Contacts of the helix formed by residues 186 - 204 (chain B) in PDB entry 3MYV
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 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B THR* 3.7 15.0 - - + -
155B GLY* 3.8 13.0 - - - -
156B TYR 3.6 12.6 - - - +
158B TYR* 3.9 21.3 - - + +
163B GLY* 3.8 8.7 - - - -
165B SER* 2.8 35.8 + - - +
167B GLY* 3.8 15.0 - - - +
185B THR* 1.3 72.5 - - - +
187B ALA* 1.3 63.4 + - - +
189B ALA* 3.2 2.7 + - - +
190B TYR* 3.0 49.7 + - + -
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B TYR* 4.1 12.8 - - + -
162B LYS 3.6 16.8 - - - +
163B GLY* 2.8 21.4 + - - +
164B ALA* 5.4 0.2 - - - -
185B THR* 3.2 5.1 - - - +
186B VAL* 1.3 76.0 - - - +
188B GLN* 1.3 62.6 + - + +
190B TYR* 3.3 2.8 + - - +
191B ASP* 3.0 32.6 + - - +
229B HIS* 5.1 0.2 + - - -
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Residues in contact with GLN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.9 9.5 - - + +
184B SER* 3.4 19.1 + - - -
185B THR* 2.9 46.7 + - - +
187B ALA* 1.3 75.3 - - + +
189B ALA* 1.3 62.1 + - - +
191B ASP* 3.4 10.6 + - - +
192B PHE* 3.2 22.2 + - - +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLN* 4.8 2.2 - - + +
151B THR* 3.4 30.5 - - + +
167B GLY* 5.9 2.0 - - - -
168B ALA 5.7 4.0 - - - +
170B LEU* 3.7 23.6 - - + +
184B SER* 5.8 0.4 - - - -
185B THR 3.0 12.7 + - - +
186B VAL* 3.5 8.7 - - - +
188B GLN* 1.3 77.6 - - - +
190B TYR* 1.3 57.3 + - - +
192B PHE* 3.2 3.5 + - - +
193B ILE* 2.8 37.3 + - + +
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 3.4 20.5 - + - -
151B THR* 3.9 13.5 - - + +
152B ARG* 5.2 4.3 - - - +
158B TYR* 3.6 22.1 + + + +
186B VAL* 3.0 47.5 + - + +
187B ALA 3.3 3.1 + - - +
189B ALA* 1.3 77.0 - - - +
191B ASP* 1.3 56.8 + - - +
193B ILE* 4.2 6.3 - - + -
194B ILE* 2.8 38.7 + - + +
225B ILE* 3.9 35.9 - - + -
228B TYR* 3.4 27.4 + - + +
229B HIS* 3.5 39.0 - + + +
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Residues in contact with ASP 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ALA* 3.0 23.4 + - - +
188B GLN* 3.6 12.5 - - - +
189B ALA 3.3 0.2 - - - -
190B TYR* 1.3 73.9 - - - +
192B PHE* 1.3 61.8 + - - +
194B ILE* 4.1 3.1 - - - +
195B GLU* 3.1 40.4 + - - +
229B HIS* 4.4 14.0 + - - -
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TRP* 4.1 11.9 - + - -
143B ILE* 3.8 24.7 - - + -
144B ALA 5.8 0.2 - - - -
147B GLN* 4.4 9.4 - - + -
170B LEU* 3.6 27.6 - - + -
171B ILE 3.5 26.7 - - - -
172B ASP* 3.5 26.7 - - + +
188B GLN 3.2 10.5 + - - +
189B ALA 3.6 5.6 - - - +
191B ASP* 1.3 78.6 - - - +
193B ILE* 1.3 65.4 + - + +
195B GLU* 3.5 4.9 + - + +
196B THR* 2.7 57.7 + - + -
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA* 3.8 19.9 - - + +
147B GLN* 3.9 22.4 - - + -
148B PHE* 3.6 31.0 - - + +
151B THR* 3.9 13.9 - - - +
189B ALA 2.8 35.1 + - - +
190B TYR* 3.8 10.8 - - + +
192B PHE* 1.3 77.7 - - + +
194B ILE* 1.3 60.2 + - - +
196B THR* 3.7 4.0 - - - -
197B LEU* 2.9 29.5 + - + +
225B ILE* 3.8 37.2 - - + -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B TYR* 2.8 23.3 + - + +
191B ASP* 4.1 3.1 - - - +
193B ILE* 1.3 77.8 - - - +
195B GLU* 1.3 58.3 + - + +
197B LEU* 3.3 1.2 + - - +
198B GLU* 2.9 60.6 + - + +
222B LEU* 4.5 6.7 - - + -
225B ILE* 3.8 20.4 - - + -
226B TYR* 3.8 18.6 - - + -
229B HIS* 3.3 46.9 - - + +
231B ASP* 3.8 7.6 - - - +
234B LYS* 5.8 2.7 - - - +
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ASP* 3.1 28.9 + - - +
192B PHE* 4.0 5.2 - - - +
194B ILE* 1.3 76.5 - - + +
196B THR* 1.3 61.5 + - - +
198B GLU* 3.6 14.0 + - - +
199B GLU* 3.2 24.7 + - - +
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Residues in contact with THR 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B TRP* 6.4 0.9 - - + -
116B LEU* 6.3 0.2 - - + -
140B MSE 3.5 54.3 - - + +
143B ILE* 4.6 11.7 - - + -
144B ALA* 4.6 4.0 - - + -
192B PHE* 2.7 44.5 + - + -
193B ILE* 3.7 5.4 - - - -
195B GLU* 1.3 77.7 - - - +
197B LEU* 1.3 58.1 + - - +
199B GLU* 3.4 1.3 + - - -
200B ALA* 2.9 26.7 + - - +
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ALA* 3.8 34.1 - - + -
144B ALA* 4.1 8.3 - - + -
193B ILE* 2.9 16.3 + - + +
196B THR* 1.3 74.8 - - - +
198B GLU* 1.3 65.3 + - - +
200B ALA* 3.2 4.5 + - + +
201B VAL* 3.0 30.1 + - + +
218B ALA* 4.0 17.0 - - + +
221B LEU* 3.8 13.2 - - + -
222B LEU* 3.6 48.9 - - + +
225B ILE* 3.7 24.0 - - + -
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ILE* 2.9 32.7 + - + +
195B GLU* 3.8 13.7 - - - +
197B LEU* 1.3 76.4 - - - +
199B GLU* 1.3 62.4 + - - +
201B VAL* 3.6 8.7 + - - +
202B THR* 3.4 19.1 + - - +
222B LEU* 3.8 14.1 - - + -
226B TYR* 2.5 38.3 + - - +
234B LYS* 4.7 8.5 + - - +
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Residues in contact with GLU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LYS* 4.2 19.9 + - - -
140B MSE 3.5 22.5 - - + +
195B GLU 3.2 19.1 + - - +
196B THR* 3.8 3.8 - - - +
198B GLU* 1.3 72.8 - - - +
200B ALA* 1.3 66.2 + - - +
202B THR* 2.6 31.5 + - - +
203B LEU* 3.5 12.6 + - + +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLY* 3.1 32.1 - - - +
140B MSE 3.9 11.6 - - + +
141B ALA 3.9 6.7 - - - +
196B THR 2.9 18.9 + - - +
197B LEU* 3.2 15.7 + - + +
199B GLU* 1.3 77.4 - - - +
201B VAL* 1.3 61.9 + - - +
203B LEU* 3.0 13.0 + - - +
204B MSE 3.1 23.4 + - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B LEU* 3.0 21.2 + - + +
198B GLU* 3.8 7.2 - - - +
199B GLU 3.2 0.4 - - - -
200B ALA* 1.3 75.6 - - - +
202B THR* 1.3 64.1 + - + +
203B LEU 3.3 0.9 + - - -
204B MSE 3.6 9.8 + - - -
215B LYS* 3.3 35.0 - - + +
218B ALA* 3.9 29.2 - - + +
219B ARG* 3.7 32.5 - - + +
222B LEU* 4.5 11.2 - - + -
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Residues in contact with THR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLU 3.4 17.3 - - - +
199B GLU* 2.6 23.5 + - - +
201B VAL* 1.3 80.4 - - + +
203B LEU* 1.3 68.1 + - - +
204B MSE 3.6 1.3 - - - +
215B LYS* 5.1 5.8 + - - +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS 4.8 0.9 - - - +
133B ASN* 3.4 39.2 - - + +
134B ALA* 3.3 19.6 + - - +
136B LYS* 3.9 31.2 - - + +
137B GLY* 3.8 22.7 - - - +
140B MSE 4.0 10.1 - - - -
199B GLU* 3.7 19.5 - - + +
200B ALA 3.0 7.2 + - - +
202B THR* 1.3 86.4 - - - +
204B MSE 1.3 61.6 + - - +
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Residues in contact with MSE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA* 3.9 7.4 - - - +
137B GLY* 3.6 27.6 - - - +
138B GLU* 3.7 19.7 - - + +
141B ALA* 4.1 4.9 - - + -
200B ALA 3.1 20.3 + - - +
201B VAL 3.6 3.9 + - - +
202B THR 5.0 0.9 - - - +
203B LEU* 1.3 80.1 - - - +
205B SER* 1.3 61.8 + - - +
206B GLU 4.2 0.2 + - - -
213B MSE 3.4 30.5 - - + +
214B ASN* 3.4 18.6 - - - +
215B LYS* 3.6 29.4 + - + +
218B ALA* 3.5 27.1 - - + -
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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