Contacts of the helix formed by residues 274 - 289 (chain D) in PDB entry 2XH2
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 274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256D GLY 5.3 2.7 - - - +
257D LYS* 3.5 27.4 - - + +
258D TYR* 4.4 3.6 - - - -
273D LEU* 1.3 75.5 - - - +
275D GLY* 1.3 65.8 + - - +
276D PRO* 3.6 15.2 - - - +
277D GLN* 3.1 29.6 + - - +
278D LEU* 2.9 21.8 + - - +
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Residues in contact with GLY 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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256D GLY 5.5 1.4 + - - -
258D TYR* 4.4 8.9 - - - -
274D THR* 1.3 75.3 - - - +
276D PRO* 1.4 65.8 - - - +
278D LEU 3.3 0.3 + - - -
279D ALA* 3.0 21.6 + - - +
298D PHE* 3.4 22.2 - - - -
302D ASP* 5.4 0.4 - - - -
305D ALA* 4.3 16.8 - - - -
308D HIS* 5.0 3.1 - - - -
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Residues in contact with PRO 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D THR* 3.6 14.8 - - - +
275D GLY* 1.4 88.9 - - - +
277D GLN* 1.3 60.7 + - + +
279D ALA* 3.4 4.1 - - + +
280D ASP* 3.1 30.4 + - - +
308D HIS* 3.9 31.0 - - + +
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Residues in contact with GLN 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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257D LYS* 4.9 0.9 + - - -
272D TRP 3.8 5.2 - - - +
273D LEU* 3.4 30.3 - - + +
274D THR* 3.1 40.7 + - - +
275D GLY 3.2 0.6 - - - -
276D PRO* 1.3 76.9 - - + +
278D LEU* 1.3 65.2 + - - +
280D ASP* 3.1 11.7 + - - +
281D LEU* 3.1 19.2 + - - +
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Residues in contact with LEU 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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252D PHE* 4.3 4.0 - - + -
258D TYR* 3.5 34.5 - - + -
260D LEU* 3.9 26.5 - - + -
273D LEU* 4.0 11.8 - - + +
274D THR 2.9 16.5 + - - +
277D GLN* 1.3 72.5 - - - +
279D ALA* 1.3 66.2 + - - +
281D LEU* 3.0 25.8 + - + +
282D TYR* 3.0 51.4 + - + +
297D PRO 3.5 12.3 - - - +
298D PHE* 3.7 12.1 - - + -
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Residues in contact with ALA 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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275D GLY 3.0 12.8 + - - +
276D PRO* 3.4 14.4 - - + +
277D GLN 3.3 0.2 - - - -
278D LEU* 1.3 76.3 - - - +
280D ASP* 1.3 57.7 + - - +
282D TYR* 3.2 10.6 + - - +
283D HIS* 2.8 37.3 + - + +
298D PHE* 3.7 13.3 - - + -
308D HIS* 4.6 10.3 - - + +
309D PHE* 3.6 25.5 - - + -
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Residues in contact with ASP 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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276D PRO* 3.1 17.7 + - - +
277D GLN* 3.1 11.9 + - - +
279D ALA* 1.3 73.0 - - - +
281D LEU* 1.3 61.5 + - - +
283D HIS* 3.2 18.5 + - - +
284D SER* 2.9 30.1 + - - -
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Residues in contact with LEU 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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166D LEU* 5.4 3.4 - - + -
221D ALA* 5.7 2.9 - - + -
222D GLU* 6.1 0.9 - - - +
260D LEU* 3.9 24.9 - - + -
273D LEU* 3.8 24.0 - - + -
277D GLN 3.1 11.0 + - - +
278D LEU* 3.0 14.3 + - + +
280D ASP* 1.3 74.8 - - - +
282D TYR* 1.3 77.4 + - + +
284D SER* 3.2 9.4 + - - -
285D LEU* 3.1 41.1 + - + +
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Residues in contact with TYR 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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166D LEU* 4.5 9.2 - - + -
245D LEU* 5.4 1.1 - - + -
247D CYS* 3.5 33.3 - - - +
249D SER* 4.3 1.7 - - - -
252D PHE* 4.5 2.9 - - - -
278D LEU* 3.0 45.7 + - + +
279D ALA* 3.2 9.8 + - - +
281D LEU* 1.3 83.8 - - + +
283D HIS* 1.3 68.1 + - - +
285D LEU* 3.1 13.7 + - + +
286D MET* 2.8 30.7 + - + +
294D ILE* 4.3 12.1 - - + -
297D PRO* 2.6 44.5 + - + -
298D PHE* 3.8 4.9 - + - -
309D PHE* 3.8 28.3 - + + -
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Residues in contact with HIS 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 ALA* 2.8 36.4 + - + +
280D ASP* 3.2 20.2 + - - +
282D TYR* 1.3 72.0 - - - +
284D SER* 1.3 62.2 + - - +
286D MET* 3.2 15.1 + - + +
287D LYS* 3.1 22.5 + - - +
309D PHE* 3.6 24.2 - + - -
312D THR* 3.2 44.2 + - - -
313D ALA* 4.2 2.4 + - - -
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Residues in contact with SER 284 (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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222D GLU* 5.3 4.6 + - - -
280D ASP 2.9 12.7 + - - -
281D LEU* 3.4 12.6 - - - -
282D TYR 3.2 0.2 - - - -
283D HIS* 1.3 75.4 - - - +
285D LEU* 1.3 64.1 - - - +
287D LYS* 3.4 14.8 - - - +
288D ARG* 3.5 17.5 - - - +
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Residues in contact with LEU 285 (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 LEU* 4.3 12.6 - - + -
221D ALA* 4.1 22.4 - - + -
222D GLU* 4.1 22.7 - - + +
225D LEU* 3.9 23.1 - - + -
245D LEU* 4.5 9.4 - - + -
281D LEU* 3.1 34.6 + - + +
282D TYR* 3.1 12.8 + - + +
284D SER* 1.3 77.8 + - - +
286D MET* 1.3 63.7 + - - +
288D ARG 3.1 2.4 + - - -
289D TYR* 3.0 41.2 + - + +
291D ILE* 4.0 13.7 - - + -
294D ILE* 6.4 0.4 - - + -
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Residues in contact with MET 286 (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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282D TYR* 2.8 29.1 + - + +
283D HIS* 3.2 24.7 + - + +
285D LEU* 1.3 77.0 - - - +
287D LYS* 1.3 60.6 + - - +
289D TYR 3.2 17.8 - - - +
291D ILE* 4.4 15.8 - - + +
294D ILE* 4.2 11.2 - - + -
309D PHE* 3.6 29.2 - - + -
313D ALA 3.9 11.9 - - - +
315D ILE* 3.4 39.9 - - + -
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Residues in contact with LYS 287 (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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283D HIS 3.1 12.5 + - - +
284D SER* 3.7 11.9 - - - +
285D LEU 3.2 0.6 - - - -
286D MET* 1.3 77.9 - - - +
288D ARG* 1.3 68.0 + - + +
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Residues in contact with ARG 288 (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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229D VAL* 5.4 0.5 - - - +
284D SER* 3.5 13.9 - - - +
285D LEU 3.1 2.0 + - - -
287D LYS* 1.3 88.0 - - + +
289D TYR* 1.3 89.1 + - + +
290D PRO* 4.6 1.0 - - - +
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Residues in contact with TYR 289 (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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222D GLU* 3.4 24.3 + - + +
225D LEU* 3.5 46.7 - - + -
226D ASP* 2.7 31.5 + - - -
229D VAL* 3.7 19.1 - - + -
243D ILE* 4.5 4.9 - - + -
285D LEU* 3.0 36.3 + - + +
286D MET 3.2 17.7 - - - +
287D LYS 3.6 0.8 - - - -
288D ARG* 1.3 100.3 - - + +
290D PRO* 1.3 59.9 - - + +
291D ILE* 2.8 31.1 + - + +
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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