Contacts of the helix formed by residues 860 - 870 (chain A) in PDB entry 1E42
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 ASN 860 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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858A HIS 3.8 4.7 + - - +
859A LEU* 1.3 76.1 - - - +
861A ALA* 1.3 68.1 + - - +
862A ASP* 2.6 25.1 + - - +
863A THR* 2.7 20.3 + - - +
864A VAL* 2.9 10.9 + - - +
905A ILE* 5.4 1.1 - - - -
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Residues in contact with ALA 861 (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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859A LEU 4.0 0.6 + - - -
860A ASN* 1.3 73.1 - - - +
862A ASP* 1.3 58.1 + - - +
864A VAL* 3.1 4.4 + - - +
865A SER* 2.8 33.6 + - - -
878A LYS* 4.0 18.2 - - + +
885A ASP* 4.1 22.6 + - + -
887A LEU* 3.8 27.2 - - + +
905A ILE* 3.9 15.9 - - + +
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Residues in contact with ASP 862 (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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860A ASN* 2.6 34.6 + - + +
861A ALA* 1.3 80.7 - - - +
863A THR* 1.3 84.8 + - - +
865A SER* 3.3 7.5 + - - -
866A SER* 2.9 28.8 + - - -
878A LYS* 4.8 7.6 - - - +
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Residues in contact with THR 863 (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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859A LEU* 3.8 26.7 - - + -
860A ASN* 2.7 20.6 + - - +
862A ASP* 1.3 93.4 + - - +
864A VAL* 1.3 64.6 + - - +
866A SER* 3.3 7.8 + - - +
867A LYS* 3.1 37.1 + - + +
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Residues in contact with VAL 864 (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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859A LEU* 3.8 26.0 - - + +
860A ASN 2.9 16.6 + - - +
861A ALA* 3.4 11.0 - - - +
863A THR* 1.3 76.4 - - - +
865A SER* 1.3 64.4 + - - +
867A LYS* 3.8 1.2 - - - +
868A LEU* 3.0 46.5 + - + +
887A LEU* 3.9 8.3 - - + -
903A LEU* 3.7 23.6 - - + -
905A ILE* 4.5 1.8 - - + -
912A TYR* 4.3 13.9 - - + -
935A LEU* 4.2 20.6 - - + +
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Residues in contact with SER 865 (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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861A ALA 2.8 18.4 + - - -
862A ASP* 3.6 6.5 - - - -
863A THR 3.2 0.2 - - - -
864A VAL* 1.3 79.4 - - - +
866A SER* 1.3 58.0 + - - +
868A LEU* 3.9 3.4 - - - +
869A GLN* 3.0 29.8 + - - +
873A VAL 4.7 1.0 - - - +
875A THR* 2.8 38.4 + - - +
887A LEU* 3.6 13.2 - - - +
889A GLN* 4.9 0.7 - - - +
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Residues in contact with SER 866 (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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862A ASP 2.9 15.6 + - - -
863A THR* 3.3 14.7 + - - +
864A VAL 3.3 0.2 - - - -
865A SER* 1.3 74.3 - - - +
867A LYS* 1.3 70.5 + - - +
869A GLN* 3.4 8.2 + - - +
870A ASN* 3.1 29.3 + - - -
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Residues in contact with LYS 867 (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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859A LEU* 3.8 23.0 - - + +
863A THR* 3.1 26.5 + - + +
864A VAL 3.8 2.9 - - - +
866A SER* 1.3 83.9 + - - +
868A LEU* 1.3 64.6 + - - +
870A ASN* 3.0 21.1 + - - +
871A ASN* 3.1 19.5 + - - +
934A ILE* 3.3 28.2 + - + +
935A LEU* 3.6 14.7 + - + -
937A ASN* 2.4 33.5 + - - -
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Residues in contact with LEU 868 (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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864A VAL* 3.0 29.1 + - + +
865A SER* 4.0 2.7 - - - +
867A LYS* 1.3 76.9 - - - +
869A GLN* 1.3 57.3 + - - +
871A ASN* 2.8 22.6 + - - +
872A ASN 3.2 0.2 + - - -
873A VAL* 2.9 44.2 + - + +
889A GLN* 3.2 20.2 - - - +
931A TYR* 3.1 58.3 - - + +
934A ILE* 4.3 22.9 - - + -
935A LEU* 4.5 6.7 - - + -
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Residues in contact with GLN 869 (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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865A SER 3.0 18.5 + - - +
866A SER* 3.5 7.6 + - - +
868A LEU* 1.3 76.7 - - - +
870A ASN* 1.3 81.0 + - - +
872A ASN* 3.1 18.1 + - - +
873A VAL 3.2 12.0 + - - +
874A TYR* 4.4 25.8 - - + -
875A THR 6.0 0.7 - - - +
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Residues in contact with ASN 870 (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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705A GLY* 3.6 25.0 + - - +
706A GLY 3.2 21.0 + - - -
866A SER* 3.1 22.3 + - - -
867A LYS* 3.0 15.6 + - - +
869A GLN* 1.3 89.7 + - - +
871A ASN* 1.3 59.5 + - - +
872A ASN* 3.4 3.8 + - - +
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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