Contacts of the helix formed by residues 274 - 289 (chain B) in PDB entry 2XGZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256B GLY 4.8 6.3 - - - -
257B LYS* 3.6 25.8 - - + +
258B TYR* 4.2 2.2 - - - -
273B LEU* 1.3 76.1 - - - +
275B GLY* 1.3 65.2 + - - +
276B PRO* 3.3 18.5 - - - +
277B GLN* 3.1 26.4 + - - +
278B LEU* 2.9 21.3 + - - +
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Residues in contact with GLY 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B GLY 5.0 2.2 + - - -
258B TYR* 4.2 14.9 - - - -
274B THR* 1.3 72.7 - - - +
276B PRO* 1.4 55.4 - - - +
278B LEU 3.1 3.3 + - - -
279B ALA* 2.8 31.3 + - - +
298B PHE* 3.3 24.6 - - - -
302B ASP* 5.0 0.8 + - - -
305B ALA* 4.3 13.5 - - - -
308B HIS* 5.4 1.8 - - - -
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Residues in contact with PRO 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B THR* 3.3 14.6 - - - +
275B GLY* 1.4 89.7 - - - +
277B GLN* 1.3 56.4 + - + +
279B ALA* 3.3 10.9 + - + +
280B ASP* 3.1 33.4 + - - +
305B ALA* 6.3 0.4 - - - -
308B HIS* 4.2 25.0 - - + +
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Residues in contact with GLN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B LYS* 4.7 2.1 + - - -
272B TRP 4.1 4.4 + - - +
273B LEU* 3.5 32.2 - - + +
274B THR* 3.1 40.6 + - - +
276B PRO* 1.3 73.9 - - + +
278B LEU* 1.3 65.2 + - - +
280B ASP* 3.2 22.2 + - - +
281B LEU* 3.4 9.2 + - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B PHE* 4.2 3.6 - - + -
258B TYR* 3.5 37.5 - - + -
260B LEU* 4.3 16.4 - - + -
273B LEU* 3.9 16.2 - - + +
274B THR 2.9 13.1 + - - +
275B GLY 3.4 7.6 - - - +
277B GLN* 1.3 76.1 - - - +
279B ALA* 1.3 63.0 + - - +
281B LEU* 3.2 30.2 + - + +
282B TYR* 3.2 50.9 + - + +
297B PRO 3.5 12.1 - - - +
298B PHE* 4.0 5.4 - - + -
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLY 2.8 12.9 + - - +
276B PRO* 3.4 15.0 - - + +
277B GLN 3.2 0.2 - - - -
278B LEU* 1.3 78.8 - - - +
280B ASP* 1.3 56.6 + - - +
282B TYR* 3.4 7.4 + - - +
283B HIS* 2.9 39.9 + - + +
298B PHE* 4.0 11.8 - - + -
308B HIS* 5.0 9.2 - - + +
309B PHE* 3.6 25.1 - - + -
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276B PRO 3.1 20.2 + - - +
277B GLN* 3.4 15.8 - - - +
278B LEU 3.2 0.6 - - - -
279B ALA* 1.3 73.5 - - - +
281B LEU* 1.3 60.5 + - - +
283B HIS* 3.3 13.3 + - - +
284B SER* 2.9 29.0 + - - -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LEU* 5.7 3.4 - - + -
221B ALA* 5.7 5.6 - - + -
222B GLU* 4.2 19.3 - - - +
260B LEU* 3.5 33.7 - - + -
273B LEU* 5.0 3.6 - - + -
277B GLN 3.4 6.9 + - - +
278B LEU* 3.2 21.4 + - + +
280B ASP* 1.3 78.4 - - - +
282B TYR* 1.3 69.0 + - + +
284B SER* 2.8 27.7 + - - +
285B LEU* 3.0 23.8 + - + +
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Residues in contact with TYR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.4 11.9 - - + -
245B LEU* 5.5 1.1 - - + -
247B CYS* 3.6 33.7 - - - +
249B SER* 4.3 2.3 - - - -
252B PHE* 4.3 3.3 - - - -
278B LEU* 3.2 44.1 + - + +
279B ALA* 3.8 10.3 - - - +
280B ASP 3.4 0.2 - - - -
281B LEU* 1.3 80.0 - - + +
283B HIS* 1.3 57.4 + - - +
285B LEU* 3.2 18.0 + - + +
286B MET* 2.8 34.4 + - - +
294B ILE* 4.4 13.6 - - + +
297B PRO* 2.7 48.5 + - + -
298B PHE* 4.0 4.7 - + - -
309B PHE* 3.8 24.0 - + + -
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Residues in contact with HIS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ALA* 2.9 34.2 + - + +
280B ASP* 3.5 14.4 - - - +
282B TYR* 1.3 76.9 - - - +
284B SER* 1.3 60.1 + - - +
286B MET* 3.2 17.4 + - + +
287B LYS* 3.1 46.1 + - - +
309B PHE* 3.6 23.3 - + - -
312B THR* 3.7 40.4 + - - -
313B ALA* 4.3 3.8 - - - -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B GLU* 5.0 2.9 + - - -
280B ASP 2.9 12.7 + - - -
281B LEU* 2.8 31.0 + - - +
283B HIS* 1.3 72.1 - - - +
285B LEU* 1.3 66.1 + - - +
287B LYS* 3.5 14.0 + - - +
288B ARG* 3.4 26.3 + - - +
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.4 14.6 - - + -
221B ALA* 4.0 20.6 - - + -
222B GLU* 4.0 29.4 - - + +
225B LEU* 3.8 22.2 - - + -
245B LEU* 4.4 9.4 - - + -
281B LEU* 3.0 31.7 + - + +
282B TYR* 3.5 15.7 - - + +
284B SER* 1.3 78.5 + - - +
286B MET* 1.3 62.8 + - - +
288B ARG 3.1 2.3 + - - -
289B TYR* 3.0 37.6 + - + +
291B ILE* 3.9 14.3 - - + +
294B ILE* 6.4 0.7 - - + -
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B TYR 2.8 28.9 + - - +
283B HIS* 3.2 21.1 + - - +
285B LEU* 1.3 72.8 - - - +
287B LYS* 1.3 60.5 + - + +
289B TYR 3.1 20.3 - - - +
291B ILE* 4.6 12.4 - - + +
294B ILE* 3.9 22.7 - - + -
309B PHE* 4.2 11.4 - - - -
313B ALA* 3.0 33.9 - - - +
315B ILE* 3.9 29.4 - - + -
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Residues in contact with LYS 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B HIS* 3.1 36.6 + - - +
284B SER* 3.9 11.2 - - - +
285B LEU 3.2 0.4 - - - -
286B MET* 1.3 77.7 - - + +
288B ARG* 1.3 65.2 + - + +
289B TYR 4.0 0.2 + - - -
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B SER 3.4 13.4 + - - +
285B LEU 3.1 2.4 + - - -
287B LYS* 1.3 85.3 - - + +
289B TYR* 1.3 89.7 + - + +
290B PRO* 4.8 0.2 - - - +
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Residues in contact with TYR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B GLU* 3.4 19.2 + - + +
225B LEU* 3.6 46.0 - - + -
226B ASP* 2.7 37.3 + - - -
229B VAL* 4.0 19.5 - - + -
243B ILE* 4.5 4.5 - - + -
285B LEU* 3.0 30.2 + - + +
286B MET 3.1 19.1 - - - +
287B LYS 3.6 0.6 + - - -
288B ARG* 1.3 98.9 - - + +
290B PRO* 1.4 61.3 - - + +
291B ILE* 2.8 30.0 + - + +
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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