Contacts of the helix formed by residues 203 - 215 (chain B) in PDB entry 3UMO
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 ASP 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B GLN* 3.2 2.6 - - + +
202B PRO* 1.3 80.7 - - + +
204B ASP* 1.3 60.8 + - - +
205B VAL 3.4 2.0 - - - -
206B ARG* 2.4 50.0 + - - +
207B LYS* 3.0 41.9 + - - +
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Residues in contact with ASP 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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197B ARG* 4.8 5.0 + - - +
198B GLU 3.9 5.1 - - - +
199B LEU* 3.6 26.8 - - + +
200B THR* 3.0 10.0 + - - -
201B GLN* 2.9 50.1 + - - +
202B PRO 3.4 0.2 - - - -
203B ASP* 1.3 75.8 - - - +
205B VAL* 1.3 62.0 + - - +
207B LYS* 3.4 10.9 + - - +
208B ALA* 2.9 32.3 + - - +
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Residues in contact with VAL 205 (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 GLN* 4.7 22.7 - - + +
191B LEU* 3.8 9.1 - - + +
199B LEU* 4.1 24.0 - - + +
201B GLN 4.7 1.2 + - - +
202B PRO 4.8 5.0 + - - +
203B ASP 3.4 0.4 - - - -
204B ASP* 1.3 77.3 - - - +
206B ARG* 1.3 63.9 + - - +
208B ALA* 3.7 1.4 - - - +
209B ALA* 2.9 22.7 + - - +
223B VAL* 3.8 33.0 - - + -
225B LEU* 4.4 10.3 - - + -
231B LEU* 4.2 11.4 - - + -
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Residues in contact with ARG 206 (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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202B PRO 5.5 0.2 + - - -
203B ASP* 2.4 55.7 + - - +
204B ASP 3.3 0.2 - - - -
205B VAL* 1.3 79.3 - - - +
207B LYS* 1.3 82.3 + - - +
209B ALA* 3.3 3.3 + - - +
210B GLN* 2.9 68.6 + - + +
231B LEU* 3.6 17.0 - - + +
233B VAL* 4.6 0.6 - - + +
238B CYS* 3.5 32.1 - - - -
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Residues in contact with LYS 207 (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 ARG* 4.3 6.7 + - - +
203B ASP* 3.0 31.4 + - - +
204B ASP* 3.8 11.4 - - - +
205B VAL 3.3 0.2 - - - -
206B ARG* 1.3 103.6 - - - +
208B ALA* 1.3 57.5 + - - +
210B GLN* 3.4 9.5 + - - +
211B GLU* 2.9 28.9 + - - +
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Residues in contact with ALA 208 (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* 3.9 18.8 - - + -
195B VAL* 4.0 19.4 - - + +
197B ARG* 3.5 22.1 - - - +
199B LEU* 4.2 5.8 - - + -
204B ASP 2.9 18.3 + - - +
205B VAL 3.7 3.1 - - - +
207B LYS* 1.3 73.7 - - - +
209B ALA* 1.3 65.2 + - - +
211B GLU* 3.2 12.8 + - - +
212B ILE* 3.2 18.2 + - - +
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Residues in contact with ALA 209 (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* 4.4 1.9 - - - +
205B VAL 2.9 17.2 + - - +
206B ARG* 3.6 4.9 - - - +
208B ALA* 1.3 76.5 - - - +
210B GLN* 1.3 62.2 + - - +
212B ILE* 3.1 17.4 + - - +
213B VAL* 3.2 16.1 + - - +
221B VAL* 3.9 16.4 - - + +
223B VAL* 3.8 22.4 - - + -
231B LEU* 4.9 0.7 - - + -
233B VAL* 3.8 23.1 - - + -
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Residues in contact with GLN 210 (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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206B ARG* 2.9 64.4 + - + +
207B LYS* 3.7 7.6 - - - +
209B ALA* 1.3 77.2 - - - +
211B GLU* 1.3 56.9 + - - +
213B VAL* 3.3 2.3 + - - +
214B ASN* 2.8 48.0 + - - +
233B VAL* 3.7 21.7 - - + +
234B ASP 5.5 1.0 + - - +
237B ASN 6.2 0.2 - - - -
238B CYS* 4.9 8.9 - - - +
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Residues in contact with GLU 211 (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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195B VAL* 4.2 16.9 - - + +
197B ARG* 2.8 39.9 + - - +
207B LYS 2.9 12.6 + - - +
208B ALA 3.4 8.5 - - - +
209B ALA 3.2 0.2 - - - -
210B GLN* 1.3 78.4 - - - +
212B ILE* 1.3 61.6 + - + +
214B ASN* 4.0 6.6 - - - +
215B SER* 3.1 25.3 + - - -
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Residues in contact with ILE 212 (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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176B LEU* 4.5 9.4 - - + -
184B VAL* 4.9 1.1 - - + -
186B PRO* 5.5 0.7 - - + -
191B LEU* 3.5 32.1 - - + -
194B LEU* 3.6 22.9 - - + -
195B VAL* 4.1 13.2 - - + -
208B ALA 3.5 9.9 - - - +
209B ALA* 3.1 10.6 + - - +
211B GLU* 1.3 76.3 - - + +
213B VAL* 1.3 62.6 + - - +
215B SER* 2.7 22.5 + - - -
217B LYS* 3.4 32.2 + - + -
218B ALA* 3.8 10.4 + - + -
221B VAL* 3.6 23.1 - - + -
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Residues in contact with VAL 213 (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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209B ALA 3.2 12.6 + - - +
210B GLN* 3.8 7.9 - - - +
212B ILE* 1.3 77.0 - - - +
214B ASN* 1.3 66.5 + - - +
216B GLY* 3.0 15.4 + - - -
218B ALA 3.4 18.6 - - - +
219B LYS* 4.0 8.5 - - - +
221B VAL* 3.8 18.8 - - + +
233B VAL* 3.8 26.7 - - + +
234B ASP 4.0 2.5 - - - +
235B SER* 3.9 35.0 - - - +
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Residues in contact with ASN 214 (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 GLN* 2.8 36.6 + - - +
211B GLU* 4.0 6.3 - - - +
213B VAL* 1.3 78.8 - - - +
215B SER* 1.3 60.1 + - - +
216B GLY 3.4 0.7 + - - -
235B SER* 5.4 4.3 - - - -
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Residues in contact with SER 215 (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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211B GLU* 3.1 16.6 + - - -
212B ILE* 2.7 21.5 + - - -
214B ASN* 1.3 77.1 - - - +
216B GLY* 1.3 57.6 + - - +
217B LYS* 3.3 31.3 + - - +
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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