Contacts of the helix formed by residues 240 - 251 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300S GLU 4.0 6.4 - - - +
301S HIS 3.9 14.0 - - - +
303S ASN* 2.8 44.3 + - - +
212X THR 4.2 3.3 - - - +
236X LEU* 4.9 3.8 - - + +
237X GLN* 3.1 25.3 + - + +
238X HIS 3.2 0.8 - - - -
239X ASP* 1.3 74.6 - - - +
241X LEU* 1.3 62.4 + - - +
243X GLY* 3.6 13.6 + - - -
244X HIS* 2.7 34.2 + - - +
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Residues in contact with LEU 241 (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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238X HIS 4.0 11.0 - - - +
239X ASP* 3.1 13.5 + - - +
240X ASP* 1.3 74.5 + - - +
242X ILE* 1.3 58.4 + - + +
244X HIS* 3.3 1.7 + - - -
245X GLN* 3.0 25.3 + - - +
269X GLU* 3.3 40.8 - - + +
270X TRP* 3.9 39.9 - - + +
273X LYS* 4.2 24.7 - - + +
274X THR* 3.1 24.5 - - + +
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Residues in contact with ILE 242 (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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301S HIS* 3.4 51.5 + - + +
302S HIS* 3.8 31.4 - - + +
240X ASP* 3.3 1.2 + - - -
241X LEU* 1.3 75.7 - - + +
243X GLY* 1.3 66.2 + - - +
245X GLN* 3.3 14.2 + - + +
246X LYS* 3.0 42.0 + - + +
273X LYS* 4.2 21.5 - - - +
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Residues in contact with GLY 243 (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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303S ASN* 3.6 31.1 - - - +
214X TRP* 3.6 8.3 - - - +
236X LEU* 3.4 13.3 - - - +
240X ASP* 3.6 16.7 + - - -
241X LEU 3.4 0.2 - - - -
242X ILE* 1.3 76.9 - - - +
244X HIS* 1.3 55.8 + - - +
246X LYS* 3.3 1.8 + - - +
247X LEU* 2.9 25.8 + - - +
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Residues in contact with HIS 244 (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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209X TYR* 6.0 0.4 - - - -
234X ALA* 5.5 1.8 - - - -
235X CYS 4.8 3.2 + - - -
236X LEU* 3.3 40.9 + - + +
237X GLN 3.1 26.2 - - - -
240X ASP 2.7 26.8 + - - -
241X LEU 3.6 7.2 - - - +
242X ILE 3.3 0.4 - - - -
243X GLY* 1.3 74.4 - - - +
245X GLN* 1.3 58.8 + - - +
247X LEU* 4.5 0.2 - - - -
248X ALA* 2.8 32.2 + - - +
255X LEU* 3.4 26.9 - - + +
256X CYS 4.2 9.6 + - - -
257X GLY* 5.3 0.6 - - - -
270X TRP* 3.6 32.8 - + + -
274X THR* 3.9 15.3 - - + -
276X ILE* 4.9 0.7 - - + -
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Residues in contact with GLN 245 (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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241X LEU 3.0 10.3 + - - +
242X ILE* 3.3 22.4 + - + +
244X HIS* 1.3 75.9 - - - +
246X LYS* 1.3 92.6 + - - +
248X ALA* 4.0 1.0 - - - +
249X ALA* 3.1 27.7 + - - +
273X LYS* 3.2 28.0 - - + +
274X THR* 3.4 19.9 - - - +
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Residues in contact with LYS 246 (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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271S LEU 5.4 0.4 + - - -
275S GLY* 4.5 23.6 + - - -
276S ILE 5.3 3.0 + - - -
302S HIS* 3.8 27.7 + - - +
214X TRP* 3.5 48.5 - - + +
242X ILE* 3.0 31.1 + - + +
243X GLY 3.7 1.3 - - - +
245X GLN* 1.3 93.4 - - - +
247X LEU* 1.3 65.7 + - - +
249X ALA* 3.4 5.7 + - - +
250X ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 247 (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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214X TRP* 3.5 13.8 - - + +
217X ALA* 3.9 7.6 - - + +
218X ARG* 3.7 37.7 - - + +
221X PHE* 5.4 2.5 - - + -
235X CYS* 3.6 31.2 - - + -
236X LEU* 4.1 14.4 - - + -
243X GLY 2.9 17.1 + - - +
244X HIS 3.8 3.6 - - - +
246X LYS* 1.3 76.7 - - - +
248X ALA* 1.3 57.7 + - - +
250X ALA* 2.9 18.5 + - - +
251X ILE* 3.0 31.5 + - + +
255X LEU* 3.8 21.8 - - + -
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Residues in contact with ALA 248 (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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218R ARG* 5.6 1.9 + - - -
244X HIS 2.8 22.1 + - - +
245X GLN 4.0 0.7 - - - +
247X LEU* 1.3 73.1 - - - +
249X ALA* 1.3 61.2 + - - +
250X ALA 3.5 0.3 + - - -
251X ILE* 3.6 24.1 - - - +
253X THR 5.0 2.1 - - - +
255X LEU* 3.8 19.4 - - + +
274X THR 3.7 19.3 - - - +
275X GLY 4.2 13.7 - - - +
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Residues in contact with ALA 249 (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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218R ARG* 5.6 0.9 + - - -
245X GLN* 3.1 23.9 + - - +
246X LYS* 4.0 5.4 - - - +
247X LEU 3.2 0.2 - - - -
248X ALA* 1.3 75.3 - - - +
250X ALA* 1.3 59.9 + - - +
251X ILE 4.1 3.3 - - - +
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Residues in contact with ALA 250 (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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214X TRP* 3.9 10.8 - - + -
218X ARG* 3.7 39.2 + - + +
225X GLU* 5.2 3.5 - - - +
246X LYS 3.1 15.2 + - - +
247X LEU* 2.9 5.1 + - - +
249X ALA* 1.3 77.6 - - - +
251X ILE* 1.3 64.8 + - + +
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Residues in contact with ILE 251 (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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218R ARG* 3.6 13.3 + - - -
218X ARG* 5.3 4.9 - - + +
221X PHE* 4.3 24.7 - - + +
222X ARG 5.6 0.2 - - - +
225X GLU* 5.3 4.7 - - - -
232X ILE* 4.3 16.8 - - + -
247X LEU* 3.0 34.3 + - + +
248X ALA* 3.6 16.3 - - - +
249X ALA 4.1 3.6 - - - +
250X ALA* 1.3 81.8 - - + +
252X ASN* 1.3 61.9 + - - +
253X THR* 3.3 24.9 - - - +
254X ARG 4.3 2.0 - - - -
255X LEU* 4.1 30.1 - - + +
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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