Contacts of the helix formed by residues 159 - 190 (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 VAL 159 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158U GLU* 3.8 29.2 - - - +
160U ASP* 3.8 28.5 - - - +
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Residues in contact with ASP 160 (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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159U VAL* 3.8 26.5 - - - +
161U LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 161 (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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160U ASP* 3.8 28.7 - - - +
162U ILE* 3.8 26.7 - - - +
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Residues in contact with ILE 162 (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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161U LEU* 3.8 28.7 - - - +
163U ARG* 3.8 26.7 - - - +
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Residues in contact with ARG 163 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157U LEU* 4.7 19.3 - - - +
162U ILE* 3.8 29.2 - - - +
164U SER* 3.8 26.5 - - - +
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Residues in contact with SER 164 (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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163U ARG* 3.8 28.9 - - - +
165U GLN* 3.8 25.6 - - - +
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Residues in contact with GLN 165 (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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164U SER* 3.8 28.5 - - - +
166U VAL* 3.8 28.0 - - - +
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Residues in contact with VAL 166 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165U GLN* 3.8 29.4 - - - +
167U GLN* 3.8 26.2 - - - +
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Residues in contact with GLN 167 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166U VAL* 3.8 26.0 - - - +
168U GLN* 3.8 28.9 - - - +
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Residues in contact with GLN 168 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167U GLN* 3.8 28.5 - - - +
169U LEU* 3.8 26.5 - - - +
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Residues in contact with LEU 169 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168U GLN* 3.8 27.1 - - - +
170U ILE* 3.8 28.7 - - - +
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Residues in contact with ILE 170 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169U LEU* 3.8 29.4 - - - +
171U SER* 3.8 28.7 - - - +
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Residues in contact with SER 171 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170U ILE* 3.8 28.9 - - - +
172U LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 172 (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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171U SER* 3.8 28.7 - - - +
173U PRO* 3.8 26.0 - - - -
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Residues in contact with PRO 173 (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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172U LEU* 3.8 25.8 - - - -
174U MSE 3.8 28.5 - - - -
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Residues in contact with MSE 174 (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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173U PRO* 3.8 24.2 - - - -
175U TRP* 3.8 29.4 - - - +
219U ARG* 4.2 24.5 - - - +
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Residues in contact with TRP 175 (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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174U MSE 3.8 26.5 - - - +
176U MSE 3.8 28.5 - - - +
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Residues in contact with MSE 176 (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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175U TRP* 3.8 24.0 - - - +
177U GLY* 3.8 28.9 - - - +
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Residues in contact with GLY 177 (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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176U MSE 3.8 28.7 - - - +
178U LEU* 3.8 25.6 - - - +
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Residues in contact with LEU 178 (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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177U GLY* 3.8 29.2 - - - +
179U GLN* 3.8 29.2 - - - +
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Residues in contact with GLN 179 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178U LEU* 3.8 29.4 - - - +
180U LEU* 3.8 28.9 - - - +
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Residues in contact with LEU 180 (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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179U GLN* 3.8 29.2 - - - +
181U ALA* 3.8 26.2 - - - +
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Residues in contact with ALA 181 (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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180U LEU* 3.8 29.6 - - - +
182U ARG* 3.8 26.0 - - - +
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Residues in contact with ARG 182 (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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181U ALA* 3.8 26.5 - - - +
183U LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 183 (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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182U ARG* 3.8 25.8 - - - +
184U GLU* 3.8 29.4 - - - +
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Residues in contact with GLU 184 (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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183U LEU* 3.8 28.7 - - - +
185U LEU* 3.8 26.2 - - - +
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Residues in contact with LEU 185 (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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184U GLU* 3.8 29.4 - - - +
186U GLU* 3.8 25.8 - - - +
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Residues in contact with GLU 186 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185U LEU* 3.8 26.5 - - - +
187U LEU* 3.8 29.2 - - - +
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Residues in contact with LEU 187 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186U GLU* 3.8 28.5 - - - +
188U LYS* 3.8 25.8 - - - +
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Residues in contact with LYS 188 (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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187U LEU* 3.8 25.1 - - - +
189U LYS* 3.8 29.2 - - - +
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Residues in contact with LYS 189 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188U LYS* 3.8 29.4 - - - +
190U THR* 3.8 25.8 - - - +
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Residues in contact with THR 190 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189U LYS* 3.8 28.7 - - - +
191U PRO* 3.8 28.3 - - - -
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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
------------------------------------------------------------
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