Contacts of the helix formed by residues 182 - 198 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181W VAL* 1.3 76.3 - - - +
183W ASP* 1.3 59.0 + - - +
184W LYS* 3.3 11.2 + - - +
185W GLU* 3.0 39.5 + - - +
186W ILE* 3.0 26.2 + - - +
210W ARG* 3.5 2.9 - - - +
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Residues in contact with ASP 183 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182W SER* 1.3 71.4 - - - +
184W LYS* 1.3 56.3 + - - +
186W ILE* 2.9 7.5 + - - +
187W VAL* 2.8 37.1 + - - +
210W ARG* 2.8 32.4 + - - +
211W TRP* 2.7 26.4 + - - -
216W LYS* 3.1 33.1 - - - +
219W TRP* 4.0 13.5 - - + -
220W THR* 3.3 16.8 + - - +
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Residues in contact with LYS 184 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182W SER* 3.3 8.7 + - - +
183W ASP* 1.3 77.2 - - - +
185W GLU* 1.3 62.3 + - + +
187W VAL* 3.4 22.9 + - + +
188W ALA* 3.2 21.7 + - + +
191W ARG* 5.5 1.8 - - - +
219W TRP* 3.5 37.4 - - + -
223W GLN* 4.5 8.5 + - - +
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Residues in contact with GLU 185 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149W LEU* 3.7 19.3 - - + +
180W LYS 4.5 2.1 - - - +
181W VAL* 3.4 17.1 - - + +
182W SER* 3.0 44.5 + - - +
184W LYS* 1.3 75.3 - - + +
186W ILE* 1.3 59.1 + - - +
188W ALA* 3.4 7.0 + - - +
189W TYR* 3.0 27.7 + - - +
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Residues in contact with ILE 186 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149W LEU* 4.2 17.9 - - + -
175W ILE* 3.6 45.5 - - + -
178W ASN* 6.0 0.2 - - + -
181W VAL* 3.5 21.5 - - + -
182W SER 3.0 17.0 + - - +
183W ASP* 2.9 11.5 + - - +
185W GLU* 1.3 72.9 - - - +
187W VAL* 1.3 67.4 + - - +
189W TYR* 3.3 6.8 + - + +
190W LEU* 2.9 34.5 + - + +
210W ARG* 3.6 23.6 - - - +
211W TRP* 4.3 11.4 - - + -
220W THR* 4.6 3.6 - - + -
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Residues in contact with VAL 187 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183W ASP 2.8 21.5 + - - +
184W LYS* 3.5 19.5 - - - +
186W ILE* 1.3 73.3 - - - +
188W ALA* 1.3 57.2 + - - +
190W LEU 3.4 0.2 + - - -
191W ARG* 3.0 58.0 + - - +
219W TRP* 3.9 17.7 - - + -
220W THR* 4.0 16.8 - - + +
223W GLN* 3.8 22.7 - - + -
224W LEU* 3.5 19.8 - - + +
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Residues in contact with ALA 188 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195H GLU* 5.0 17.3 - - - +
184W LYS* 3.2 13.0 + - + +
185W GLU* 3.8 9.6 - - - +
186W ILE 3.3 0.2 - - - -
187W VAL* 1.3 81.1 - - - +
189W TYR* 1.3 56.8 + - - +
191W ARG* 3.4 8.8 + - - +
192W GLU* 2.9 30.4 + - - +
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Residues in contact with TYR 189 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149W LEU* 3.9 41.7 - - + -
152W ILE* 3.6 17.0 - - + +
153W VAL* 3.6 28.9 - - + +
156W TYR* 3.5 17.2 - - - -
174W CYS 2.6 28.9 + - - -
175W ILE* 4.2 12.9 - - + -
176W ILE 4.8 1.7 + - - -
185W GLU 3.0 18.9 + - - +
186W ILE* 3.4 11.9 - - + +
188W ALA* 1.3 76.5 - - - +
190W LEU* 1.3 80.9 + - + +
192W GLU* 3.3 10.3 + - - +
193W LEU* 3.1 37.7 + - + +
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Residues in contact with LEU 190 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173W VAL* 4.4 5.2 - - + -
174W CYS 5.4 0.2 - - - +
175W ILE* 4.3 6.5 - - + -
186W ILE* 2.9 31.7 + - + +
189W TYR* 1.3 96.4 - - + +
191W ARG* 1.3 66.4 + - - +
193W LEU* 3.3 11.7 + - + +
194W ARG 3.1 17.3 + - - -
203W MET* 3.7 4.9 - - + +
205W VAL* 4.0 40.8 - - + -
221W PHE* 4.4 7.4 - - + -
224W LEU* 3.5 32.3 - - + -
227W ILE* 3.6 18.4 - - + +
229W LEU* 5.2 0.4 - - + -
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Residues in contact with ARG 191 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184W LYS* 5.5 1.8 - - - +
187W VAL* 3.0 37.5 + - - +
188W ALA* 3.6 8.3 - - - +
190W LEU* 1.3 75.9 - - - +
192W GLU* 1.3 63.4 + - - +
194W ARG* 3.4 4.3 + - - +
195W GLU* 3.2 23.9 + - - +
223W GLN* 2.7 32.3 + - - +
224W LEU* 3.8 4.0 - - + +
226W ASP* 2.4 43.5 + - - -
227W ILE* 3.8 18.8 - - + +
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Residues in contact with GLU 192 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150H SER* 5.3 2.6 + - - -
192H GLU* 5.2 12.3 - - - +
150W SER* 5.3 8.7 + - - -
153W VAL* 3.4 37.0 - - + +
154W GLU* 4.4 6.8 - - - +
157W LYS* 4.6 5.5 + - - -
188W ALA 2.9 14.8 + - - +
189W TYR* 3.6 10.9 - - - +
191W ARG* 1.3 76.8 - - - +
193W LEU* 1.3 56.9 + - - +
195W GLU* 3.1 22.3 + - + +
196W VAL* 3.0 33.8 + - + +
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Residues in contact with LEU 193 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153W VAL* 4.0 24.0 - - + -
156W TYR* 3.9 29.8 - - + -
160W ILE* 4.5 9.0 - - + -
173W VAL* 3.8 30.5 - - + -
189W TYR* 3.1 50.1 + - + +
190W LEU* 3.8 10.3 - - + +
191W ARG 3.3 0.4 - - - -
192W GLU* 1.3 76.3 - - - +
194W ARG* 1.3 56.2 + - - +
196W VAL* 3.2 7.3 + - + +
197W ILE* 2.8 35.9 + - + +
203W MET* 4.0 9.6 - - + -
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Residues in contact with ARG 194 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190W LEU 3.1 13.3 + - - +
191W ARG 3.9 4.7 - - - +
193W LEU* 1.3 74.5 - - - +
195W GLU* 1.3 61.2 + - - +
197W ILE* 4.2 4.6 - - - +
198W GLY* 2.7 58.8 + - - -
199W TRP* 3.7 43.1 + - + +
201W MET 3.0 21.0 + - - -
202W ASP* 5.1 2.2 + - - +
203W MET* 3.6 46.3 - - - +
227W ILE* 2.9 42.2 + - + -
228W ASP* 3.3 19.0 + - - +
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Residues in contact with GLU 195 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H ALA* 4.7 16.5 - - - +
191W ARG 3.2 13.9 + - - +
192W GLU* 3.1 27.6 + - + +
194W ARG* 1.3 77.6 - - - +
196W VAL* 1.3 64.0 + - + +
198W GLY* 3.7 8.7 + - - -
199W TRP* 5.8 3.4 - - - +
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Residues in contact with VAL 196 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153W VAL* 4.5 9.9 - - + -
157W LYS* 3.8 45.3 - - + +
160W ILE* 3.8 28.5 - - + -
164W LYS* 2.9 23.9 + - - -
192W GLU* 3.0 24.5 + - + +
193W LEU* 3.5 10.3 - - + +
194W ARG 3.2 0.2 - - - -
195W GLU* 1.3 79.6 - - + +
197W ILE* 1.3 57.8 + - - +
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Residues in contact with ILE 197 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160W ILE* 3.8 26.2 - - + -
164W LYS* 3.1 20.9 - - - -
171W VAL* 3.5 23.6 - - + -
173W VAL* 4.2 16.4 - - + -
193W LEU 2.8 23.7 + - - +
194W ARG* 3.9 12.6 - - - +
196W VAL* 1.3 73.8 - - - +
198W GLY* 1.3 68.4 + - - +
200W ASP 5.0 1.2 + - - -
201W MET* 3.6 35.3 - - + +
203W MET* 3.8 28.9 - - + -
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Residues in contact with GLY 198 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164W LYS* 5.0 2.0 - - - -
194W ARG* 2.7 42.6 + - - -
195W GLU* 4.1 7.2 - - - -
196W VAL 3.4 2.0 - - - -
197W ILE* 1.3 78.2 - - - +
199W TRP* 1.3 72.5 + - - -
200W ASP 3.5 1.5 + - - -
201W MET 4.2 0.3 - - - +
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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
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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