Contacts of the helix formed by residues 870 - 881 (chain C) in PDB entry 2OO9
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 870 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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893B ARG* 4.8 8.5 - - - +
894B GLU* 3.3 13.7 - - - -
868C GLY 3.7 2.6 + - - -
869C TYR* 1.3 76.4 - - - +
871C TYR* 1.3 62.6 + - - +
872C GLN* 3.8 9.3 + - - +
873C ASP* 3.2 33.7 + - - +
874C ILE* 3.1 22.7 + - - +
897C ALA 4.7 2.8 + - - -
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Residues in contact with TYR 871 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A GLN* 4.2 22.6 - - + -
875A GLN* 3.4 26.5 + - + +
876A LYS* 3.6 37.2 - - + -
879A VAL* 4.3 12.1 - - + +
894B GLU* 2.9 28.1 + - - +
861C ILE* 4.0 27.0 - - + +
865C MSE 4.2 12.3 - - - -
869C TYR 3.8 0.6 + - - -
870C SER* 1.3 72.0 - - - +
872C GLN* 1.3 54.6 + - + +
874C ILE* 3.4 11.5 + - - +
875C GLN* 2.7 71.8 + - + +
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Residues in contact with GLN 872 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A GLN* 5.5 9.4 - - - +
876A LYS* 6.3 0.9 - - - +
894B GLU* 4.9 1.2 + - - +
870C SER* 3.3 9.1 + - - +
871C TYR* 1.3 81.5 - - + +
873C ASP* 1.3 61.6 + - - +
875C GLN* 3.3 9.9 - - - +
876C LYS* 3.0 56.6 + - + +
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Residues in contact with ASP 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869C TYR* 5.5 0.7 - - + -
870C SER* 3.2 23.8 + - - +
872C GLN* 1.3 80.8 + - - +
874C ILE* 1.3 65.3 + - - +
875C GLN 3.2 1.1 - - - -
876C LYS* 3.7 24.7 + - - +
877C ALA* 3.0 27.0 + - - +
892C LEU* 3.5 16.9 - - + +
896C ALA* 3.9 17.1 - - + +
897C ALA* 4.4 11.4 + - - +
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Residues in contact with ILE 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861C ILE* 3.8 29.6 - - + +
864C LEU* 3.7 33.2 - - + -
865C MSE 3.4 31.0 - - + -
869C TYR* 3.7 11.4 - - + +
870C SER 3.1 17.5 + - - +
871C TYR* 3.6 5.6 - - - +
873C ASP* 1.3 74.7 - - - +
875C GLN* 1.3 69.9 + - - +
877C ALA* 3.6 1.7 + - - +
878C LEU* 3.2 34.4 + - + +
888C ALA* 5.3 0.6 - - + +
892C LEU* 3.9 23.5 - - + +
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Residues in contact with GLN 875 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A GLN* 5.1 6.0 + - - +
861C ILE* 4.2 12.3 - - - +
871C TYR* 2.7 65.1 + - + +
872C GLN* 3.3 10.5 - - - +
873C ASP 3.2 0.2 - - - -
874C ILE* 1.3 72.6 - - - +
876C LYS* 1.3 57.1 + - + +
878C LEU* 2.7 45.2 + - - +
879C VAL* 2.9 17.2 + - + +
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Residues in contact with LYS 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872C GLN* 3.0 33.6 + - + +
873C ASP* 3.7 27.6 + - - +
875C GLN* 1.3 79.1 - - + +
877C ALA* 1.3 56.6 + - - +
879C VAL* 3.3 14.2 + - + +
880C ILE* 3.0 38.4 + - + +
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Residues in contact with ALA 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873C ASP 3.0 18.8 + - - +
874C ILE 3.8 4.7 - - - +
876C LYS* 1.3 76.3 - - - +
878C LEU* 1.3 53.1 + - - +
880C ILE* 3.8 3.3 - - - +
881C ALA* 2.9 35.0 + - - +
888C ALA* 3.8 16.4 - - + +
891C ILE* 3.9 24.0 - - + +
892C LEU* 3.8 25.6 - - + -
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Residues in contact with LEU 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861C ILE* 4.2 13.2 - - + -
874C ILE* 3.2 35.6 + - + +
875C GLN* 2.7 27.4 + - - +
877C ALA* 1.3 69.6 - - - +
879C VAL* 1.3 63.2 + - - -
880C ILE 3.1 1.1 - - - -
881C ALA* 4.1 2.0 - - - +
882C GLN* 3.0 3.8 + - - -
883C ASN* 2.8 64.1 + - + +
884C ASN 4.6 1.8 - - - +
885C ILE* 4.8 8.3 - - + +
888C ALA* 3.6 24.0 - - + -
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Residues in contact with VAL 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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875C GLN* 2.9 18.6 + - + +
876C LYS* 3.3 14.3 + - + +
878C LEU* 1.3 75.7 - - - +
880C ILE* 1.3 66.4 + - + +
882C GLN* 3.5 17.7 + - - +
883C ASN* 5.0 2.2 - - - -
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Residues in contact with ILE 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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876C LYS* 3.0 29.0 + - + +
877C ALA* 3.8 1.3 - - - +
879C VAL* 1.3 77.5 - - + +
881C ALA* 1.3 54.0 + - - +
882C GLN* 2.8 17.6 + - - +
887C MSE 3.6 20.9 - - + +
891C ILE* 3.7 24.7 - - + -
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Residues in contact with ALA 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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877C ALA 2.9 25.4 + - - +
878C LEU* 3.4 1.5 + - - -
880C ILE* 1.3 70.8 - - - +
882C GLN* 1.3 58.6 + - - +
883C ASN 3.2 0.4 - - - -
884C ASN* 2.7 58.2 + - - +
887C MSE 3.4 25.6 - - + +
888C ALA* 3.6 13.5 - - + +
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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