Contacts of the helix formed by residues 183 - 194 (chain Q) in PDB entry 2X86
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 SER 183 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170Q VAL 4.1 5.6 + - - -
171Q TYR* 3.5 24.1 - - - +
175Q GLU* 2.7 35.8 + - - -
181Q MET 3.9 0.6 + - - -
182Q ALA* 1.3 76.2 - - - +
184Q VAL* 1.3 64.4 + - - +
185Q ALA* 3.5 10.1 - - - +
186Q PHE* 3.0 16.1 + - - +
187Q HIS* 3.1 18.0 + - - -
211Q PHE* 6.5 0.7 - - - -
302Q TYR* 3.9 0.2 - - - -
401Q ADP 5.2 1.6 - - - -
402Q BMA 5.7 0.6 + - - -
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Residues in contact with VAL 184 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Q ALA 3.7 0.2 + - - -
183Q SER* 1.3 70.6 - - - +
185Q ALA* 1.3 67.1 + - - +
187Q HIS* 3.1 8.9 + - + +
188Q LEU* 2.9 43.9 + - + +
199Q LYS 4.8 0.2 - - - +
200Q LEU* 3.9 23.6 - - + -
211Q PHE* 5.6 5.8 - - + -
243Q PHE* 3.6 31.4 - - + -
246Q VAL* 4.9 8.3 - - + -
401Q ADP 3.6 37.0 - - + +
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Residues in contact with ALA 185 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171Q TYR* 4.6 11.0 - - + -
183Q SER* 3.5 11.4 + - - +
184Q VAL* 1.3 77.6 - - - +
186Q PHE* 1.3 62.8 + - - +
188Q LEU* 3.3 2.9 + - - +
189Q ASN* 3.0 24.3 + - - +
246Q VAL* 4.2 23.5 - - + +
250Q THR* 4.6 2.5 - - - -
299Q VAL* 4.7 4.7 - - + -
302Q TYR* 4.0 19.5 - - + -
303Q MET* 3.6 18.7 - - + +
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Residues in contact with PHE 186 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175Q GLU* 3.6 7.4 - - + +
176Q GLY* 3.5 38.4 - - - -
179Q GLY* 5.5 2.2 - - - -
182Q ALA* 3.7 20.2 - - + -
183Q SER* 3.0 15.1 + - - +
185Q ALA* 1.3 80.7 - - - +
187Q HIS* 1.3 71.9 + + - +
189Q ASN* 3.2 5.9 + - - +
190Q THR* 3.1 53.6 + - + +
302Q TYR* 3.3 30.0 - - - +
306Q LEU* 4.1 20.4 - - + -
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Residues in contact with HIS 187 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179Q GLY 2.9 26.6 + - - -
180Q SER* 3.8 12.4 - - - -
182Q ALA* 3.1 24.0 + - - +
183Q SER 3.1 15.4 + - - -
184Q VAL* 3.1 12.5 + - + +
186Q PHE* 1.3 85.9 - + - +
188Q LEU* 1.3 59.0 + - + +
190Q THR* 3.3 9.0 + - - -
191Q GLN* 2.9 47.7 + - - +
199Q LYS 6.1 0.2 - - - +
401Q ADP 3.2 18.8 + - - -
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Residues in contact with LEU 188 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184Q VAL* 2.9 37.0 + - + +
185Q ALA 3.7 3.6 - - - +
187Q HIS* 1.3 77.3 - - + +
189Q ASN* 1.3 64.2 + - - +
191Q GLN* 3.4 19.4 + - - +
192Q LEU* 3.0 30.5 + - - +
198Q PRO* 3.8 14.4 - - + -
199Q LYS 3.4 28.9 - - - +
200Q LEU* 5.0 1.6 - - + -
246Q VAL* 4.6 2.5 - - + -
247Q ALA* 3.8 35.7 - - + +
250Q THR* 4.1 19.5 - - + +
251Q LEU* 5.5 1.1 - - + -
259Q ILE* 4.8 3.8 - - + -
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Residues in contact with ASN 189 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Q ALA 3.0 14.0 + - - +
186Q PHE 3.6 7.4 - - - +
188Q LEU* 1.3 77.7 - - - +
190Q THR* 1.3 67.5 + - - +
192Q LEU* 3.3 2.6 + - - +
193Q ASN* 3.0 43.3 + - - +
250Q THR* 4.5 1.7 - - - +
254Q HIS* 2.8 35.1 + - - -
303Q MET* 3.6 9.5 - - - +
306Q LEU* 3.6 40.3 + - + +
307Q ASN* 3.4 13.2 + - - -
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Residues in contact with THR 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Q PHE* 3.1 48.2 + - + +
187Q HIS* 3.4 12.8 + - - -
189Q ASN* 1.3 84.0 - - - +
191Q GLN* 1.3 68.1 + - - +
193Q ASN* 3.4 6.6 + - - +
194Q ASN* 3.1 36.5 + - - -
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Residues in contact with GLN 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Q HIS* 2.9 31.4 + - - +
188Q LEU* 3.4 15.4 - - - +
190Q THR* 1.3 80.1 + - - +
192Q LEU* 1.3 57.7 + - - +
194Q ASN* 3.3 6.1 + - - +
196Q GLU* 2.9 53.6 + - - +
197Q SER 3.9 14.4 - - - +
198Q PRO* 3.3 6.7 - - + +
199Q LYS* 3.0 49.6 + - + +
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Residues in contact with LEU 192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Q LEU 3.0 21.1 + - - +
189Q ASN 3.7 3.6 - - - +
190Q THR 3.2 0.2 - - - -
191Q GLN* 1.3 72.9 - - - +
193Q ASN* 1.3 64.5 + - - +
194Q ASN 3.1 4.3 - - - -
195Q GLY* 3.2 6.9 + - - -
196Q GLU 4.2 5.8 - - - +
198Q PRO* 3.8 30.7 - - + -
250Q THR* 3.9 8.1 - - + -
251Q LEU* 3.8 22.2 - - + -
254Q HIS* 3.8 39.5 - - + +
256Q LYS* 2.8 43.8 + - - +
257Q GLY* 4.1 18.2 - - - -
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Residues in contact with ASN 193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Q ASN* 3.0 41.1 + - - +
190Q THR* 3.9 7.0 - - - +
191Q GLN 3.4 0.2 - - - -
192Q LEU* 1.3 75.7 - - - +
194Q ASN* 1.3 60.5 + - - +
195Q GLY 3.3 1.9 + - - -
254Q HIS* 3.4 18.1 + - - -
306Q LEU 5.2 1.2 + - - -
307Q ASN* 3.4 18.3 + - - +
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Residues in contact with ASN 194 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190Q THR* 3.1 26.7 + - - +
191Q GLN* 3.6 6.4 - - - +
192Q LEU 3.1 1.0 - - - -
193Q ASN* 1.3 81.1 - - - +
195Q GLY* 1.3 55.6 + - - +
196Q GLU* 3.0 32.2 + - - +
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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