Contacts of the helix formed by residues 251 - 265 (chain B) in PDB entry 2QU7
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 ASN 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASN* 3.8 11.6 - - - +
186B ALA* 3.8 13.9 - - - +
196B ARG* 4.4 6.5 - - - +
228B GLN* 3.4 22.2 + - - +
249B ALA 3.4 1.3 - - - +
250B THR* 1.3 79.2 + - - +
252B HIS* 1.3 55.7 + - - +
253B LEU* 3.1 10.0 + - - +
254B LEU* 2.8 49.6 + - - +
255B LEU* 2.8 33.3 + - - +
278B PHE* 3.7 7.9 - - - -
279B ASP* 3.5 12.8 - - - +
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Residues in contact with HIS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 3.6 33.8 + + - -
75B ASN* 3.4 20.4 - - - +
76B PRO* 3.5 32.3 - - + +
251B ASN* 1.3 71.7 - - - +
253B LEU* 1.3 59.6 + - + +
255B LEU* 3.2 11.3 - - + +
256B LEU* 2.8 59.4 + - + +
278B PHE 3.3 6.9 + - - -
279B ASP* 2.7 34.7 + - + +
280B ASP 4.8 1.9 + - - -
281B SER* 3.9 18.2 - - - -
284B ASN* 5.1 1.8 - - - -
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Residues in contact with LEU 253 (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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73B ASP* 4.2 14.1 - - - +
74B GLN 4.5 3.1 - - - +
75B ASN* 4.3 24.9 - - + +
76B PRO* 4.7 0.9 - - + -
225B THR* 3.8 40.2 - - + +
228B GLN* 3.9 32.1 - - + +
229B ILE* 3.5 30.5 - - + +
251B ASN* 3.1 6.2 + - - +
252B HIS* 1.3 79.2 - - + +
254B LEU* 1.3 64.4 + - - +
256B LEU* 3.2 17.9 + - + +
257B GLY 3.0 18.7 + - - -
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Residues in contact with LEU 254 (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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184B LEU* 3.3 39.1 - - + +
185B LEU* 3.4 26.7 - - - +
186B ALA* 3.5 4.7 - - - +
219B SER* 4.4 6.1 - - - -
228B GLN* 3.4 26.0 - - + +
231B SER* 3.9 11.7 - - - +
232B GLY* 3.8 19.4 - - - +
249B ALA* 4.1 4.7 - - + -
250B THR* 3.7 7.4 - - - +
251B ASN* 2.8 37.1 + - - +
253B LEU* 1.3 71.8 - - - +
255B LEU* 1.3 53.0 + - - +
257B GLY* 3.1 2.9 + - - -
258B ALA* 2.8 33.6 + - - +
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 5.4 1.6 - - + -
249B ALA* 3.6 12.8 - - + +
251B ASN 2.8 13.2 + - - +
252B HIS* 3.2 17.9 - - + +
254B LEU* 1.3 76.7 - - - +
256B LEU* 1.3 63.9 + - + +
258B ALA* 3.0 4.6 + - - +
259B LEU* 2.9 48.4 + - + +
275B ILE* 4.0 22.9 - - + -
277B GLY* 4.2 17.5 - - - +
278B PHE 4.5 6.7 - - - +
279B ASP 4.9 2.2 - - - +
284B ASN* 4.3 13.5 - - - +
291B LEU* 4.6 6.3 - - + -
293B VAL* 4.1 25.1 - - + -
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A TYR* 4.6 19.3 - - + -
283A TRP* 3.9 46.2 - - + +
286A ILE* 4.2 12.8 - - + +
229B ILE* 4.5 16.4 - - + -
252B HIS* 2.8 46.4 + - + +
253B LEU* 3.2 19.7 + - + +
255B LEU* 1.3 73.3 - - + +
257B GLY* 1.3 57.7 + - - +
259B LEU* 3.4 6.6 + - + +
260B GLN* 3.1 33.7 + - + +
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Residues in contact with GLY 257 (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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229B ILE* 3.2 27.5 - - - +
233B TYR* 3.1 25.7 - - - +
253B LEU 3.0 10.9 + - - -
254B LEU 3.5 2.9 - - - -
256B LEU* 1.3 73.5 - - - +
258B ALA* 1.3 63.9 + - - +
260B GLN* 3.4 11.0 + - - +
261B ALA 3.1 12.6 + - - -
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Residues in contact with ALA 258 (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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184B LEU* 3.9 8.7 - - + -
232B GLY 3.8 1.4 - - - -
236B THR* 3.4 27.1 - - + +
247B ILE* 4.8 0.4 - - + -
254B LEU 2.8 16.6 + - - +
255B LEU* 3.0 10.1 + - - +
257B GLY* 1.3 71.7 - - - +
259B LEU* 1.3 57.6 + - - +
261B ALA* 3.0 19.1 + - - +
262B ILE* 3.0 20.4 + - - +
275B ILE* 3.7 27.1 - - + -
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 4.4 13.0 - - + -
286A ILE* 4.0 11.1 - - + +
255B LEU* 2.9 40.5 + - + +
256B LEU* 3.9 6.5 - - - +
258B ALA* 1.3 75.6 - - - +
260B GLN* 1.3 58.1 + - - +
262B ILE* 3.9 6.9 - - + +
263B LYS* 2.9 32.4 + - - +
269B ILE* 4.2 15.3 - - + -
275B ILE* 4.7 7.2 - - + -
287B TYR* 3.9 29.1 + - + +
291B LEU* 3.6 43.7 - - + -
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Residues in contact with GLN 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A TYR* 3.4 40.5 - - - +
285A GLU* 4.9 5.5 + - + +
286A ILE* 3.8 22.2 - - + +
229B ILE* 3.5 26.3 - - - +
230B TYR* 5.6 0.3 - - - -
233B TYR* 3.8 24.8 - - + +
256B LEU* 3.1 18.4 + - - +
257B GLY* 3.5 6.4 - - - +
258B ALA 3.3 0.2 - - - -
259B LEU* 1.3 77.0 - - - +
261B ALA* 1.3 60.9 + - - +
263B LYS* 3.9 1.4 - - - +
264B GLU* 3.1 25.1 + - - +
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Residues in contact with ALA 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TYR* 3.3 41.9 - - + +
236B THR* 3.7 15.7 - - + -
237B LYS* 3.7 14.5 - - + +
240B LEU* 4.1 3.5 - - + +
257B GLY 3.1 2.9 + - - +
258B ALA 3.0 9.4 + - - +
260B GLN* 1.3 76.4 - - - +
262B ILE* 1.3 61.3 + - - +
264B GLU* 3.6 4.0 + - - +
265B SER* 3.0 28.8 + - - -
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Residues in contact with ILE 262 (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 THR* 4.1 9.0 - - + -
240B LEU* 3.8 18.8 - - + -
247B ILE* 5.0 0.9 - - + -
258B ALA 3.0 24.7 + - - +
259B LEU* 3.9 8.3 - - + +
261B ALA* 1.3 74.5 - - - +
263B LYS* 1.3 65.7 + - - +
265B SER* 2.7 28.0 + - - +
267B LYS* 3.7 19.0 - - + +
269B ILE* 3.8 34.5 - - + -
273B VAL* 4.4 26.0 - - + -
275B ILE* 4.3 21.3 - - + -
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Residues in contact with LYS 263 (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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285A GLU 3.9 16.4 - - - +
286A ILE* 2.8 37.6 + - + +
287A TYR 2.9 12.7 + - - -
288A THR* 2.8 29.3 + - - +
289A PRO* 5.6 0.4 - - - +
290A LYS* 4.0 19.0 - - - +
331A GLU* 5.6 1.0 + - - -
259B LEU 2.9 19.2 + - - +
260B GLN 3.9 4.0 - - - +
262B ILE* 1.3 77.7 - - - +
264B GLU* 1.3 55.1 + - - +
265B SER 2.8 18.5 - - - +
267B LYS 5.6 0.2 - - - -
287B TYR* 4.3 6.0 + - - +
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Residues in contact with GLU 264 (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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233B TYR* 2.8 37.4 + - - -
237B LYS* 4.3 13.2 - - - +
260B GLN 3.1 16.1 + - - +
261B ALA 3.8 3.7 - - - +
263B LYS* 1.3 80.4 - - - +
265B SER* 1.3 61.1 + - - +
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Residues in contact with SER 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.7 10.7 - - - +
261B ALA 3.0 15.2 + - - -
262B ILE* 2.7 26.2 + - - +
263B LYS 2.8 17.3 - - - +
264B GLU* 1.3 79.2 - - - +
266B GLU* 1.3 64.5 + - - +
267B LYS* 3.3 23.6 + - - +
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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
------------------------------------------------------------
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