Contacts of the helix formed by residues 185 - 193 (chain F) in PDB entry 1MKD
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 GLN 185 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183F THR* 4.9 0.2 - - - +
184F GLU* 1.3 94.5 - - + +
186F GLU* 1.3 81.5 + - - +
187F ASP 2.9 6.5 - - - -
188F VAL* 2.8 33.5 + - + +
189F LEU* 2.9 14.2 + - - +
209F LEU* 4.2 32.5 - - + +
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Residues in contact with GLU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F THR* 3.2 48.8 + - - +
184F GLU 3.1 1.2 - - - -
185F GLN* 1.3 95.9 + - - +
187F ASP* 1.3 60.4 + - - +
189F LEU* 3.8 17.1 - - + +
190F ALA* 3.3 21.0 + - - +
209F LEU 5.8 1.3 - - - +
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Residues in contact with ASP 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F THR* 2.7 28.5 + - - +
184F GLU* 2.9 11.6 - - - +
185F GLN 2.9 0.2 - - - -
186F GLU* 1.3 79.6 - - - +
188F VAL* 1.3 60.3 + - + +
190F ALA* 3.4 6.7 + - - +
191F LYS* 3.0 28.6 + - - +
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Residues in contact with VAL 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F GLU* 4.5 5.2 - - - +
185F GLN* 2.8 26.6 + - + +
187F ASP* 1.3 76.9 - - + +
189F LEU* 1.3 59.7 + - - +
191F LYS* 3.1 29.2 + - - +
192F GLU* 2.8 38.3 + - + +
205F ARG* 5.7 3.6 - - - -
209F LEU* 4.0 20.6 - - + -
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Residues in contact with LEU 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185F GLN 2.9 10.6 + - - +
186F GLU* 3.8 18.2 - - + +
188F VAL* 1.3 76.7 - - - +
190F ALA* 1.3 64.7 + - + +
192F GLU* 3.0 5.3 + - - +
193F LEU* 2.9 37.5 + - + +
206F ILE* 3.9 20.0 - - + +
209F LEU* 3.6 48.1 - - + +
210F SER* 3.9 15.7 - - - +
217F VAL* 4.6 10.1 - - + -
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Residues in contact with ALA 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186F GLU 3.3 15.2 + - - +
187F ASP* 3.7 7.6 - - - +
188F VAL 3.3 0.2 - - - -
189F LEU* 1.3 81.8 - - + +
191F LYS* 1.3 57.6 + - - +
193F LEU* 3.6 13.9 + - - +
194F GLU* 3.1 23.4 + - - +
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Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F ASP 3.0 14.0 + - - +
188F VAL* 3.1 31.7 + - - +
190F ALA* 1.3 77.1 - - - +
192F GLU* 1.3 79.5 + - - +
194F GLU* 3.1 37.5 - - - +
195F ASP* 4.2 5.5 - - - +
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Residues in contact with GLU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F VAL* 2.8 22.8 + - + +
189F LEU* 3.0 6.7 + - - +
191F LYS* 1.3 88.3 - - - +
193F LEU* 1.3 57.9 + - - +
194F GLU 2.9 10.8 + - - -
195F ASP* 3.0 21.9 + - - +
201F LEU* 3.5 13.4 - - + +
202F HIS* 4.5 7.3 - - - +
205F ARG* 3.0 43.6 + - - +
206F ILE* 3.7 23.3 - - + -
209F LEU* 3.8 17.5 - - + -
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Residues in contact with LEU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F LEU* 2.9 31.4 + - + +
190F ALA* 3.9 11.7 - - - +
191F LYS 3.3 0.2 - - - -
192F GLU* 1.3 75.2 - - - +
194F GLU* 1.3 60.5 + - - +
195F ASP 3.1 1.2 + - - -
196F VAL* 3.3 28.0 + - + +
201F LEU* 4.8 2.0 - - + -
206F ILE* 3.8 24.5 - - + -
217F VAL* 3.4 36.1 - - + -
218F ILE* 4.2 8.3 - - + -
221F THR* 3.7 35.1 - - + +
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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