Contacts of the helix formed by residues 225 - 239 (chain B) in PDB entry 1MGV
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 PRO 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B MET* 3.7 36.6 - - + -
213B ILE* 3.6 17.9 - - + -
223B TYR 3.6 0.2 - - - -
224B HIS* 1.3 97.3 - - + +
226B GLU* 1.3 64.3 + - - +
227B TRP 3.0 2.9 - - - -
228B LEU* 2.9 13.3 + - - +
229B LYS* 3.5 10.0 + - - +
262B HIS* 3.4 33.2 - - + +
263B ALA* 3.5 11.3 - - + +
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Residues in contact with GLU 226 (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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186B TRP* 3.6 31.9 - - + +
224B HIS* 2.9 26.6 + - + +
225B PRO* 1.3 77.4 - - - +
227B TRP* 1.3 62.9 + - - +
229B LYS* 3.2 32.7 + - - +
230B ARG* 2.1 63.1 + - - +
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Residues in contact with TRP 227 (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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140B PHE* 3.6 31.0 - + - -
176B PRO* 5.4 3.1 - - + -
177B ALA 5.6 0.2 - - - -
178B PRO* 3.4 26.1 - - + +
180B SER* 4.8 1.8 - - - -
186B TRP* 3.4 24.6 - + - -
190B ASP* 2.8 60.4 + - + -
191B MET* 3.3 31.6 - - + -
194B PHE* 4.0 21.8 - + + -
223B TYR* 3.7 19.7 - + + -
224B HIS 3.1 19.2 + - - +
225B PRO 3.0 0.2 - - - -
226B GLU* 1.3 79.2 - - - +
228B LEU* 1.3 57.0 + - - +
230B ARG* 3.3 3.2 + - - +
231B ILE* 2.8 40.4 + - + +
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Residues in contact with LEU 228 (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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210B ILE* 3.2 36.1 - - + -
212B PRO* 3.7 28.0 - - + -
213B ILE* 3.7 25.6 - - + -
223B TYR* 3.8 13.0 - - + +
225B PRO 2.9 4.0 + - - +
227B TRP* 1.3 75.0 - - - +
229B LYS* 1.3 60.8 + - - +
231B ILE* 3.9 4.0 - - + +
232B ARG* 2.9 30.3 + - - +
242B LEU* 5.1 2.1 - - + +
244B ALA* 6.5 0.4 - - + -
259B ALA 4.4 5.2 - - - +
260B CYS* 4.5 6.3 - - - -
263B ALA* 3.6 22.4 - - + -
265B ILE* 3.9 17.9 - - + +
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Residues in contact with LYS 229 (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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225B PRO* 3.5 9.3 + - - -
226B GLU* 3.4 38.6 - - - +
228B LEU* 1.3 76.9 - - - +
230B ARG* 1.3 65.3 + - - +
232B ARG* 3.1 4.3 + - - +
233B LYS* 3.0 43.0 + - - +
262B HIS 4.8 2.4 + - - -
263B ALA* 3.2 40.8 + - - +
264B GLU* 5.1 7.7 + - - +
265B ILE* 4.0 12.6 - - + -
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Residues in contact with ARG 230 (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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186B TRP* 3.3 15.1 - - + +
188B GLU* 2.3 39.4 + - - -
191B MET* 3.9 33.6 - - + +
226B GLU* 2.1 58.0 + - + +
227B TRP 3.5 4.5 - - - +
229B LYS* 1.3 80.5 - - - +
231B ILE* 1.3 63.4 + - - +
233B LYS* 3.1 11.0 + - - +
234B ILE* 2.9 31.5 + - + +
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Residues in contact with ILE 231 (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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140B PHE* 3.4 35.0 - - + -
194B PHE* 4.0 21.1 - - + -
208B VAL* 3.9 13.5 - - + -
210B ILE* 3.6 22.7 - - + -
227B TRP* 2.8 35.1 + - + +
228B LEU* 3.9 5.4 - - + +
229B LYS 3.3 0.2 - - - -
230B ARG* 1.3 72.5 - - + +
232B ARG* 1.3 63.5 + - - +
234B ILE* 3.3 7.8 + - + +
235B CYS* 2.9 28.8 + - - -
242B LEU* 3.8 28.0 - - + -
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Residues in contact with ARG 232 (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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228B LEU 2.9 19.2 + - - +
229B LYS 3.5 4.5 - - - +
231B ILE* 1.3 76.4 - - - +
233B LYS* 1.3 62.1 + - + +
235B CYS* 3.5 19.6 + - - +
236B ASP* 2.9 58.4 + - - +
240B ILE 4.0 3.4 + - - -
242B LEU* 3.8 15.9 - - + +
265B ILE* 4.0 26.7 - - + -
266B ALA 2.6 40.0 + - - +
267B PRO* 3.6 3.8 - - - +
268B ASP* 2.8 41.6 + - - +
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Residues in contact with LYS 233 (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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229B LYS* 3.0 32.7 + - - +
230B ARG* 3.5 13.2 - - - +
232B ARG* 1.3 80.1 - - + +
234B ILE* 1.3 60.9 + - - +
236B ASP* 3.3 11.5 + - + +
237B ARG* 2.9 46.4 + - - +
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Residues in contact with ILE 234 (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 MET* 3.6 30.7 - - + -
194B PHE* 3.9 22.0 - - + -
195B ALA* 5.9 3.6 - - + -
198B MET* 3.8 34.1 - - + -
230B ARG* 2.9 26.7 + - + +
231B ILE* 3.7 4.7 - - - +
233B LYS* 1.3 74.7 - - - +
235B CYS* 1.3 57.9 + - - +
237B ARG* 3.3 26.1 - - - +
238B GLU* 3.0 39.0 + - + +
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Residues in contact with CYS 235 (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 PHE* 5.6 0.4 - - - -
198B MET* 5.4 2.0 - - - -
208B VAL* 3.5 38.6 - - - -
231B ILE* 2.9 26.2 + - - +
232B ARG* 3.7 16.2 - - - +
234B ILE* 1.3 75.8 - - - +
236B ASP* 1.3 65.7 + - - +
238B GLU* 3.4 0.4 + - - -
239B GLY* 2.9 4.7 + - - -
240B ILE* 2.9 53.6 + - - +
241B LEU 4.3 1.3 - - - -
242B LEU* 4.1 9.6 - - + -
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Residues in contact with ASP 236 (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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232B ARG* 2.9 60.8 + - - +
233B LYS* 3.5 13.0 - - + +
235B CYS* 1.3 77.8 - - - +
237B ARG* 1.3 63.8 + - - +
239B GLY* 3.1 10.4 + - - -
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Residues in contact with ARG 237 (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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233B LYS* 2.9 24.9 + - - +
234B ILE* 3.3 40.1 - - - +
236B ASP* 1.3 77.6 - - - +
238B GLU* 1.3 71.2 + - + +
239B GLY 3.5 0.3 + - - -
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Residues in contact with GLU 238 (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 ARG* 4.3 12.8 + - - -
198B MET* 3.9 22.5 - - + +
202B ARG* 3.9 41.9 + - + +
234B ILE* 3.0 21.9 + - + +
235B CYS 4.2 0.4 - - - +
237B ARG* 1.3 85.4 + - + +
239B GLY* 1.3 60.6 + - - +
240B ILE* 3.5 25.1 + - + +
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Residues in contact with GLY 239 (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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126B TYR* 5.4 0.7 + - - -
127B TRP* 3.1 31.2 - - - -
235B CYS 2.9 6.7 + - - -
236B ASP* 3.1 10.2 + - - -
237B ARG 3.3 1.2 + - - -
238B GLU* 1.3 78.5 - - - +
240B ILE* 1.3 60.9 + - - +
241B LEU* 5.5 0.7 - - - +
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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