Contacts of the helix formed by residues 870 - 881 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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868A GLY 3.7 2.8 + - - -
869A TYR* 1.3 75.6 - - - +
871A TYR* 1.3 63.8 + - - +
872A GLN* 3.9 7.0 + - - +
873A ASP* 3.0 36.7 + - - +
874A ILE* 3.1 21.0 + - - +
897A ALA 4.6 3.8 + - - -
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Residues in contact with TYR 871 (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 ILE* 4.5 15.9 - - + -
865A MSE 4.3 30.7 - - + +
869A TYR 3.7 2.2 + - - -
870A SER* 1.3 71.4 - - - +
872A GLN* 1.3 60.8 + - + +
874A ILE* 3.3 10.5 + - + +
875A GLN* 2.9 74.4 + - + +
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Residues in contact with GLN 872 (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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870A SER* 3.2 7.1 + - - +
871A TYR* 1.3 83.0 - - + +
873A ASP* 1.3 68.0 + - - +
875A GLN* 3.4 8.3 + - - +
876A LYS* 2.9 35.1 + - + +
871C TYR* 4.2 26.2 - - + -
872C GLN* 5.5 9.7 - - - +
875C GLN* 5.1 6.3 + - - +
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Residues in contact with ASP 873 (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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869A TYR* 5.1 0.4 - - + -
870A SER* 3.0 32.4 + - - +
872A GLN* 1.3 79.3 - - - +
874A ILE* 1.3 56.9 + - - +
876A LYS* 3.3 19.7 + - - -
877A ALA* 2.9 31.4 + - - +
892A LEU* 3.8 10.8 - - + -
896A ALA* 3.8 18.2 - - + +
897A ALA* 4.4 9.9 + - - +
895B PHE* 3.6 25.5 - - + -
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Residues in contact with ILE 874 (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 ILE* 3.8 35.0 - - + +
864A LEU* 3.5 34.1 - - + -
865A MSE 3.5 32.3 - - + +
869A TYR* 3.7 21.3 - - + +
870A SER 3.1 15.1 + - - +
871A TYR* 3.3 7.8 + - + +
873A ASP* 1.3 71.6 - - - +
875A GLN* 1.3 69.7 + - - +
877A ALA* 3.3 2.3 + - - +
878A LEU* 2.9 32.4 + - + +
892A LEU* 4.0 12.3 - - + +
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Residues in contact with GLN 875 (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 ILE* 4.3 18.2 - - - +
871A TYR* 2.9 61.1 + - + +
872A GLN* 3.8 4.0 - - - +
874A ILE* 1.3 77.7 - - - +
876A LYS* 1.3 62.7 + - - +
878A LEU* 3.2 10.9 + - - +
879A VAL* 3.0 28.8 + - + +
871C TYR* 3.4 21.4 + - - +
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Residues in contact with LYS 876 (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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872A GLN* 2.9 29.1 + - + +
873A ASP* 3.6 26.4 + - - +
875A GLN* 1.3 76.5 - - - +
877A ALA* 1.3 57.8 + - - +
879A VAL* 3.3 3.2 + - - +
880A ILE* 3.0 36.0 + - + +
894B GLU* 2.9 60.4 + - + +
895B PHE* 3.9 13.0 - - + -
865C MSE 5.2 1.0 - - - +
871C TYR* 3.6 38.7 - - + +
872C GLN* 6.3 0.4 - - - +
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Residues in contact with ALA 877 (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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873A ASP 2.9 17.2 + - - +
874A ILE 3.7 3.8 - - - +
876A LYS* 1.3 75.5 - - - +
878A LEU* 1.3 58.9 + - - +
880A ILE* 3.4 1.0 + - - -
881A ALA* 2.8 32.1 + - - +
888A ALA* 3.9 15.3 - - + +
891A ILE* 3.8 21.2 - - + +
892A LEU* 3.8 26.0 - - + -
895B PHE* 4.1 6.5 - - + -
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Residues in contact with LEU 878 (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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857A LEU* 4.1 18.6 - - + -
861A ILE* 4.1 21.3 - - + -
864A LEU* 6.0 0.7 - - + -
874A ILE* 2.9 37.8 + - + +
875A GLN* 3.8 10.3 - - - +
877A ALA* 1.3 76.6 - - - +
879A VAL* 1.3 60.4 + - + +
881A ALA* 3.5 1.0 + - - -
882A GLN 3.2 2.6 + - - -
883A ASN* 2.8 62.2 + - - +
885A ILE* 4.3 14.6 - - + -
888A ALA* 3.8 21.3 - - + -
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Residues in contact with VAL 879 (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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875A GLN* 3.0 19.5 + - + +
876A LYS* 3.6 7.9 - - - +
878A LEU* 1.3 75.2 - - + +
880A ILE* 1.3 64.9 + - + +
882A GLN 2.9 4.5 + - - -
883A ASN* 5.2 1.1 - - - +
858C SER* 3.6 28.7 - - - +
861C ILE* 4.3 11.2 - - + -
862C GLU* 2.8 65.8 - - + +
865C MSE 4.8 6.5 - - - -
871C TYR* 4.3 17.7 - - + +
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Residues in contact with ILE 880 (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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876A LYS 3.0 21.0 + - - +
877A ALA* 3.9 3.8 - - - +
879A VAL* 1.3 77.2 - - - +
881A ALA* 1.3 57.6 + - - +
882A GLN* 3.2 8.1 + - - +
891A ILE* 4.0 5.4 - - + -
887B MSE 3.8 30.6 - - + +
890B ASN* 3.7 37.0 + - + +
891B ILE* 3.7 27.8 - - + -
894B GLU* 3.9 11.9 - - + -
895B PHE* 3.8 26.9 - - + -
862C GLU* 4.8 3.2 - - - +
865C MSE 3.7 21.3 - - + -
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Residues in contact with ALA 881 (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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877A ALA 2.8 18.2 + - - +
878A LEU* 3.9 3.8 - - - +
879A VAL 3.2 0.2 - - - -
880A ILE* 1.3 75.4 - - - +
882A GLN* 1.3 70.4 + - - +
884A ASN* 3.0 38.4 + - - +
887A MSE 3.8 24.0 - - + +
888A ALA* 3.7 15.9 - - + +
891A ILE* 4.3 2.0 - - + -
887B MSE 5.0 1.4 - - - +
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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