Contacts of the helix formed by residues 183 - 198 (chain B) in PDB entry 1MDU
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 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B SER* 4.5 4.0 - - - -
158B GLY 3.1 16.2 - - - +
159B ASP 3.6 6.1 - - - -
160B GLY 3.6 1.3 + - - -
161B VAL 3.4 33.0 - - - +
162B THR* 4.0 3.4 - - - +
182B LEU* 1.3 77.9 - - - +
184B GLY* 1.3 69.2 + - - +
185B ARG 3.4 2.0 - - - -
186B ASP* 2.9 21.4 + - - +
187B LEU* 3.1 18.5 + - - +
263B LEU* 4.9 0.4 - - - -
305B THR* 4.2 2.9 - - - -
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Residues in contact with GLY 184 (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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158B GLY 2.8 17.0 + - - -
159B ASP* 4.0 1.6 - - - -
183B ALA* 1.3 71.5 - - - +
185B ARG* 1.3 51.8 + - - +
187B LEU* 2.8 10.7 + - - +
188B THR* 2.8 36.0 + - - -
215B LYS* 3.3 15.3 + - - -
305B THR* 3.2 17.2 + - - -
400B ATP 4.1 5.6 - - - -
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Residues in contact with ARG 185 (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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16B SER* 3.1 31.3 + - - -
71B TYR* 3.4 49.9 + - - +
73B ILE 4.8 2.2 + - - -
74B GLU* 6.3 0.8 - - - +
159B ASP* 2.9 54.4 + - - +
160B GLY* 5.3 3.1 - - - -
184B GLY* 1.3 71.6 - - - +
186B ASP* 1.3 60.2 + - - +
188B THR* 3.4 6.6 + - - +
189B ASP* 3.0 40.4 + - - +
208B ARG* 4.3 22.9 - - - +
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Residues in contact with ASP 186 (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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75B HIC 5.5 2.6 - - - -
159B ASP 4.7 2.6 - - - +
160B GLY* 4.7 5.0 - - - +
181B ASP 4.0 8.7 - - - +
182B LEU* 3.4 24.0 + - + -
183B ALA* 2.9 33.2 + - - +
185B ARG* 1.3 80.0 - - - +
187B LEU* 1.3 57.5 + - - +
189B ASP* 3.5 8.7 + - - +
190B TYR* 3.1 28.2 + - - +
269B ILE* 4.4 17.8 - - + +
271B MET* 5.8 0.5 - - - +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU* 3.7 22.4 - - + -
183B ALA 3.1 14.6 + - - +
184B GLY* 2.8 10.6 + - - +
186B ASP* 1.3 77.5 - - - +
188B THR* 1.3 59.7 + - - +
190B TYR* 3.8 3.7 - - + +
191B LEU* 3.0 22.9 + - - +
215B LYS* 4.0 4.5 - - + -
259B CYS* 3.3 37.7 - - - +
260B PRO* 4.6 2.2 - - + -
262B THR* 4.3 12.1 - - + -
263B LEU* 4.0 12.6 - - + -
305B THR* 3.8 18.4 - - + -
308B TYR* 3.2 42.2 - - + +
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Residues in contact with THR 188 (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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184B GLY 2.8 10.4 + - - -
185B ARG* 3.8 7.8 - - - -
187B LEU* 1.3 74.5 - - - +
189B ASP* 1.3 59.7 + - - +
191B LEU* 3.3 3.0 + - - -
192B MET* 2.8 35.4 + - + +
208B ARG* 3.8 24.0 - - - +
211B VAL* 3.8 4.6 - - + +
212B ARG* 4.1 33.7 - - + +
215B LYS* 2.9 33.7 + - - -
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Residues in contact with ASP 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B ARG* 3.0 29.1 + - - +
186B ASP* 3.8 8.5 - - - +
188B THR* 1.3 76.7 - - - +
190B TYR* 1.3 57.9 + - - +
192B MET* 3.3 9.8 + - - +
193B LYS* 2.8 30.1 + - - +
208B ARG* 2.7 36.6 + - - -
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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
----------------------------------------------------------
186B ASP 3.1 17.5 + - - +
187B LEU* 3.8 5.4 - - + +
189B ASP* 1.3 75.9 - - - +
191B LEU* 1.3 66.7 + - - +
193B LYS* 3.0 20.7 + - + +
194B ILE* 3.0 48.5 + - + +
258B ARG* 3.5 42.9 + - - -
259B CYS* 3.8 17.9 - - + -
262B THR* 3.5 18.4 - - - +
268B PHE* 3.9 34.9 + + + +
269B ILE* 3.9 18.6 - - + -
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LEU 3.0 18.0 + - - +
188B THR* 3.8 4.3 - - - +
190B TYR* 1.3 75.6 - - - +
192B MET* 1.3 63.5 + - - +
194B ILE* 3.2 21.9 - - + +
195B LEU* 3.0 44.3 + - + +
211B VAL* 3.8 30.7 - - + +
214B ILE* 4.2 12.6 - - + -
215B LYS* 3.8 24.5 - - + +
219B CYS* 4.3 7.6 - - - -
252B ILE* 5.3 4.7 - - + -
255B GLU* 4.5 11.7 - - + +
259B CYS* 4.0 15.0 - - + -
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Residues in contact with MET 192 (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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188B THR* 2.8 21.6 + - + +
189B ASP* 3.4 9.0 - - - +
191B LEU* 1.3 77.7 - - - +
193B LYS* 1.3 53.7 + - - +
195B LEU* 3.5 3.8 + - - +
196B THR* 2.7 41.3 + - - +
202B PHE* 4.1 18.4 - - + -
203B VAL* 3.9 40.6 - - + -
208B ARG* 3.0 55.2 - - + +
211B VAL* 3.7 15.2 - - + +
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Residues in contact with LYS 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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189B ASP 2.8 14.5 + - - +
190B TYR* 3.0 22.9 + - + +
192B MET* 1.3 74.6 - - - +
194B ILE* 1.3 66.9 + - + +
196B THR* 3.3 7.0 + - - -
197B GLU* 3.1 42.6 + - - +
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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
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190B TYR* 3.0 48.2 + - + +
191B LEU* 3.2 38.1 - - + +
193B LYS* 1.3 79.4 - - + +
195B LEU* 1.3 63.8 + - + +
197B GLU* 3.6 19.8 - - - +
198B ARG* 3.5 24.1 + - - +
255B GLU* 4.2 24.5 - - + +
258B ARG* 4.0 27.8 - - + +
259B CYS* 4.9 2.5 - - + +
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Residues in contact with LEU 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 LEU* 3.0 49.1 + - + +
192B MET 4.0 3.4 - - - +
194B ILE* 1.3 80.7 - - + +
196B THR* 1.3 65.7 + - - +
198B ARG* 3.3 11.5 + - - +
200B TYR* 3.0 36.1 - - + -
202B PHE* 4.0 27.8 - - + -
211B VAL* 4.5 6.3 - - + -
214B ILE* 4.2 22.9 - - + -
250B ILE* 4.8 7.6 - - + -
252B ILE* 4.3 22.2 - - + -
255B GLU* 4.5 8.3 - - + +
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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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192B MET* 2.7 30.2 + - - +
193B LYS* 3.3 7.5 + - - -
195B LEU* 1.3 77.1 - - - +
197B GLU* 1.3 57.3 + - - +
199B GLY* 2.8 21.7 + - - -
200B TYR* 3.5 22.9 + - - +
201B SER* 4.9 2.6 - - - -
202B PHE* 4.4 7.0 - - - -
203B VAL* 4.9 9.4 - - + +
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Residues in contact with GLU 197 (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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193B LYS* 3.1 39.4 + - - +
194B ILE* 3.6 23.8 - - - +
195B LEU 3.2 0.2 - - - -
196B THR* 1.3 77.9 - - - +
198B ARG* 1.3 58.0 + - + +
199B GLY* 3.0 4.6 + - - -
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Residues in contact with ARG 198 (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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194B ILE 3.5 12.2 + - - +
195B LEU* 3.3 14.4 + - - +
196B THR 3.1 1.0 - - - -
197B GLU* 1.3 77.3 - - + +
199B GLY* 1.3 64.1 + - - +
200B TYR* 3.9 31.8 + - + -
250B ILE* 5.8 0.6 - - - +
251B THR 3.3 25.0 + - - +
252B ILE* 5.1 3.0 - - - +
255B GLU* 3.3 26.9 + - - -
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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