Contacts of the helix formed by residues 181 - 195 (chain Z) in PDB entry 1MVW
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 ALA 181 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155Z SER* 4.5 0.4 - - - +
156Z GLY 3.3 15.5 - - - +
157Z ASP 3.4 17.7 - - - +
158Z GLY 3.7 14.6 + - - -
159Z VAL 3.8 10.1 - - - +
160Z THR* 4.3 2.7 - - - +
180Z LEU* 1.3 77.2 - - - +
182Z GLY* 1.3 61.5 + - - +
183Z ARG 3.2 2.9 + - - -
184Z ASP* 3.2 10.8 + - - +
185Z LEU* 3.0 33.3 + - - +
303Z THR* 4.2 7.0 - - - -
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Residues in contact with GLY 182 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156Z GLY 3.0 11.5 + - - -
157Z ASP* 4.4 4.9 - - - -
181Z ALA* 1.3 76.5 - - - +
183Z ARG* 1.3 54.2 + - - +
185Z LEU* 3.5 8.0 - - - +
186Z THR* 3.0 18.2 + - - -
213Z LYS* 2.8 30.8 + - - -
303Z THR* 3.1 21.4 + - - -
306Z TYR* 4.6 0.2 - - - -
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Residues in contact with ARG 183 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Z SER* 2.8 35.8 + - - -
69Z TYR* 3.5 29.4 + - - +
71Z ILE 4.8 5.3 + - - -
72Z GLU* 4.6 14.5 + - - +
73Z HIS* 5.2 7.4 - - - +
157Z ASP* 2.9 47.9 + - - +
158Z GLY* 4.4 15.0 - - - -
181Z ALA 3.2 0.2 - - - -
182Z GLY* 1.3 71.8 - - - +
184Z ASP* 1.3 70.4 + - - +
186Z THR* 3.3 14.0 + - - -
187Z ASP* 3.3 24.7 + - - +
206Z ARG* 6.1 2.7 - - - +
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Residues in contact with ASP 184 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73Z HIS* 5.4 3.1 - - - -
157Z ASP 4.5 0.7 - - - +
158Z GLY* 4.7 4.9 - - - +
179Z ASP 3.9 12.5 - - - +
180Z LEU* 3.8 11.0 - - + +
181Z ALA* 3.2 29.2 + - - +
183Z ARG* 1.3 81.0 - - - +
185Z LEU* 1.3 61.6 + - + +
187Z ASP* 3.2 9.0 + - - +
188Z TYR* 3.1 27.5 + - - +
267Z ILE* 5.0 13.2 - - + +
269Z MET* 5.6 0.9 - - - +
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Residues in contact with LEU 185 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180Z LEU* 3.9 24.2 - - + -
181Z ALA 3.0 16.3 + - - +
182Z GLY 3.5 7.0 - - - +
184Z ASP* 1.3 78.4 - - + +
186Z THR* 1.3 61.9 + - - +
188Z TYR* 3.7 5.5 + - + +
189Z LEU* 3.3 8.5 + - - +
213Z LYS* 4.1 3.4 - - + -
257Z CYS* 3.2 38.9 - - - +
258Z PRO* 5.1 0.2 - - + -
260Z THR* 4.3 20.0 - - + -
261Z LEU* 4.0 10.8 - - + -
303Z THR* 3.8 18.2 - - + -
306Z TYR* 3.0 40.8 - - + +
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Residues in contact with THR 186 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Z GLY 3.0 8.6 + - - -
183Z ARG* 3.3 8.1 + - - -
185Z LEU* 1.3 75.2 - - - +
187Z ASP* 1.3 66.9 + - - +
189Z LEU* 3.4 5.2 + - - +
190Z MET* 3.1 25.3 + - - +
206Z ARG* 4.6 10.1 - - - +
209Z VAL* 3.6 26.7 - - + +
210Z ARG* 3.7 25.1 - - + +
213Z LYS* 2.7 37.8 + - - +
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Residues in contact with ASP 187 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183Z ARG* 3.3 18.0 + - - +
184Z ASP* 3.2 10.6 + - - +
186Z THR* 1.3 79.4 - - - +
188Z TYR* 1.3 64.3 + - - +
190Z MET* 3.1 19.6 - - - +
191Z LYS* 3.3 9.5 + - - +
206Z ARG* 3.4 35.3 + - - -
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Residues in contact with TYR 188 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184Z ASP 3.1 14.7 + - - +
185Z LEU* 4.1 6.1 - - - +
186Z THR 3.3 0.2 - - - -
187Z ASP* 1.3 76.3 - - - +
189Z LEU* 1.3 66.4 + - - +
191Z LYS* 3.2 39.6 + - + +
192Z ILE* 3.0 44.7 + - + +
256Z ARG* 3.3 21.6 + - - +
257Z CYS* 3.8 11.2 - - + -
260Z THR* 3.2 24.5 - - + -
266Z PHE* 3.1 40.3 - + + +
267Z ILE* 3.5 24.9 - - + -
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Residues in contact with LEU 189 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Z LEU 3.3 13.1 + - - +
186Z THR* 3.7 7.0 - - - +
187Z ASP 3.4 0.2 - - - -
188Z TYR* 1.3 77.9 - - - +
190Z MET* 1.3 54.3 - - - +
192Z ILE* 3.0 25.7 + - + +
193Z LEU* 2.8 52.4 + - + +
209Z VAL* 3.5 32.3 - - + +
212Z ILE* 3.7 12.1 - - + -
213Z LYS* 3.5 28.9 - - + +
217Z CYS* 4.6 7.4 - - - -
250Z ILE* 5.5 2.2 - - + -
253Z GLU* 4.6 16.6 - - + +
254Z ARG 5.3 0.7 - - - +
257Z CYS* 3.8 9.0 - - + -
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Residues in contact with MET 190 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Z THR 3.1 9.4 + - - +
187Z ASP* 3.1 18.2 - - - +
189Z LEU* 1.3 78.3 - - - +
191Z LYS* 1.3 57.6 + - - +
193Z LEU* 3.3 3.7 + - - +
194Z THR* 2.9 37.5 + - + +
200Z PHE* 3.7 29.7 - - + +
206Z ARG* 3.7 44.4 - - + +
209Z VAL* 3.2 35.4 - - + -
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Residues in contact with LYS 191 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187Z ASP 3.3 5.1 + - - +
188Z TYR* 3.2 48.7 + - + +
190Z MET* 1.3 78.6 - - - +
192Z ILE* 1.3 64.8 + - - +
193Z LEU 2.8 7.1 + - - -
194Z THR* 2.9 10.5 + - - -
195Z GLU* 2.8 55.0 + - + +
266Z PHE 5.0 3.2 + - - -
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Residues in contact with ILE 192 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Z TYR* 3.0 49.7 + - + +
189Z LEU* 3.0 23.5 + - + +
191Z LYS* 1.3 90.2 - - - +
193Z LEU* 1.3 55.1 + - - +
195Z GLU* 3.5 25.0 - - - +
196Z ARG* 3.2 20.8 + - - +
253Z GLU* 3.6 39.4 - - + +
256Z ARG* 3.6 32.5 + - + +
257Z CYS* 4.0 3.1 - - + +
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Residues in contact with LEU 193 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Z LEU* 2.8 35.0 + - + +
190Z MET 3.6 4.5 - - - +
191Z LYS 2.8 0.6 + - - -
192Z ILE* 1.3 79.0 - - - +
194Z THR* 1.3 63.3 + - - +
195Z GLU 3.2 0.9 - - - -
196Z ARG* 3.3 7.0 + - + +
198Z TYR* 2.8 40.1 - - + +
200Z PHE* 3.6 27.1 - - + -
209Z VAL* 4.1 10.5 - - + -
212Z ILE* 4.2 17.7 - - + -
248Z ILE* 5.2 0.2 - - + -
249Z THR 4.5 0.9 - - - +
250Z ILE* 3.3 33.7 - - + -
253Z GLU* 4.1 13.7 - - + -
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Residues in contact with THR 194 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190Z MET* 2.9 27.4 + - + +
191Z LYS* 3.0 14.4 + - - +
193Z LEU* 1.3 75.9 - - - +
195Z GLU* 1.3 59.5 + - - +
197Z GLY* 2.9 9.5 + - - -
198Z TYR 2.9 38.5 + - - +
199Z SER* 4.9 0.2 - - - -
200Z PHE* 3.5 26.0 - - + +
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Residues in contact with GLU 195 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Z LYS* 2.8 44.8 + - + +
192Z ILE* 3.5 22.9 - - - +
194Z THR* 1.3 77.1 + - - +
196Z ARG* 1.3 56.2 + - - +
197Z GLY* 3.0 8.9 + - - -
256Z ARG* 3.7 15.5 + - - +
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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