Contacts of the helix formed by residues 182 - 198 (chain U) in PDB entry 3MQT
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 SER 182 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181U VAL* 1.3 76.6 - - - +
183U ASP* 1.3 59.3 + - - +
184U LYS* 3.4 10.9 + - - +
185U GLU* 3.0 39.8 + - - +
186U ILE* 3.0 27.9 + - - +
210U ARG* 3.6 3.6 - - - +
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Residues in contact with ASP 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 SER* 1.3 71.2 - - - +
184U LYS* 1.3 57.9 + - - +
186U ILE* 3.2 7.7 + - - +
187U VAL* 2.9 32.2 + - - +
210U ARG* 2.9 32.9 + - - +
211U TRP* 2.8 26.8 + - - -
216U LYS* 3.4 33.9 - - - +
219U TRP* 3.8 13.9 - - + -
220U THR* 3.5 16.9 + - - +
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Residues in contact with LYS 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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182U SER* 3.4 10.7 + - - +
183U ASP* 1.3 76.5 - - - +
185U GLU* 1.3 63.5 + - + +
187U VAL* 3.1 21.8 + - + +
188U ALA* 3.1 20.5 + - + +
191U ARG* 4.5 8.3 - - - +
219U TRP* 3.3 41.0 - - + -
223U GLN* 4.7 7.1 + - - +
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Residues in contact with GLU 185 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149U LEU* 3.9 20.3 - - + +
180U LYS 4.6 1.2 - - - +
181U VAL* 3.5 17.8 - - + +
182U SER* 3.0 39.0 + - - +
184U LYS* 1.3 74.5 - - + +
186U ILE* 1.3 53.3 + - - +
188U ALA* 3.1 10.0 + - - +
189U TYR* 2.8 35.2 + - - +
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Residues in contact with ILE 186 (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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149U LEU* 4.5 8.7 - - + -
175U ILE* 3.6 45.8 - - + -
181U VAL* 3.9 17.5 - - + -
182U SER 3.0 17.9 + - - +
183U ASP* 3.3 10.5 - - - +
185U GLU* 1.3 72.6 - - - +
187U VAL* 1.3 64.5 + - - +
189U TYR* 3.1 16.0 + - + +
190U LEU* 2.8 35.7 + - + +
210U ARG* 3.7 24.2 - - - +
211U TRP* 4.4 2.7 - - + -
220U THR* 4.4 13.7 - - + -
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Residues in contact with VAL 187 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183U ASP 2.9 17.5 + - - +
184U LYS* 3.3 22.4 - - + +
186U ILE* 1.3 76.4 - - - +
188U ALA* 1.3 62.8 + - - +
190U LEU* 3.3 0.7 + - - -
191U ARG* 2.9 61.9 + - - +
219U TRP* 4.0 11.2 - - + -
220U THR* 3.8 33.9 - - + +
223U GLN* 4.0 11.9 - - + -
224U LEU* 3.8 13.4 - - + +
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Residues in contact with ALA 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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184U LYS* 3.1 13.7 + - + +
185U GLU* 3.1 11.0 + - - +
187U VAL* 1.3 77.2 - - - +
189U TYR* 1.3 58.0 + - - +
191U ARG* 3.3 8.6 + - - +
192U GLU* 2.9 31.3 + - - +
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Residues in contact with TYR 189 (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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149U LEU* 4.2 34.1 - - + -
152U ILE* 3.4 29.3 - - + +
153U VAL* 3.6 31.0 - - + -
156U TYR* 3.4 8.0 - - - -
174U CYS 2.8 27.9 + - - -
175U ILE* 4.4 12.7 - - + -
176U ILE 5.0 2.1 + - - -
185U GLU 2.8 12.9 + - - +
186U ILE* 3.2 24.9 - - + +
188U ALA* 1.3 76.2 - - - +
190U LEU* 1.3 76.4 + - + +
192U GLU* 3.0 11.8 + - - +
193U LEU* 3.0 37.9 + - + +
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Residues in contact with LEU 190 (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 VAL* 4.2 14.1 - - + -
174U CYS 5.6 0.2 - - - +
175U ILE* 4.2 6.7 - - + -
186U ILE* 2.8 32.2 + - + +
189U TYR* 1.3 91.3 - - + +
191U ARG* 1.3 66.2 + - - +
193U LEU* 3.4 4.8 + - + -
194U ARG 3.1 17.3 + - - -
203U MET* 3.6 10.1 - - + +
205U VAL* 4.0 41.3 - - + -
221U PHE* 4.4 7.4 - - + -
224U LEU* 3.6 33.7 - - + -
227U ILE* 3.8 11.1 - - + +
229U LEU* 5.3 0.7 - - + -
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Residues in contact with ARG 191 (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 LYS* 4.5 7.3 - - - +
187U VAL* 2.9 42.6 + - - +
188U ALA* 3.7 7.0 - - - +
190U LEU* 1.3 76.4 - - - +
192U GLU* 1.3 62.3 + - - +
194U ARG* 3.2 4.3 + - - +
195U GLU* 3.2 28.6 + - - +
223U GLN* 2.8 36.3 + - - +
224U LEU* 3.8 10.9 - - + +
226U ASP* 3.0 26.2 + - - -
227U ILE* 4.0 15.4 - - + +
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Residues in contact with GLU 192 (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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150U SER* 5.1 9.4 + - - -
153U VAL* 3.6 33.7 - - + +
154U GLU* 5.4 0.9 - - - +
157U LYS* 4.6 6.9 + - - -
188U ALA 2.9 13.7 + - - +
189U TYR* 3.3 11.5 - - - +
191U ARG* 1.3 74.4 - - - +
193U LEU* 1.3 64.4 - - - +
195U GLU* 3.1 21.7 + - - +
196U VAL* 3.0 27.5 + - + +
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Residues in contact with LEU 193 (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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153U VAL* 3.8 26.2 - - + -
156U TYR* 4.0 27.8 - - + -
160U ILE* 4.5 9.9 - - + -
173U VAL* 3.7 31.6 - - + -
189U TYR* 3.0 43.9 + - + +
190U LEU* 3.7 11.9 - - + +
191U ARG 3.3 0.2 - - - -
192U GLU* 1.3 78.0 - - - +
194U ARG* 1.3 56.1 + - - +
196U VAL* 3.3 5.3 + - + +
197U ILE* 2.8 36.8 + - + +
203U MET* 3.8 10.5 - - + -
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Residues in contact with ARG 194 (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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190U LEU 3.1 11.4 + - - +
191U ARG 3.2 6.9 + - - +
193U LEU* 1.3 72.7 - - - +
195U GLU* 1.3 58.4 + - + +
197U ILE* 3.1 3.8 + - - +
198U GLY* 2.7 55.7 + - - -
199U TRP* 3.7 41.5 + - + +
201U MET 3.1 22.0 + - - -
202U ASP* 5.0 1.8 + - - +
203U MET* 3.6 42.6 - - - +
227U ILE* 2.9 43.0 + - + -
228U ASP* 3.1 22.0 + - - +
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Residues in contact with GLU 195 (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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191U ARG* 3.2 17.5 + - - +
192U GLU* 3.1 20.7 + - - +
194U ARG* 1.3 79.7 - - + +
196U VAL* 1.3 64.2 + - + +
198U GLY* 3.5 9.1 + - - -
199U TRP* 5.7 3.1 - - - +
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Residues in contact with VAL 196 (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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153U VAL* 4.7 9.9 - - + -
157U LYS* 4.2 42.2 - - + +
160U ILE* 3.8 29.1 - - + +
164U LYS* 2.6 33.5 + - - +
192U GLU* 3.0 19.3 + - + +
193U LEU* 3.7 9.0 - - + +
195U GLU* 1.3 78.6 - - + +
197U ILE* 1.3 52.4 + - - +
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Residues in contact with ILE 197 (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 ILE* 3.9 26.5 - - + -
164U LYS* 3.0 21.4 - - - -
171U VAL* 4.0 13.5 - - + -
173U VAL* 3.9 24.0 - - + -
193U LEU 2.8 24.8 + - - +
194U ARG* 3.8 12.1 - - - +
196U VAL* 1.3 72.1 - - - +
198U GLY* 1.3 69.3 + - - +
200U ASP* 5.0 1.9 + - - +
201U MET* 3.8 34.8 - - + +
203U MET* 3.6 33.4 - - + -
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Residues in contact with GLY 198 (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 LYS* 4.9 2.5 - - - -
194U ARG* 2.7 44.3 + - - -
195U GLU* 3.5 7.3 + - - -
196U VAL 3.3 2.4 - - - -
197U ILE* 1.3 78.9 - - - +
199U TRP* 1.3 70.8 + - - -
200U ASP 3.6 1.5 + - - -
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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