +
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Residues in contact with ASP 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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840A MET* 3.5 17.1 - - + +
841A SER* 3.0 29.7 + - - +
843A GLN* 1.3 74.5 - - - +
845A VAL* 1.3 59.8 - - - +
847A LYS* 3.7 21.6 - - - +
848A ALA* 3.0 30.1 + - - +
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Residues in contact with VAL 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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800A VAL* 4.5 7.0 - - + +
801A ARG* 3.9 28.9 - - + +
837A TYR* 3.6 46.9 - - + -
840A MET* 3.8 13.0 - - + -
841A SER 2.9 17.2 + - - +
842A ASN* 3.2 9.4 + - - +
844A ASP* 1.3 75.0 - - - +
846A ILE* 1.3 64.9 + - + +
848A ALA* 3.2 3.3 + - - +
849A ILE* 2.9 48.6 + - + +
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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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800A VAL* 3.8 26.9 - - + -
808A ILE* 4.1 28.5 - - + -
809A GLN* 3.7 22.2 - - - +
842A ASN* 3.1 14.2 + - + +
843A GLN* 3.5 35.7 - - - +
845A VAL* 1.3 76.2 - - + +
847A LYS* 1.3 58.8 + - + +
849A ILE* 3.3 7.2 + - - +
850A GLU* 2.9 49.0 + - + +
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Residues in contact with LYS 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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843A GLN* 3.1 36.5 + - - +
844A ASP* 3.7 24.0 - - - +
845A VAL 3.3 0.2 - - - -
846A ILE* 1.3 77.1 - - + +
848A ALA* 1.3 64.8 + - - +
850A GLU* 3.2 17.9 + - - +
851A GLU* 2.9 24.0 + - - +
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Residues in contact with ALA 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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837A TYR* 6.0 0.4 - - + -
840A MET* 4.0 16.8 - - + -
844A ASP 3.0 19.7 + - - +
845A VAL* 3.7 3.1 - - - +
847A LYS* 1.3 75.9 - - - +
849A ILE* 1.3 60.1 + - + +
851A GLU* 2.9 24.7 - - - +
853A TYR* 2.8 46.9 + - + -
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Residues in contact with ILE 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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800A VAL 5.8 2.2 - - - +
801A ARG 5.7 1.3 - - - +
803A THR 5.6 3.1 - - - +
805A PRO* 4.1 15.5 - - + -
808A ILE* 6.0 4.3 - - + -
820A TRP* 3.7 31.4 - - + +
837A TYR* 3.4 32.1 - - + +
845A VAL* 2.9 38.2 + - + +
846A ILE* 3.7 6.7 - - - +
848A ALA* 1.3 76.8 - - + +
850A GLU* 1.3 62.7 - - + +
852A GLY* 3.0 6.1 + - - -
853A TYR 3.9 9.4 - - - +
854A ARG* 3.0 37.8 + - - +
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Residues in contact with GLU 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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805A PRO* 6.1 5.4 - - + -
809A GLN* 4.3 12.1 + - - +
846A ILE* 2.9 35.9 + - + +
847A LYS* 3.4 19.6 - - - +
849A ILE* 1.3 76.7 - - + +
851A GLU* 1.3 59.6 + - - +
852A GLY* 3.2 1.3 + - - -
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Residues in contact with GLU 851 (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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847A LYS 2.9 11.4 + - - +
848A ALA* 2.9 29.1 + - - +
850A GLU* 1.3 75.2 - - - +
852A GLY* 1.3 55.8 + - - +
853A TYR* 4.0 15.3 - - - +
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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