Contacts of the helix formed by residues 250 - 267 (chain B) in PDB entry 2AXZ
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 250 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244B GLN 5.0 0.4 + - - -
245B PHE* 3.3 18.5 + - - +
248B ASP* 3.5 11.6 - - + +
249B LYS* 1.3 75.3 - - - +
251B ILE* 1.3 94.7 + - - +
252B ASP* 3.1 28.3 + - - +
253B SER* 2.8 25.0 + - - +
290I THR 4.3 2.4 + - - -
292I PRO* 5.7 0.9 - - - +
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Residues in contact with ILE 251 (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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245B PHE* 4.0 15.6 - - + -
249B LYS 4.3 0.4 - - - -
250B ASN* 1.3 90.3 - - - +
252B ASP* 1.3 60.8 + - - +
254B TYR* 3.1 5.7 + - + +
255B LEU* 2.8 41.5 + - + +
254C TYR* 5.5 3.6 - - + +
290I THR* 3.0 57.0 - - - +
291I PRO* 3.6 10.1 - - + -
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Residues in contact with ASP 252 (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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250B ASN* 2.8 29.8 + - - +
251B ILE* 1.3 82.8 - - - +
253B SER* 1.3 62.2 + - - +
255B LEU* 3.2 10.1 + - - +
256B ASN* 2.9 36.9 + - - +
291I PRO* 3.7 9.6 - - - +
292I PRO* 2.7 48.1 - - - +
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Residues in contact with SER 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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241B GLN* 3.3 39.0 + - - +
244B GLN* 3.1 29.5 + - - +
245B PHE* 3.7 12.6 - - - -
248B ASP* 5.9 0.7 - - - +
250B ASN* 2.8 21.8 + - - +
252B ASP* 1.3 74.3 - - - +
254B TYR* 1.3 63.4 + - - +
256B ASN* 3.3 4.8 + - - +
257B ALA* 3.1 17.2 + - - +
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Residues in contact with TYR 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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242B ILE* 4.5 9.6 - - + -
245B PHE* 3.5 48.1 - + + -
250B ASN 3.6 1.8 + - - -
251B ILE* 3.1 9.5 + - + +
253B SER* 1.3 77.3 - - - +
255B LEU* 1.3 70.9 + - + +
257B ALA* 3.0 10.0 + - - +
258B VAL* 3.0 44.8 + - + +
280B LEU* 4.3 15.3 - - + +
284B SER* 4.4 17.0 + - - -
251C ILE* 3.9 31.3 - - + +
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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
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251B ILE* 2.8 35.2 + - + +
252B ASP* 3.5 12.6 - - - +
254B TYR* 1.3 81.1 - - + +
256B ASN* 1.3 62.2 + - - +
258B VAL* 3.2 6.4 + - + +
259B ASN* 2.8 29.2 + - - +
251C ILE* 4.0 30.3 - - + -
254C TYR* 5.3 9.0 - - + -
255C LEU* 3.9 32.1 - - + -
291I PRO* 4.5 14.8 - - + -
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Residues in contact with ASN 256 (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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266A ILE* 4.4 23.8 - - + +
241B GLN* 3.6 29.6 + - + +
252B ASP* 2.9 25.9 + - - +
253B SER* 3.4 8.2 - - - +
254B TYR 3.2 0.2 - - - -
255B LEU* 1.3 78.2 - - - +
257B ALA* 1.3 66.0 + - - +
259B ASN* 3.1 7.6 + - - +
260B ILE* 2.9 30.2 + - - +
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Residues in contact with ALA 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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238B TYR* 3.9 16.7 - - + +
241B GLN* 4.0 7.1 - - + +
242B ILE* 3.7 36.3 - - + -
253B SER 3.1 11.6 + - - +
254B TYR 3.0 9.8 + - - +
256B ASN* 1.3 76.9 - - - +
258B VAL* 1.3 63.7 + - + +
260B ILE* 3.3 6.9 + - - +
261B ILE* 3.0 28.8 + - - +
280B LEU* 5.2 2.7 - - + -
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Residues in contact with VAL 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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254B TYR* 3.0 44.4 + - + +
255B LEU* 3.5 10.1 - - + +
257B ALA* 1.3 76.7 - - - +
259B ASN* 1.3 63.5 + - - +
261B ILE* 3.1 10.9 + - + +
262B ASN* 2.9 25.6 + - + +
280B LEU* 3.8 15.7 - - + -
251C ILE* 4.3 24.2 - - + -
252C ASP* 6.0 1.3 - - - +
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Residues in contact with ASN 259 (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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259A ASN* 2.9 37.5 + - - +
262A ASN* 5.5 1.6 - - - +
263A ILE* 3.7 23.8 - - + +
266A ILE* 3.8 13.5 - - + +
255B LEU 2.8 14.4 + - - +
256B ASN* 3.1 12.1 + - - +
258B VAL* 1.3 77.4 - - - +
260B ILE* 1.3 62.1 + - - +
262B ASN* 3.2 8.3 + - - +
263B ILE* 3.0 28.9 + - - +
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Residues in contact with ILE 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A ILE* 3.5 23.6 - - + -
266A ILE* 4.4 10.8 - - + -
267A ILE* 4.8 1.6 - - + -
234B LEU* 3.3 44.0 - - + +
237B ASN* 3.9 14.1 - - + +
238B TYR* 3.5 34.1 - - + +
241B GLN* 4.0 11.2 - - + -
256B ASN 2.9 20.5 + - - +
257B ALA 3.6 4.9 - - - +
259B ASN* 1.3 73.2 - - - +
261B ILE* 1.3 67.2 + - - +
263B ILE* 3.1 17.5 + - - +
264B PHE* 3.5 11.9 + - + -
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Residues in contact with ILE 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TYR* 3.5 37.9 - - + -
257B ALA 3.0 16.9 + - - +
258B VAL* 3.5 7.4 - - + +
260B ILE* 1.3 74.8 - - - +
262B ASN* 1.3 63.0 + - - +
264B PHE* 3.2 19.6 - - - +
273B HIS* 3.0 22.9 - - + +
276B LEU* 3.8 31.2 - - + +
277B VAL* 3.9 22.7 - - + +
280B LEU* 3.7 35.0 - - + -
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Residues in contact with ASN 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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259A ASN* 3.7 18.6 - - - +
258B VAL* 2.9 16.8 + - + +
259B ASN* 3.4 13.0 + - - +
261B ILE* 1.3 75.3 - - - +
263B ILE* 1.3 56.1 + - - +
265B LYS* 2.7 35.9 + - - +
266B ILE* 3.1 33.2 + - - +
273B HIS* 4.3 8.3 + - - -
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Residues in contact with ILE 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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234A LEU* 3.4 30.3 - - + -
259A ASN* 3.0 41.1 - - - +
260A ILE* 4.5 15.9 - - + -
263A ILE* 3.4 26.2 - - + -
234B LEU* 3.8 18.2 - - + -
259B ASN* 3.0 25.6 + - - +
260B ILE 3.1 8.2 + - - +
262B ASN* 1.3 75.5 - - - +
264B PHE* 1.3 62.6 + - - +
266B ILE* 3.2 8.4 + - + +
267B ILE* 3.1 27.2 + - + +
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Residues in contact with PHE 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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231B TYR* 3.8 44.2 - + + -
234B LEU* 4.0 24.9 - - + -
235B GLU* 4.2 16.2 - - + -
238B TYR* 6.4 0.2 - - + -
260B ILE* 3.5 19.2 + - + -
261B ILE* 3.2 13.4 + - - +
262B ASN 3.0 0.4 + - - -
263B ILE* 1.3 79.1 - - - +
265B LYS* 1.3 58.9 + - - +
267B ILE* 3.3 11.5 - - + +
269B LYS* 3.0 50.9 + - + +
272B ILE* 3.7 22.7 - - + -
273B HIS* 4.0 14.8 - - + -
276B LEU* 3.6 23.6 - - + -
302B TYR* 4.7 2.7 - + - -
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Residues in contact with LYS 265 (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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262B ASN* 2.7 17.0 + - - +
264B PHE* 1.3 78.8 - - - +
266B ILE* 1.3 67.8 + - + +
267B ILE 3.1 1.1 + - - -
268B GLY* 3.2 12.3 + - - -
269B LYS 4.8 0.9 - - - +
270B GLU* 4.1 23.8 - - - +
273B HIS* 3.2 45.1 - - + +
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Residues in contact with ILE 266 (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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237A ASN* 3.6 8.3 + - - -
241A GLN* 4.2 21.0 - - + +
256A ASN* 4.3 27.8 - - + +
259A ASN* 4.9 5.8 - - - +
260A ILE* 4.3 21.5 - - + -
262B ASN* 3.1 38.3 + - - +
263B ILE* 3.2 13.0 + - + +
265B LYS* 1.3 80.8 - - + +
267B ILE* 1.3 60.8 + - + +
268B GLY 3.7 0.3 + - - -
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Residues in contact with ILE 267 (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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221A LYS* 4.0 14.6 + - - -
233A ASP* 4.1 17.6 - - + +
234A LEU* 4.2 31.2 - - + -
237A ASN* 3.2 42.8 + - + +
260A ILE* 4.4 9.0 - - + -
231B TYR* 4.4 10.3 - - + -
234B LEU* 5.2 2.9 - - + -
263B ILE* 3.1 20.6 + - + +
264B PHE* 3.3 18.6 - - + +
266B ILE* 1.3 79.4 - - + +
268B GLY* 1.3 57.9 + - - +
269B LYS* 3.6 19.5 + - + +
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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