Contacts of the helix formed by residues 240 - 251 (chain Q) in PDB entry 3MQT
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 240 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212Q THR 4.3 3.5 - - - +
236Q LEU* 4.7 5.0 - - + +
237Q GLN* 3.0 26.3 + - + +
238Q HIS 3.3 0.4 - - - -
239Q ASP* 1.3 73.7 - - - +
241Q LEU* 1.3 60.7 + - - +
242Q ILE 3.8 1.9 + - - -
243Q GLY* 3.3 17.0 + - - -
244Q HIS* 2.7 32.7 + - - +
300R GLU 4.2 7.1 - - - +
301R HIS 4.2 9.7 - - - +
303R ASN* 2.9 42.6 + - - +
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Residues in contact with LEU 241 (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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238Q HIS 3.9 8.1 - - - +
239Q ASP* 3.2 10.9 + - - +
240Q ASP* 1.3 74.9 + - - +
242Q ILE* 1.3 58.5 + - + +
244Q HIS 3.3 0.7 + - - -
245Q GLN* 3.0 26.3 + - - +
269Q GLU* 3.6 38.8 - - + +
270Q TRP* 3.7 47.1 - - + +
273Q LYS* 4.1 27.1 - - + +
274Q THR* 3.2 24.4 - - + +
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Residues in contact with ILE 242 (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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240Q ASP* 3.3 1.2 + - - -
241Q LEU* 1.3 76.0 - - + +
243Q GLY* 1.3 64.4 + - - +
245Q GLN* 3.2 14.5 + - + +
246Q LYS* 3.1 39.4 + - + +
273Q LYS* 4.3 21.3 - - - +
301R HIS* 3.5 49.3 + - + +
302R HIS* 3.7 33.4 - - + +
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Residues in contact with GLY 243 (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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214Q TRP* 3.4 9.7 - - - +
236Q LEU* 3.4 14.6 - - - +
240Q ASP* 3.3 27.6 + - - -
242Q ILE* 1.3 79.8 - - - +
244Q HIS* 1.3 55.2 + - - +
246Q LYS* 3.5 0.3 + - - +
247Q LEU 3.0 22.7 + - - -
303R ASN* 3.6 19.1 - - - +
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Residues in contact with HIS 244 (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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209Q TYR* 6.1 0.4 - - - -
234Q ALA* 5.5 1.6 - - - -
235Q CYS 4.8 3.6 + - - -
236Q LEU* 3.6 38.6 + - + +
237Q GLN 3.3 24.0 - - - -
238Q HIS* 4.8 0.4 - - - -
240Q ASP 2.7 24.4 + - - -
241Q LEU 3.6 6.7 - - - +
243Q GLY* 1.3 75.5 - - - +
245Q GLN* 1.3 54.6 + - - +
247Q LEU* 4.5 0.2 - - - -
248Q ALA* 2.7 36.9 + - - +
255Q LEU* 3.5 27.6 - - + +
256Q CYS 4.0 11.0 + - - -
257Q GLY* 5.1 0.4 - - - -
270Q TRP* 3.6 31.2 - + + -
274Q THR* 3.8 16.4 - - + -
276Q ILE* 4.7 0.9 - - + -
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Residues in contact with GLN 245 (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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241Q LEU 3.0 10.1 + - - +
242Q ILE* 3.2 19.4 + - + +
244Q HIS* 1.3 76.8 - - - +
246Q LYS* 1.3 81.0 + - - +
248Q ALA* 3.9 1.6 - - - +
249Q ALA* 3.2 27.1 + - - +
273Q LYS 3.1 27.3 - - - +
274Q THR* 3.3 21.0 - - - +
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Residues in contact with LYS 246 (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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214Q TRP* 3.5 56.5 - - + +
242Q ILE* 3.1 30.1 + - + +
243Q GLY 3.9 1.1 - - - +
245Q GLN* 1.3 89.7 - - - +
247Q LEU* 1.3 64.8 + - - +
249Q ALA* 3.6 4.6 + - - +
250Q ALA* 3.1 17.5 + - - +
271R LEU 5.7 0.4 + - - -
275R GLY* 4.9 22.1 + - - -
276R ILE 5.2 4.0 + - - -
277R SER* 6.3 0.4 - - - +
302R HIS* 3.1 33.7 + - - +
304R ALA* 6.0 0.6 - - - +
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Residues in contact with LEU 247 (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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214Q TRP* 3.6 14.2 - - + +
217Q ALA* 3.9 7.4 - - + +
218Q ARG* 3.6 39.7 - - + +
221Q PHE* 5.3 2.9 - - + -
235Q CYS* 3.6 31.0 - - + -
236Q LEU* 4.0 14.8 - - + -
243Q GLY 3.0 18.1 + - - +
244Q HIS 3.8 2.5 - - - +
246Q LYS* 1.3 73.1 - - - +
248Q ALA* 1.3 65.8 + - - +
250Q ALA* 3.0 11.0 + - - +
251Q ILE* 3.1 36.9 + - + +
255Q LEU* 4.0 20.6 - - + -
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Residues in contact with ALA 248 (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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244Q HIS 2.7 22.0 + - - +
245Q GLN 3.9 0.9 - - - +
247Q LEU* 1.3 74.8 - - - +
249Q ALA* 1.3 61.6 + - - +
251Q ILE* 3.6 21.7 - - - +
253Q THR 4.9 2.3 - - - +
255Q LEU* 4.0 20.6 - - + +
274Q THR 3.5 20.6 - - - +
275Q GLY 4.3 13.7 - - - +
276Q ILE 4.7 0.4 - - - +
218S ARG* 5.7 1.4 + - - -
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Residues in contact with ALA 249 (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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245Q GLN* 3.2 20.9 + - - +
246Q LYS* 4.0 5.4 - - - +
247Q LEU 3.2 0.2 - - - -
248Q ALA* 1.3 78.4 - - - +
250Q ALA* 1.3 60.9 + - - +
251Q ILE 4.0 3.5 - - - +
218S ARG* 5.6 1.7 + - - -
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Residues in contact with ALA 250 (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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214Q TRP* 4.0 10.1 - - + -
218Q ARG* 3.7 40.5 + - + +
225Q GLU* 5.2 3.6 - - - +
246Q LYS 3.1 16.7 + - - +
247Q LEU* 3.0 5.5 + - - +
249Q ALA* 1.3 75.5 - - - +
251Q ILE* 1.3 65.6 + - + +
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Residues in contact with ILE 251 (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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218Q ARG* 5.1 5.6 - - + +
221Q PHE* 4.4 22.2 - - + -
225Q GLU* 5.4 3.1 - - - -
232Q ILE* 4.1 23.6 - - + -
247Q LEU* 3.1 37.7 + - + +
248Q ALA 3.6 12.7 - - - +
249Q ALA 4.0 2.9 - - - +
250Q ALA* 1.3 82.2 - - + +
252Q ASN* 1.3 60.1 + - - +
253Q THR* 3.3 25.6 - - - +
255Q LEU* 4.2 26.7 - - + +
218S ARG* 3.6 13.0 + - - -
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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