Contacts of the helix formed by residues 895 - 905 (chain A) in PDB entry 2OOQ
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 ASP 895 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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891A ILE* 4.2 8.7 - - + -
892A ARG* 2.8 58.8 + - + +
894A ALA* 1.3 72.9 - - - +
896A LEU* 1.3 58.4 + - - +
897A LEU 3.4 2.2 - - - -
898A GLN* 3.4 14.0 + - + +
899A HIS* 2.9 27.9 + - + +
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Residues in contact with LEU 896 (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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891A ILE* 4.2 13.5 - - + -
892A ARG 3.2 5.9 + - - +
893A VAL* 3.0 19.0 + - - +
894A ALA 3.5 0.4 - - - -
895A ASP* 1.3 74.9 - - - +
897A LEU* 1.3 61.3 + - - +
899A HIS* 3.3 10.6 + - + +
900A ILE* 2.9 54.1 + - + +
1132A VAL* 4.2 22.2 - - + -
1134A ILE* 4.9 8.7 - - + -
1159A HIS 5.2 0.2 - - - +
1162A ILE* 3.8 28.5 - - + -
1163A LEU* 3.9 22.2 - - + +
1166A CYS* 4.4 12.1 - - + -
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Residues in contact with LEU 897 (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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893A VAL 4.7 0.6 + - - -
894A ALA 5.2 1.9 + - - +
895A ASP 3.4 0.4 - - - -
896A LEU* 1.3 78.7 - - - +
898A GLN* 1.3 64.9 + - + +
900A ILE* 3.2 2.8 + - - +
901A THR* 3.0 37.9 + - - +
1163A LEU* 3.7 34.6 - - + +
1167A LEU* 4.8 16.6 - - + -
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Residues in contact with GLN 898 (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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895A ASP* 3.4 15.1 + - + +
896A LEU 3.3 0.2 - - - -
897A LEU* 1.3 82.0 - - + +
899A HIS* 1.3 62.5 + - - +
901A THR* 3.4 7.0 + - - +
902A GLN* 3.0 25.7 + - - +
905A ARG* 5.5 1.1 + - - +
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Residues in contact with HIS 899 (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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891A ILE* 3.7 45.1 - - + +
895A ASP 2.9 15.3 + - - +
896A LEU* 3.4 20.0 - - + +
898A GLN* 1.3 76.1 - - - +
900A ILE* 1.3 62.8 + - + +
902A GLN* 3.3 6.5 + - - +
903A MET* 2.9 66.9 + - + +
909A TYR* 5.8 1.3 - + - -
914A GLU* 4.9 7.0 + - - -
1159A HIS* 4.6 14.8 + + - -
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Residues in contact with ILE 900 (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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896A LEU* 2.9 37.1 + - + +
897A LEU* 3.8 4.0 - - - +
899A HIS* 1.3 75.5 - - + +
901A THR* 1.3 57.2 + - - +
903A MET* 3.2 8.2 + - - +
904A LYS* 2.9 59.1 + - + +
911A PHE* 4.3 7.2 - - + -
1159A HIS* 3.6 44.9 - - + +
1160A ASP* 4.0 6.5 - - - +
1163A LEU* 3.7 28.0 - - + -
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Residues in contact with THR 901 (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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897A LEU* 3.0 30.2 + - - +
898A GLN* 3.6 7.4 - - - -
900A ILE* 1.3 75.7 - - - +
902A GLN* 1.3 65.8 + - - +
904A LYS* 2.9 9.8 + - - +
905A ARG* 2.9 59.1 + - + +
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Residues in contact with GLN 902 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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898A GLN 3.0 17.2 + - - +
899A HIS* 3.7 6.3 - - - +
901A THR* 1.3 79.0 - - - +
903A MET* 1.3 62.6 + - + +
905A ARG* 3.3 35.6 + - - +
908A GLY 5.6 0.9 + - - -
909A TYR 3.9 10.2 - - - +
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Residues in contact with MET 903 (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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899A HIS* 2.9 51.5 + - + +
900A ILE 3.5 4.7 - - - +
901A THR 3.1 0.2 - - - -
902A GLN* 1.3 78.3 - - + +
904A LYS* 1.3 57.4 + - - +
905A ARG 4.2 1.4 - - - +
909A TYR* 3.7 28.0 - - + +
910A GLY* 3.2 39.8 - - - +
911A PHE* 3.2 47.3 + - + +
914A GLU* 3.5 35.0 - - + +
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Residues in contact with LYS 904 (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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900A ILE* 2.9 32.5 + - + +
901A THR* 2.9 7.8 + - - +
903A MET* 1.3 77.4 - - - +
905A ARG* 1.3 61.3 + - - +
906A GLY* 3.4 3.3 + - - -
911A PHE* 3.7 13.5 - - + -
1156A VAL* 4.0 19.7 - - + -
1160A ASP* 2.9 33.6 + - - -
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Residues in contact with ARG 905 (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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898A GLN 5.5 0.8 + - - -
901A THR* 2.9 42.1 + - + +
902A GLN* 3.3 27.6 + - - +
903A MET 4.2 4.0 - - - +
904A LYS* 1.3 75.6 - - - +
906A GLY* 1.3 58.5 - - - +
907A GLN* 2.9 38.5 + - - +
908A GLY 4.0 9.2 + - - +
910A GLY* 5.0 1.2 - - - -
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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