Contacts of the helix formed by residues 910 - 918 (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 GLY 910 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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902A GLN 5.0 0.4 - - - -
903A MET* 3.2 27.8 - - - +
905A ARG 5.0 2.0 - - - -
908A GLY 3.2 5.8 + - - -
909A TYR* 1.3 74.6 - - - +
911A PHE* 1.3 61.7 + - - -
912A LYS 3.4 2.5 - - - -
913A GLU* 3.4 8.1 + - - +
914A GLU* 3.1 25.5 + - - +
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Residues in contact with PHE 911 (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* 3.9 11.9 - - + -
903A MET* 3.2 55.8 + - + +
904A LYS* 3.7 23.8 - - + -
910A GLY* 1.3 69.2 - - - -
912A LYS* 1.3 61.0 + - - +
914A GLU* 4.0 1.3 - - - +
915A TYR* 2.9 32.7 + - - +
1152A GLU* 4.1 6.9 - - + +
1155A TYR* 3.9 18.6 - + + -
1156A VAL* 3.6 35.7 - - + -
1159A HIS* 3.6 49.8 - + + -
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Residues in contact with LYS 912 (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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910A GLY 3.4 0.6 - - - -
911A PHE* 1.3 77.8 - - - +
913A GLU* 1.3 58.0 + - - +
915A TYR* 3.8 1.7 - - - +
916A GLU* 2.9 55.7 + - + +
1152A GLU* 3.7 29.6 + - - +
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Residues in contact with GLU 913 (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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909A TYR* 3.4 34.3 - - + +
910A GLY 3.4 10.5 + - - +
911A PHE 3.3 0.2 - - - -
912A LYS* 1.3 79.6 - - - +
914A GLU* 1.3 63.1 + - - +
916A GLU* 3.1 12.3 + - + +
917A ALA* 3.1 22.3 + - + +
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Residues in contact with GLU 914 (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* 4.9 7.3 + - - -
903A MET* 3.5 18.4 - - + +
909A TYR* 2.6 41.4 + - + +
910A GLY 3.1 16.2 + - - +
911A PHE 4.0 2.2 - - - +
912A LYS 3.3 0.2 - - - -
913A GLU* 1.3 78.6 - - - +
915A TYR* 1.3 63.8 + - - +
917A ALA* 2.9 20.3 + - - +
918A LEU 3.5 0.3 + - - -
1135A PHE* 3.4 38.7 + - + +
1155A TYR* 2.5 31.1 + - + +
1159A HIS* 4.1 7.6 + - - -
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Residues in contact with TYR 915 (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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911A PHE 2.9 17.9 + - - +
912A LYS 3.8 2.5 - - - +
914A GLU* 1.3 75.9 - - - +
916A GLU* 1.3 70.1 + - + +
918A LEU* 3.1 41.3 + - + +
1142A ARG* 3.2 27.4 + - - -
1149A VAL* 3.8 5.4 - - + -
1150A GLN 2.7 33.1 + - - -
1151A THR* 3.3 18.4 - - - -
1152A GLU* 3.5 31.2 - - + -
1155A TYR* 3.7 23.4 - - + -
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Residues in contact with GLU 916 (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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912A LYS* 2.9 40.9 + - + +
913A GLU* 3.1 12.0 + - + +
915A TYR* 1.3 82.6 - - + +
917A ALA* 1.3 59.4 + - - +
918A LEU 3.4 6.2 + - - +
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Residues in contact with ALA 917 (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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909A TYR* 5.5 2.5 - - + +
913A GLU* 3.1 10.5 + - + +
914A GLU* 2.9 15.5 + - - +
916A GLU* 1.3 75.2 - - - +
918A LEU* 1.3 66.0 + - - +
919A PRO* 3.7 3.1 - - - +
1135A PHE* 3.9 20.6 - - + -
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Residues in contact with LEU 918 (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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914A GLU 4.0 0.7 - - - +
915A TYR* 3.1 46.2 + - + +
916A GLU 3.9 6.9 - - - +
917A ALA* 1.3 80.2 - - - +
919A PRO* 1.3 71.1 - - + +
920A GLU* 3.2 6.1 + - - +
1135A PHE* 3.6 31.4 - - + +
1138A VAL* 3.7 22.9 - - + -
1139A ARG* 3.7 31.4 - - - +
1142A ARG* 3.4 17.8 + - - +
1155A TYR* 4.0 12.8 - - + -
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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