Contacts of the helix formed by residues 186 - 204 (chain Q) in PDB entry 5KHU
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 LEU 186 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185Q PRO* 3.8 26.9 - - - -
187Q GLU* 3.8 28.5 - - - +
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Residues in contact with GLU 187 (chain Q).
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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186Q LEU* 3.8 27.1 - - - +
188Q ARG* 3.8 28.7 - - - +
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Residues in contact with ARG 188 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Q GLU* 3.8 29.2 - - - +
189Q LEU* 3.8 25.8 - - - +
191Q SER* 4.5 15.9 - - - +
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Residues in contact with LEU 189 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Q ARG* 3.8 25.8 - - - +
190Q GLN* 3.8 28.5 - - - +
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Residues in contact with GLN 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Q LEU* 3.8 29.4 - - - +
191Q SER* 3.8 24.2 - - - +
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Residues in contact with SER 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Q ARG* 4.5 16.2 - - - +
190Q GLN* 3.8 26.5 - - - +
192Q GLN* 3.8 28.9 - - - +
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Residues in contact with GLN 192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q SER* 3.8 27.6 - - - +
193Q HIS* 3.8 30.1 - - - +
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Residues in contact with HIS 193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Q GLN* 3.8 26.5 - - - +
194Q ARG* 3.8 28.7 - - - +
196Q PHE* 4.5 15.0 - - - +
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Residues in contact with ARG 194 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Q HIS* 3.8 29.8 - - - +
195Q GLN* 3.8 25.6 - - - +
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Residues in contact with GLN 195 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194Q ARG* 3.8 24.9 - - - +
196Q PHE* 3.8 29.6 - - - +
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Residues in contact with PHE 196 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Q HIS* 4.5 16.8 - - - +
195Q GLN* 3.8 29.2 - - - +
197Q GLN* 3.8 27.1 - - - +
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Residues in contact with GLN 197 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196Q PHE* 3.8 26.2 - - - +
198Q ALA* 3.8 29.2 - - - +
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Residues in contact with ALA 198 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197Q GLN* 3.8 29.2 - - - +
199Q ARG* 3.8 27.1 - - - +
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Residues in contact with ARG 199 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198Q ALA* 3.8 25.4 - - - +
200Q VAL* 3.8 29.4 - - - +
202Q ARG* 4.3 18.4 - - - +
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Residues in contact with VAL 200 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Q ARG* 3.8 25.6 - - - +
201Q SER* 3.8 28.9 - - - +
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Residues in contact with SER 201 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200Q VAL* 3.8 29.4 - - - +
202Q ARG* 3.8 25.4 - - - +
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Residues in contact with ARG 202 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Q ARG* 4.3 19.7 - - - +
201Q SER* 3.8 29.6 - - - +
203Q GLN* 3.8 26.2 - - - +
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Residues in contact with GLN 203 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202Q ARG* 3.8 29.2 - - - +
204Q THR* 3.8 27.6 - - - +
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Residues in contact with THR 204 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203Q GLN* 3.8 28.7 - - - +
205Q LEU* 3.8 25.4 - - - +
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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