Contacts of the helix formed by residues 275 - 288 (chain B) in PDB entry 2XWU
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 TYR 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B PRO* 3.1 37.1 - - + +
236B LEU* 3.3 36.5 - - + +
237B GLN* 4.2 19.7 - - + -
271B ASP* 3.6 31.2 + - - -
272B ALA 3.3 6.0 + - - +
273B GLN 3.2 0.4 - - - -
274B ARG* 1.3 88.5 - - + +
276B VAL* 1.3 64.2 + - - +
277B ASN* 3.2 3.8 + - + -
278B THR* 3.4 23.2 + - - +
279B LEU* 3.6 13.5 + - - +
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLN 4.1 6.4 + - - +
274B ARG 3.7 4.8 + - - -
275B TYR* 1.3 75.7 - - - +
277B ASN* 1.3 63.4 + - - +
279B LEU* 3.3 18.9 + - + +
280B LEU* 3.3 23.3 + - + +
322B ALA* 5.3 13.2 - - + +
323B LEU* 4.9 2.7 - - + +
326B GLN* 4.9 19.1 - - + +
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Residues in contact with ASN 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B TYR* 3.2 1.7 - - + -
276B VAL* 1.3 76.2 - - - +
278B THR* 1.3 67.5 + - - +
280B LEU* 3.1 28.8 + - - +
281B LYS* 3.3 28.5 + - - +
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Residues in contact with THR 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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236B LEU* 3.8 23.3 - - + +
237B GLN* 3.7 16.5 - - - +
240B GLU* 3.2 46.1 + - + -
275B TYR* 3.4 17.1 + - - +
276B VAL 3.3 0.4 - - - -
277B ASN* 1.3 77.0 - - - +
279B LEU* 1.3 66.0 + - - +
281B LYS* 2.8 19.4 + - + +
282B LEU* 2.9 33.2 - - + +
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Residues in contact with LEU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 3.3 24.5 - - + -
267B ILE* 4.4 5.2 - - + -
272B ALA* 4.1 8.1 - - + +
273B GLN* 4.7 2.9 - - - +
275B TYR 3.6 10.3 - - - +
276B VAL* 3.3 20.0 - - + +
277B ASN 3.2 0.2 - - - -
278B THR* 1.3 78.5 - - - +
280B LEU* 1.3 62.3 - - - +
282B LEU* 2.9 23.7 + - + +
283B ILE* 3.2 14.0 + - - +
315B LEU* 4.1 14.7 - - + +
319B HIS* 3.3 54.7 - - + +
322B ALA* 5.4 3.8 - - + -
323B LEU* 4.3 13.7 - - + -
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Residues in contact with LEU 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 VAL* 3.3 12.3 + - + +
277B ASN* 3.1 22.4 + - - +
279B LEU* 1.3 77.1 - - - +
281B LYS* 1.3 57.3 + - + +
283B ILE* 3.2 16.5 + - + +
284B PRO* 3.1 23.9 - - - +
323B LEU* 3.8 24.6 - - + +
326B GLN* 4.5 21.5 - - + -
329B HIS* 3.6 56.5 - - + +
332B SER* 5.9 1.5 - - - -
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Residues in contact with LYS 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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237B GLN* 5.4 4.8 - - - +
240B GLU* 3.1 39.2 + - - +
277B ASN* 3.8 25.2 - - - +
278B THR* 2.8 16.4 + - + +
280B LEU* 1.3 76.3 - - + +
282B LEU* 1.3 62.0 + - + +
284B PRO* 2.9 23.5 - - - +
285B LEU* 4.1 10.5 - - - +
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Residues in contact with LEU 282 (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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236B LEU* 4.7 3.8 - - + -
240B GLU* 5.3 2.7 - - + -
243B ILE* 4.4 28.7 - - + -
247B PHE* 4.8 7.6 - - + -
267B ILE* 3.8 34.5 - - + -
278B THR* 2.9 46.8 + - + +
279B LEU* 2.9 25.7 + - + +
281B LYS* 1.3 81.8 - - + +
283B ILE* 1.3 55.2 + - - +
285B LEU* 2.7 37.9 + - + +
286B VAL* 3.0 9.5 + - - +
315B LEU* 4.2 11.4 - - + -
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Residues in contact with ILE 283 (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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279B LEU 3.2 11.4 + - - +
280B LEU* 3.4 14.4 - - + +
282B LEU* 1.3 73.9 - - - +
284B PRO* 1.3 66.6 - - + +
286B VAL* 3.0 5.6 + - - +
287B LEU* 2.8 37.5 + - + +
315B LEU* 3.8 23.7 - - + +
323B LEU* 4.0 31.6 - - + -
329B HIS* 6.2 0.2 - - + -
332B SER* 3.7 34.1 - - - +
333B PHE* 4.3 24.5 - - + +
336B LEU* 4.3 10.5 - - + -
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Residues in contact with PRO 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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280B LEU 3.1 15.3 - - - +
281B LYS* 2.9 21.8 - - - +
283B ILE* 1.3 98.5 - - + +
285B LEU* 1.3 57.7 + - + +
287B LEU* 3.7 10.1 - - + +
288B GLY* 2.8 27.9 + - - -
332B SER* 5.8 1.1 - - - +
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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
----------------------------------------------------------
243B ILE* 5.1 1.3 - - + -
244B GLN* 4.3 35.4 - - + +
247B PHE* 3.6 53.5 - - + -
281B LYS 4.1 14.8 - - - +
282B LEU* 2.7 22.9 + - + +
284B PRO* 1.3 76.0 - - + +
286B VAL* 1.3 61.3 + - - +
288B GLY* 3.6 7.5 + - - -
289B LEU* 3.7 8.5 + - - +
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Residues in contact with VAL 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE* 3.9 22.2 - - + -
267B ILE* 5.4 1.3 - - + -
282B LEU* 3.0 5.4 + - + +
283B ILE* 3.0 10.6 + - - +
285B LEU* 1.3 75.4 - - - +
287B LEU* 1.3 60.9 + - - +
289B LEU* 2.9 29.6 + - + +
308B ILE 5.9 0.2 - - - +
311B ILE* 4.1 14.8 - - + -
312B ALA* 3.9 10.3 - - + +
315B LEU* 3.7 28.0 - - + -
336B LEU* 3.5 29.4 - - + -
339B MET* 3.4 20.5 - - + +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 2.8 36.6 + - + +
284B PRO* 3.8 9.2 - - + +
286B VAL* 1.3 75.2 - - + +
288B GLY* 1.3 61.7 + - - +
289B LEU 3.0 1.4 + - - -
290B GLN* 3.0 53.5 + - - +
332B SER* 4.1 4.3 - - - +
335B ALA* 3.6 23.1 - - + +
336B LEU* 3.6 30.1 - - + +
339B MET* 4.0 7.2 - - - -
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Residues in contact with GLY 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 PRO 2.8 16.7 + - - -
285B LEU* 3.6 4.9 + - - -
286B VAL 3.1 1.2 - - - -
287B LEU* 1.3 76.6 - - - +
289B LEU* 1.3 63.6 + - - +
290B GLN 3.4 0.7 + - - -
291B GLU* 4.1 9.7 + - - +
292B GLN* 5.0 0.7 + - - +
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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