Contacts of the helix formed by residues 208 - 235 (chain U) in PDB entry 5MQF
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 208 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207U MSE 3.8 29.6 - - - +
209U PRO* 3.9 28.5 - - - -
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Residues in contact with PRO 209 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208U ASP* 3.9 27.4 - - - -
210U GLU* 3.8 28.7 - - - -
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Residues in contact with GLU 210 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209U PRO* 3.8 26.2 - - - -
211U ALA* 3.8 28.9 - - - +
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Residues in contact with ALA 211 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210U GLU* 3.8 25.4 - - - +
212U ARG* 3.8 29.4 - - - +
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Residues in contact with ARG 212 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211U ALA* 3.8 28.9 - - - +
213U GLU* 3.8 26.7 - - - +
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Residues in contact with GLU 213 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212U ARG* 3.8 28.9 - - - +
214U GLN* 3.8 26.0 - - - +
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Residues in contact with GLN 214 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213U GLU* 3.8 29.2 - - - +
215U ALA* 3.8 26.2 - - - +
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Residues in contact with ALA 215 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214U GLN* 3.8 28.7 - - - +
216U TYR* 3.8 25.8 - - - +
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Residues in contact with TYR 216 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215U ALA* 3.8 28.7 - - - +
217U GLN* 3.8 26.5 - - - +
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Residues in contact with GLN 217 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216U TYR* 3.8 26.0 - - - +
218U GLU* 3.8 28.7 - - - +
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Residues in contact with GLU 218 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217U GLN* 3.8 28.9 - - - +
219U ARG* 3.8 26.2 - - - +
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Residues in contact with ARG 219 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174U MSE 4.2 24.2 - - - +
218U GLU* 3.8 29.4 - - - +
220U ARG* 3.8 24.9 - - - +
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Residues in contact with ARG 220 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219U ARG* 3.8 28.7 - - - +
221U PHE* 3.8 26.9 - - - +
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Residues in contact with PHE 221 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220U ARG* 3.8 28.0 - - - +
222U LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 222 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221U PHE* 3.8 29.2 - - - +
223U SER* 3.8 26.5 - - - +
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Residues in contact with SER 223 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222U LEU* 3.8 25.8 - - - +
224U GLN* 3.8 29.2 - - - +
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Residues in contact with GLN 224 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223U SER* 3.8 29.4 - - - +
225U LEU* 3.8 25.6 - - - +
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Residues in contact with LEU 225 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224U GLN* 3.8 25.6 - - - +
226U ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 226 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225U LEU* 3.8 28.3 - - - +
227U GLN* 3.8 27.1 - - - +
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Residues in contact with GLN 227 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226U ILE* 3.8 26.5 - - - +
228U LYS* 3.8 28.7 - - - +
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Residues in contact with LYS 228 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227U GLN* 3.8 29.2 - - - +
229U PHE* 3.8 25.6 - - - +
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Residues in contact with PHE 229 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228U LYS* 3.8 26.7 - - - +
230U ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 230 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229U PHE* 3.8 29.2 - - - +
231U SER* 3.8 26.7 - - - +
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Residues in contact with SER 231 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230U ILE* 3.8 26.2 - - - +
232U VAL* 3.8 28.3 - - - +
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Residues in contact with VAL 232 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231U SER* 3.8 28.5 - - - +
233U LEU* 3.8 25.8 - - - +
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Residues in contact with LEU 233 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232U VAL* 3.8 25.8 - - - +
234U LYS* 3.8 29.6 - - - +
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Residues in contact with LYS 234 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233U LEU* 3.8 25.6 - - - +
235U SER* 3.8 28.7 - - - +
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Residues in contact with SER 235 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234U LYS* 3.8 29.4 - - - +
236U VAL* 3.8 25.8 - - - +
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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
------------------------------------------------------------
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