Contacts of the helix formed by residues 271 - 283 (chain D) in PDB entry 3H2U
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 271 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ARG* 3.4 10.8 - - - +
269D TYR* 3.8 3.8 - - - +
270D GLU* 1.3 82.3 - - + +
272D ALA* 1.3 60.8 + - - +
273D GLU* 2.8 29.2 + - - +
274D MET* 3.3 27.3 + - + -
275D ALA* 3.2 21.5 + - - +
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Residues in contact with ALA 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D LYS* 4.1 3.8 + - - -
216D ALA 4.7 4.7 - - - +
219D HIS* 3.3 43.1 - - + +
220D SER 3.4 15.9 - - - +
221D ARG* 3.4 8.7 - - + +
271D THR* 1.3 74.1 + - - +
273D GLU* 1.3 57.5 + - - +
275D ALA* 3.7 2.3 - - - +
276D GLU* 3.0 28.3 + - - +
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Residues in contact with GLU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D HIS* 5.6 0.7 + - - -
271D THR* 2.8 11.3 + - - +
272D ALA* 1.3 77.8 - - - +
274D MET* 1.3 60.7 - - + +
275D ALA 3.2 1.6 - - - -
276D GLU* 3.7 10.0 - - + +
277D GLU* 3.0 57.4 + - + +
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Residues in contact with MET 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D HIS* 3.3 55.1 + - + +
247D SER 3.8 17.7 - - - +
269D TYR* 4.0 8.8 - - + -
270D GLU* 3.6 42.2 - - + +
271D THR* 3.3 34.9 + - + +
273D GLU* 1.3 78.0 - - + +
275D ALA* 1.3 59.0 + - - +
277D GLU 3.7 0.2 + - - -
278D ALA* 3.1 29.1 + - - +
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Residues in contact with ALA 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D SER 3.8 4.5 - - - +
221D ARG* 3.4 36.6 - - - +
223D LEU* 3.7 6.8 - - + +
269D TYR* 3.8 16.0 - - + +
271D THR 3.2 12.9 + - - +
272D ALA 3.7 4.7 - - - +
274D MET* 1.3 76.2 - - - +
276D GLU* 1.3 66.9 + - - +
278D ALA* 3.0 4.3 + - - +
279D GLN* 3.0 23.4 + - - +
296D PHE* 4.3 8.5 - - + -
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Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D SER* 2.6 38.6 + - - -
167D GLU* 3.9 8.0 + - - +
168D ARG* 3.6 24.1 - - - +
169D THR* 4.9 0.8 - - + +
173D LYS* 3.5 18.0 + - - +
219D HIS* 4.6 2.4 + - - -
272D ALA 3.0 16.1 + - - +
273D GLU* 3.7 11.5 - - - +
275D ALA* 1.3 80.7 - - - +
277D GLU* 1.3 64.1 + - + +
279D GLN* 3.3 4.7 + - - +
280D GLN* 3.1 23.2 + - - +
296D PHE* 3.6 22.5 - - + -
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Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ARG* 3.5 32.9 + - - +
245D VAL* 4.4 10.7 - - + +
246D HIS* 2.8 41.4 + - + -
273D GLU* 3.0 40.4 + - + +
274D MET 4.1 0.2 - - - +
276D GLU* 1.3 76.7 - - + +
278D ALA* 1.3 60.9 + - - +
280D GLN* 3.4 10.5 - - - +
281D GLN* 3.3 22.2 + - - +
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 4.4 2.7 - - + -
242D LEU* 4.4 6.5 - - + +
245D VAL* 4.7 15.7 - - + -
246D HIS* 4.8 1.0 + - + +
269D TYR* 3.5 35.2 - - + +
274D MET 3.1 19.2 + - - +
275D ALA 3.0 4.8 + - - +
277D GLU* 1.3 75.3 - - - +
279D GLN* 1.3 59.9 + - - +
281D GLN* 3.3 4.6 + - - +
282D ALA* 2.9 34.2 + - + +
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Residues in contact with GLN 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LEU* 3.6 24.8 - - + +
275D ALA 3.0 7.6 + - - +
276D GLU 3.6 8.8 - - - +
278D ALA* 1.3 76.0 - - - +
280D GLN* 1.3 70.1 + - - +
283D ASP* 3.0 42.1 + - - +
294D VAL* 2.6 42.0 + - + +
295D SER* 4.8 1.0 - - - +
296D PHE* 4.0 29.2 - - + -
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Residues in contact with GLN 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ARG* 2.8 35.3 + - - +
169D THR* 4.2 21.6 - - - +
276D GLU* 3.1 10.3 + - + +
277D GLU* 3.4 14.9 - - - +
279D GLN* 1.3 88.6 + - - +
281D GLN* 1.3 60.7 + - - +
283D ASP* 4.2 8.5 + - - +
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Residues in contact with GLN 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ALA 4.3 5.0 + - - +
242D LEU* 5.6 1.4 - - - -
244D ALA* 3.7 28.5 + - - +
245D VAL* 3.9 20.7 - - + +
277D GLU 3.3 11.1 + - - +
278D ALA* 3.3 3.0 + - - +
279D GLN 3.3 0.6 - - - -
280D GLN* 1.3 82.0 - - - +
282D ALA* 1.3 69.4 + - - +
283D ASP 3.6 3.7 + - - +
285D LEU* 3.6 28.4 - - - +
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ALA 5.5 1.3 - - - +
242D LEU* 3.3 35.2 - - + -
278D ALA 2.9 22.6 + - - +
279D GLN 4.4 0.7 - - - +
281D GLN* 1.3 84.2 - - - +
283D ASP* 1.3 63.8 + - - +
284D GLY 3.4 0.3 + - - -
285D LEU* 3.1 28.1 + - + +
292D LEU* 4.6 2.4 - - - +
294D VAL* 3.9 14.4 - - + +
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Residues in contact with ASP 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D GLN* 3.0 38.4 + - - +
280D GLN* 4.2 6.8 + - - +
281D GLN 3.6 4.9 - - - +
282D ALA* 1.3 76.6 - - - +
284D GLY* 1.3 64.3 + - - +
285D LEU 3.2 1.8 + - - -
292D LEU 3.6 3.3 - - - +
293D ARG* 3.7 8.3 - - - +
294D VAL* 3.1 29.7 + - + +
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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