Contacts of the helix formed by residues 250 - 267 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245D PHE* 3.3 12.4 + - - +
248D ASP* 3.2 10.7 + - + +
249D LYS* 1.3 76.5 - - - +
251D ILE* 1.3 73.0 + - - +
252D ASP* 2.9 37.3 + - - +
253D SER* 2.8 31.5 + - - +
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Residues in contact with ILE 251 (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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254A TYR* 4.2 6.7 - - - +
277A VAL* 4.1 22.0 - - + +
280A LEU* 4.0 17.0 - - + -
281A THR* 3.1 43.2 + - - +
284A SER* 5.0 1.1 - - - +
245D PHE* 4.0 9.9 - - + -
249D LYS 4.3 0.4 - - - -
250D ASN* 1.3 79.7 - - - +
252D ASP* 1.3 67.5 + - - +
254D TYR* 3.1 6.4 + - + -
255D LEU* 2.8 54.2 + - + +
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Residues in contact with ASP 252 (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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250D ASN* 2.8 30.1 + - - +
251D ILE* 1.3 88.6 - - - +
253D SER* 1.3 63.1 + - - +
255D LEU* 3.2 10.8 + - - +
256D ASN* 2.9 35.7 + - - +
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Residues in contact with SER 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D GLN* 3.4 42.9 + - - +
244D GLN* 3.7 21.1 + - - +
245D PHE* 3.7 13.3 + - - -
248D ASP* 5.7 1.4 - - - +
250D ASN* 2.8 26.9 + - - +
252D ASP* 1.3 74.2 - - - +
254D TYR* 1.3 61.1 + - - -
256D ASN* 3.3 4.4 + - - +
257D ALA* 3.1 16.8 + - - +
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Residues in contact with TYR 254 (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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245A PHE* 4.4 9.0 - - - -
254A TYR* 3.4 29.0 - + - -
284A SER* 3.6 27.2 - - - -
242D ILE* 4.1 9.4 - - + -
245D PHE* 3.4 47.7 - + + -
250D ASN 3.6 1.4 + - - -
251D ILE* 3.1 9.2 + - + +
253D SER* 1.3 78.0 - - - +
255D LEU* 1.3 66.0 + - - +
257D ALA* 3.0 7.6 + - - +
258D VAL* 3.0 41.2 + - + -
280D LEU* 3.5 33.2 - - + +
283D ILE* 6.4 1.3 - - + -
284D SER* 3.8 18.0 + - - -
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Residues in contact with LEU 255 (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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254A TYR* 3.6 16.6 - - + +
255A LEU* 6.2 1.1 - - + -
258A VAL* 3.6 43.5 - - + -
262A ASN* 6.0 0.4 - - - +
280A LEU* 4.6 1.8 - - + -
251D ILE* 2.8 45.3 + - + +
252D ASP* 3.6 12.1 - - - +
254D TYR* 1.3 75.6 - - - +
256D ASN* 1.3 61.5 + - - +
258D VAL* 3.2 7.3 + - + +
259D ASN* 2.8 31.9 + - - +
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Residues in contact with ASN 256 (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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266C ILE* 4.3 25.8 - - + +
241D GLN* 3.4 31.7 + - + +
252D ASP* 2.9 25.7 + - - +
253D SER* 3.4 8.5 - - - +
255D LEU* 1.3 77.0 - - - +
257D ALA* 1.3 65.0 + - - +
259D ASN* 3.1 8.3 + - - +
260D ILE* 2.9 29.8 + - - +
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Residues in contact with ALA 257 (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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238D TYR* 3.9 18.7 - - + +
241D GLN* 4.0 7.3 - - + +
242D ILE* 3.4 37.7 - - + -
253D SER 3.1 11.1 + - - +
254D TYR 3.0 10.0 + - - +
256D ASN* 1.3 77.1 - - - +
258D VAL* 1.3 62.6 + - - +
260D ILE* 3.3 2.4 + - - +
261D ILE* 3.0 29.5 + - - +
280D LEU* 5.0 3.4 - - + -
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Residues in contact with VAL 258 (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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251A ILE* 3.5 27.4 - - + +
254A TYR* 3.8 27.1 - - + -
255A LEU* 4.1 18.6 - - + -
254D TYR* 3.0 40.8 + - + +
255D LEU* 3.5 10.5 - - + +
256D ASN 3.2 0.2 - - - -
257D ALA* 1.3 77.6 - - - +
259D ASN* 1.3 58.1 + - - +
261D ILE* 3.2 5.1 + - - +
262D ASN* 2.9 27.0 + - - +
280D LEU* 3.9 14.8 - - + -
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Residues in contact with ASN 259 (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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255A LEU* 4.4 15.0 - - - +
259C ASN* 3.5 35.9 + - - +
262C ASN* 4.4 10.1 - - - +
263C ILE* 4.4 11.1 - - + +
266C ILE* 5.2 3.5 - - + +
255D LEU* 2.8 18.5 + - - +
256D ASN* 3.1 12.1 + - - +
258D VAL* 1.3 76.7 - - - +
260D ILE* 1.3 61.4 + - - +
262D ASN* 3.2 11.0 + - - +
263D ILE* 3.0 23.9 + - - +
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Residues in contact with ILE 260 (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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263C ILE* 3.5 41.3 - - + -
266C ILE* 4.6 14.4 - - + -
267C ILE* 4.2 10.8 - - + -
234D LEU* 3.3 43.1 - - + +
235D GLU* 5.1 0.7 - - - -
237D ASN* 5.3 1.8 - - + -
238D TYR* 3.5 21.1 - - + +
241D GLN* 5.6 1.8 - - + -
256D ASN 2.9 18.4 + - - +
257D ALA 3.6 7.0 - - - +
259D ASN* 1.3 73.2 - - - +
261D ILE* 1.3 68.2 + - - +
263D ILE* 3.1 19.4 + - + +
264D PHE* 3.5 9.9 + - + -
276D LEU* 6.4 0.7 - - + -
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Residues in contact with ILE 261 (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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251A ILE* 4.3 7.4 - - + -
238D TYR* 3.4 37.7 - - + -
257D ALA 3.0 15.5 + - - +
258D VAL 3.6 7.2 - - - +
260D ILE* 1.3 75.7 - - + +
262D ASN* 1.3 56.0 + - - +
264D PHE* 3.3 10.6 + - - +
273D HIS* 2.8 31.4 - - + +
276D LEU* 3.8 41.1 - - + +
277D VAL* 3.9 21.5 - - + -
280D LEU* 3.7 32.8 - - + -
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Residues in contact with ASN 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ILE* 3.1 25.7 - - + +
252A ASP* 4.4 2.3 - - - +
255A LEU* 3.7 23.9 - - + +
256C ASN* 5.9 1.0 - - - +
259C ASN* 4.8 14.1 - - - +
258D VAL 2.9 13.0 + - - +
259D ASN* 3.4 13.5 + - - +
260D ILE 3.1 0.2 - - - -
261D ILE* 1.3 75.1 - - - +
263D ILE* 1.3 57.5 + - - +
265D LYS* 2.7 34.5 + - - +
266D ILE* 3.1 32.5 + - - +
273D HIS* 3.9 7.2 - - - -
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Residues in contact with ILE 263 (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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234C LEU* 3.8 24.7 - - + -
259C ASN* 4.0 11.2 - - - +
260C ILE* 3.4 36.8 - - + -
263C ILE* 3.4 31.2 - - + -
234D LEU* 4.0 9.0 - - + -
259D ASN 3.0 9.0 + - - +
260D ILE* 3.1 13.0 + - - +
262D ASN* 1.3 75.8 - - - +
264D PHE* 1.3 74.8 + - + +
266D ILE* 3.2 18.5 + - + +
267D ILE* 3.1 26.4 + - + +
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Residues in contact with PHE 264 (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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231D TYR* 3.6 29.2 - + + -
234D LEU* 3.3 45.8 - - + -
235D GLU* 4.0 12.3 - - + -
260D ILE* 3.9 12.6 - - + -
261D ILE 3.3 11.1 + - - +
262D ASN 3.0 0.6 - - - -
263D ILE* 1.3 82.9 - - + +
265D LYS* 1.3 59.4 + - - +
267D ILE* 3.5 12.6 - - + +
269D LYS* 3.0 38.4 + - + +
272D ILE* 3.6 23.6 - - + -
273D HIS* 4.1 12.1 - - + -
276D LEU* 3.2 31.9 - - + -
302D TYR* 5.4 1.8 - + - -
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Residues in contact with LYS 265 (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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250A ASN* 4.5 9.4 - - - +
251A ILE* 4.6 0.4 - - + -
252A ASP* 3.8 28.8 + - - +
262D ASN* 2.7 15.8 + - - +
264D PHE* 1.3 77.4 - - - +
266D ILE* 1.3 72.6 + - + +
267D ILE 3.2 0.9 + - - -
268D GLY* 3.2 12.8 + - - -
269D LYS 4.9 2.9 - - - +
270D GLU* 4.2 28.0 + - - +
273D HIS* 3.1 44.4 - - + +
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Residues in contact with ILE 266 (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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237C ASN* 3.1 10.3 + - - +
241C GLN* 3.7 21.3 - - - +
256C ASN* 4.4 27.6 - - + +
259C ASN* 6.3 1.6 - - - +
260C ILE* 4.6 17.5 - - + -
262D ASN* 3.1 36.9 + - - +
263D ILE* 3.2 19.5 + - + +
265D LYS* 1.3 87.8 - - + +
267D ILE* 1.3 56.9 + - - +
268D GLY 3.7 0.3 + - - -
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Residues in contact with ILE 267 (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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221C LYS* 4.5 8.8 + - - -
230C GLY 5.6 0.4 - - - +
233C ASP* 3.8 37.2 - - + +
234C LEU* 4.4 21.5 - - + -
237C ASN* 3.4 41.7 - - + +
260C ILE* 4.7 2.0 - - + -
231D TYR* 4.4 14.6 - - + -
234D LEU* 5.2 1.8 - - + -
263D ILE* 3.1 31.1 + - + +
264D PHE* 3.5 19.7 - - + +
265D LYS 3.1 0.2 - - - -
266D ILE* 1.3 77.2 - - + +
268D GLY* 1.3 57.8 + - - +
269D LYS* 3.6 6.8 + - + +
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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