Contacts of the helix formed by residues 202 - 217 (chain X) 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 THR 202 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285V CYS 2.6 18.2 - - - +
286V ASP* 2.1 19.5 - - - +
287V ILE* 0.7 451.2 - - + +
290V ARG* 2.8 13.5 - - - +
201X VAL* 1.3 60.1 - - - +
203X THR* 1.3 43.6 + - - -
205X GLU* 2.9 11.3 + - - +
206X ARG* 3.1 11.2 + - - +
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Residues in contact with THR 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286V ASP* 2.2 51.7 + - - +
287V ILE* 1.9 4.8 - - - +
288V ASP* 1.1 55.0 - - + +
62X ARG* 3.7 30.1 + - + +
202X THR 1.3 67.2 - - - -
204X ALA* 1.3 28.3 + - - +
205X GLU 3.2 0.2 - - - -
206X ARG* 3.7 11.9 - - - +
207X GLU* 3.3 25.1 + - - +
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Residues in contact with ALA 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287V ILE 3.0 2.7 - - - +
288V ASP* 0.9 242.9 + - + +
291V LYS* 5.4 0.2 - - - -
203X THR* 1.3 29.2 - - - +
205X GLU* 1.3 61.4 + - - +
207X GLU 4.6 0.7 - - - -
208X ILE* 3.6 11.4 - - - +
243X PRO* 3.5 26.8 - - + +
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Residues in contact with GLU 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287V ILE* 1.6 61.9 - - + +
290V ARG* 4.8 3.8 + - - -
199X SER 4.3 4.2 - - - +
200X PHE* 3.4 33.8 - - + -
201X VAL* 3.5 13.4 - - + +
202X THR 2.9 5.0 + - - +
204X ALA* 1.3 82.5 - - - +
206X ARG* 1.3 68.3 + - - +
207X GLU 3.4 0.2 - - - -
208X ILE* 3.1 22.1 - - - +
209X VAL 3.7 2.9 + - - -
242X LEU* 3.7 24.2 - - + +
243X PRO* 4.4 5.0 - - - +
244X ASP* 5.1 2.9 - - - +
246X GLN* 5.6 1.6 - - - +
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Residues in contact with ARG 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X ARG* 4.4 13.7 - - - +
183X ARG* 6.1 2.8 - - - +
186X THR* 4.6 11.4 - - - +
187X ASP* 3.4 31.8 + - - -
190X MET* 3.7 26.7 - - + +
200X PHE* 4.2 4.1 - - + +
201X VAL 5.9 0.4 - - - +
202X THR 3.1 8.0 + - - +
203X THR* 3.7 15.5 - - - +
205X GLU* 1.3 76.5 - - - +
207X GLU* 1.3 68.2 + - - +
209X VAL* 3.0 29.7 + - - +
210X ARG* 5.1 0.7 - - - +
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Residues in contact with GLU 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288V ASP* 4.4 8.2 - - - +
59X GLN* 3.8 12.8 - - - +
62X ARG* 2.9 39.1 + - - +
203X THR 3.3 14.5 + - - +
205X GLU 3.4 0.4 - - - -
206X ARG* 1.3 83.7 - - - +
208X ILE* 1.3 58.0 + - - +
210X ARG* 3.1 39.3 + - - +
211X ASP* 3.8 1.9 + - - +
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Residues in contact with ILE 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X PHE* 5.4 3.1 - - + -
204X ALA 3.6 14.1 - - - +
205X GLU* 3.1 20.4 - - - +
207X GLU* 1.3 75.5 - - + +
209X VAL* 1.4 57.5 + - - +
210X ARG 3.1 2.0 - - - -
211X ASP* 3.0 10.9 + - + +
212X ILE* 2.9 32.6 + - + +
240X TYR* 3.2 41.7 - - + +
242X LEU* 4.4 13.7 - - + -
243X PRO* 3.9 28.7 - - + -
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Residues in contact with VAL 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186X THR* 3.6 22.7 - - + +
189X LEU* 3.5 22.1 - - + +
190X MET* 3.2 48.7 - - + +
193X LEU* 4.1 13.2 - - + -
200X PHE* 5.1 5.2 - - + -
205X GLU 4.5 2.7 - - - +
206X ARG* 3.0 25.2 + - - +
208X ILE* 1.4 78.0 - - - +
210X ARG* 1.3 58.4 + - - +
212X ILE* 3.2 12.5 + - - +
213X LYS* 3.0 24.4 + - - +
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Residues in contact with ARG 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X LEU* 6.1 2.6 - - - +
186X THR* 3.7 31.6 - - + +
206X ARG* 5.1 0.9 - - - +
207X GLU* 3.1 25.2 + - - +
209X VAL* 1.3 82.6 - - + +
211X ASP* 1.3 61.7 + - - +
213X LYS* 3.4 13.3 - - - +
214X GLU* 2.8 68.1 + - - +
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Residues in contact with ASP 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207X GLU 3.8 1.3 + - - +
208X ILE* 3.0 20.7 + - + +
210X ARG* 1.3 83.0 + - - +
212X ILE* 1.3 60.6 + - - +
214X GLU* 4.0 12.7 - - - +
215X LYS* 2.7 63.9 + - - +
240X TYR* 2.9 21.7 + - - +
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Residues in contact with ILE 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X LEU* 3.7 17.3 - - + -
193X LEU* 4.2 24.0 - - + -
200X PHE* 5.1 7.6 - - + -
208X ILE* 2.9 19.9 + - + +
209X VAL* 3.2 13.4 + - - +
211X ASP* 1.3 74.7 - - - +
213X LYS* 1.4 60.4 + - - +
215X LYS 3.2 1.2 + - - -
216X LEU* 2.9 42.8 + - + +
217X CYS* 3.8 2.1 + - - -
240X TYR* 3.9 40.4 - - + -
242X LEU* 5.2 1.6 - - + -
248X ILE* 4.3 15.5 - - + -
250X ILE* 4.5 15.5 - - + -
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Residues in contact with LYS 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157X ASP* 5.8 0.6 + - - -
182X GLY* 2.8 25.4 + - - +
185X LEU 4.1 2.9 - - - -
186X THR* 2.7 41.9 + - - +
189X LEU* 3.5 17.9 - - + +
209X VAL 3.0 8.7 + - - +
210X ARG* 3.4 20.8 - - - +
212X ILE* 1.4 73.6 - - - +
214X GLU* 1.3 77.0 + - - +
217X CYS* 3.0 30.6 + - - +
257X CYS* 4.2 13.0 - - - -
303X THR* 5.1 1.2 + - - -
306X TYR* 3.7 32.6 - - + +
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Residues in contact with GLU 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X ARG* 2.8 55.9 + - - +
211X ASP* 4.2 10.6 - - - +
212X ILE 3.3 0.2 - - - -
213X LYS* 1.3 95.5 + - - +
215X LYS* 1.3 63.9 + - + +
217X CYS 4.3 6.1 + - - +
306X TYR* 5.6 4.0 - - - -
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Residues in contact with LYS 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X ASP* 2.7 52.2 + - - +
212X ILE* 4.1 1.1 - - - +
214X GLU* 1.3 79.6 - - + +
216X LEU* 1.3 72.5 + - + +
217X CYS 4.9 0.7 - - - +
218X TYR* 4.8 6.9 - - - -
240X TYR* 4.1 15.4 + - + -
254X ARG* 5.4 0.3 + - - -
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Residues in contact with LEU 216 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212X ILE* 2.9 25.3 + - + +
215X LYS* 1.3 86.0 - - + +
217X CYS* 1.3 61.8 + - - +
218X TYR* 3.3 5.6 - - - -
238X LYS* 3.8 46.4 - - + +
239X SER 5.8 0.9 - - - +
240X TYR* 3.9 32.5 - - + +
250X ILE* 4.6 11.4 - - + -
254X ARG* 2.9 43.4 + - + +
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Residues in contact with CYS 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X LEU* 4.6 7.9 - - - -
212X ILE* 3.8 2.7 + - - -
213X LYS* 3.0 35.9 + - - +
214X GLU 4.6 4.5 - - - +
215X LYS 3.8 0.7 - - - +
216X LEU* 1.3 72.4 - - - +
218X TYR* 1.3 73.3 - - - +
250X ILE* 6.2 0.7 - - - -
253X GLU 4.7 0.2 - - - -
254X ARG* 2.9 26.5 - - - +
257X CYS* 4.2 19.5 - - - -
258X PRO* 4.1 3.4 - - + -
306X TYR* 4.0 21.6 - - + -
307X PRO* 3.4 17.5 - - - +
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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