Contacts of the helix formed by residues 269 - 287 (chain B) in PDB entry 2AXV
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 LYS 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ASP* 4.1 7.9 - - - +
231B TYR* 3.3 60.1 + - + +
264B PHE* 3.0 28.2 + - + +
267B ILE* 4.0 15.5 - - + +
268B GLY* 1.3 78.4 - - - +
270B GLU* 1.3 58.7 + - - +
271B ASP* 3.1 28.9 - - - +
272B ILE* 3.2 12.4 + - + +
273B HIS* 2.9 27.9 + - - +
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Residues in contact with GLU 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B LYS* 4.1 15.5 - - - +
268B GLY* 3.1 9.5 + - - +
269B LYS* 1.3 72.5 + - - +
271B ASP* 1.3 69.8 + - - +
273B HIS* 3.1 23.5 + - - +
274B ARG* 2.8 28.0 + - + +
298B TYR* 2.9 37.3 + - - +
302B TYR* 5.6 2.6 - - + -
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLY 4.8 0.2 - - - +
269B LYS* 3.1 37.8 - - - -
270B GLU* 1.3 79.8 + - - +
272B ILE* 1.3 81.1 + - - +
274B ARG* 3.4 11.2 + - - +
275B SER* 3.3 18.9 + - - -
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Residues in contact with ILE 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B TYR* 4.8 9.4 - - + +
235B GLU* 4.7 16.2 - - - +
264B PHE* 3.4 52.5 - - + -
269B LYS* 3.2 26.4 + - - +
271B ASP* 1.3 94.1 - - - +
273B HIS* 1.3 67.4 + - - +
275B SER* 3.1 8.0 + - - +
276B LEU* 2.9 32.4 + - + +
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Residues in contact with HIS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ILE* 3.5 29.7 - - + +
262B ASN* 5.4 1.4 + - - -
264B PHE* 4.3 4.2 - - + +
265B LYS* 3.6 40.2 - - + +
269B LYS 2.9 16.4 + - - +
270B GLU* 3.1 31.3 + - - +
272B ILE* 1.3 78.8 - - - +
274B ARG* 1.3 57.1 + - - +
276B LEU* 3.5 4.2 + - - +
277B VAL* 3.0 37.6 + - + +
298B TYR* 3.4 33.2 - + - +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 2.8 19.0 + - - +
271B ASP* 3.7 12.1 - - - +
273B HIS* 1.3 70.6 - - - +
275B SER* 1.3 68.4 - - - +
277B VAL* 3.5 2.3 + - - +
278B GLU* 3.0 35.4 + - - +
298B TYR* 3.7 27.4 - - + +
302B TYR* 2.9 35.5 + - - +
303B VAL* 3.7 18.6 + - + +
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU* 4.4 5.4 + - - -
271B ASP 3.3 11.5 + - - -
272B ILE* 3.1 11.5 + - - +
274B ARG* 1.3 78.2 - - - +
276B LEU* 1.3 60.2 + - - +
278B GLU* 3.2 13.9 + - - +
279B GLU* 2.7 53.0 + - - +
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Residues in contact with LEU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU* 3.8 20.9 - - + +
238B TYR* 3.4 43.0 + - + -
239B LEU* 5.9 0.7 - - + -
261B ILE* 3.9 22.3 - - + +
264B PHE* 3.8 35.4 - - + -
272B ILE* 2.9 23.4 + - + +
273B HIS* 4.1 2.0 - - - +
275B SER* 1.3 76.3 + - - +
277B VAL* 1.3 67.8 + - - +
279B GLU* 3.6 19.5 - - - +
280B LEU* 2.9 25.8 + - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ILE* 3.6 22.2 - - + -
273B HIS* 3.0 35.0 + - + +
274B ARG 3.8 3.6 - - - +
275B SER 3.3 0.2 - - - -
276B LEU* 1.3 77.5 - - - +
278B GLU* 1.3 62.3 + - - +
280B LEU* 3.6 4.9 - - - +
281B THR* 2.8 28.5 + - - +
295B VAL* 3.5 37.9 - - + +
298B TYR* 4.3 14.1 - - + -
299B TYR* 4.0 22.7 - - + -
303B VAL* 4.9 1.3 - - + -
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.0 25.9 + - - +
275B SER* 3.2 14.7 - - - +
277B VAL* 1.3 74.9 - - - +
279B GLU* 1.3 69.2 + - + +
281B THR* 3.3 10.3 + - - -
282B LYS* 3.1 50.7 + - - +
299B TYR* 4.4 6.0 - - + -
303B VAL* 3.6 33.0 - - + +
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Residues in contact with GLU 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B THR* 3.4 31.2 - - - +
202B ILE* 5.8 0.3 - - - +
203B MET* 4.1 16.6 - - - +
235B GLU* 4.2 4.0 - - - +
238B TYR* 3.7 11.6 - - - +
239B LEU* 4.3 12.5 - - - +
275B SER* 2.7 43.0 + - - +
276B LEU* 3.6 17.1 - - - +
277B VAL 3.3 0.2 - - - -
278B GLU* 1.3 73.4 - - + +
280B LEU* 1.3 64.6 + - - +
282B LYS* 2.9 9.1 + - - +
283B ILE* 2.8 35.2 + - + +
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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
----------------------------------------------------------
238B TYR* 3.4 13.4 + - + +
242B ILE* 4.2 14.4 - - + -
254B TYR* 3.2 37.7 - - + +
257B ALA* 5.5 0.9 - - + -
258B VAL* 3.9 20.0 - - + -
261B ILE* 3.4 25.6 - - + -
276B LEU 2.9 15.4 + - - +
277B VAL 3.6 4.0 - - - +
279B GLU* 1.3 78.7 - - - +
281B THR* 1.3 53.3 + - - +
283B ILE* 3.8 6.0 - - + +
284B SER* 2.8 39.2 + - - +
291B PRO* 4.4 0.7 - - + -
295B VAL* 4.1 23.8 - - + -
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Residues in contact with THR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 2.8 23.8 + - - +
278B GLU 3.3 7.4 - - - -
280B LEU* 1.3 76.9 - - - +
282B LYS* 1.3 59.3 + - + +
284B SER* 3.3 6.9 - - - -
285B ALA* 2.9 29.0 + - + +
291B PRO* 4.7 9.5 - - + +
295B VAL* 4.8 4.9 - - - +
296B THR* 4.7 15.4 - - + +
299B TYR* 3.4 39.7 - - + +
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Residues in contact with LYS 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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203B MET* 3.8 23.1 - - + -
278B GLU* 3.4 39.5 + - - +
279B GLU* 2.9 8.5 + - - +
281B THR* 1.3 79.2 - - + +
283B ILE* 1.3 65.1 - - - +
284B SER 3.2 0.2 + - - -
285B ALA* 3.2 7.8 + - - +
286B LYS* 2.9 29.7 + - + +
299B TYR* 6.1 2.7 - - + -
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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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202B ILE* 4.4 17.0 - - + +
203B MET* 3.5 22.0 - - + -
205B ARG* 6.4 0.4 - - + -
238B TYR* 3.9 8.3 - - + +
239B LEU* 6.2 0.2 - - + -
242B ILE* 3.9 31.2 - - + -
245B PHE* 5.4 5.6 - - + -
246B LEU* 3.9 21.8 - - + -
254B TYR* 6.4 0.7 - - + -
279B GLU* 2.8 47.2 + - + +
280B LEU* 3.8 10.1 - - + +
282B LYS* 1.3 72.2 - - - +
284B SER* 1.3 57.0 + - - +
286B LYS* 3.3 14.3 + - + +
287B GLU* 3.0 28.0 + - + +
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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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245B PHE* 5.9 1.3 - - - -
254B TYR* 2.8 32.2 + - - -
280B LEU* 2.8 25.9 + - - +
281B THR 3.3 6.5 - - - -
282B LYS 3.1 0.2 - - - -
283B ILE* 1.3 74.5 - - - +
285B ALA* 1.3 67.1 + - - +
287B GLU* 3.0 11.4 + - - -
288B LYS 3.0 9.2 + - - -
289B PHE* 3.1 34.7 + - - +
291B PRO* 4.0 10.0 - - - +
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Residues in contact with ALA 285 (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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281B THR* 2.9 12.5 + - + +
282B LYS* 3.5 10.5 - - - +
284B SER* 1.3 79.1 - - - +
286B LYS* 1.3 63.5 + - - +
288B LYS* 3.0 27.0 + - - -
289B PHE 3.8 6.4 + - - +
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Residues in contact with LYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE 5.7 0.2 - - - -
203B MET* 2.9 46.6 + - - +
204B ASN* 4.7 4.8 + - - +
205B ARG* 4.9 15.9 - - + -
282B LYS* 2.9 18.1 + - - +
283B ILE* 3.3 13.5 - - + +
285B ALA* 1.3 78.0 - - + +
287B GLU* 1.3 68.9 + - - +
288B LYS* 3.3 12.3 + - - +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ARG* 2.9 49.1 + - - +
245B PHE* 4.6 13.9 - - + -
246B LEU* 3.5 18.6 - - + +
249B LYS* 3.1 24.2 + - + +
283B ILE 3.0 17.3 + - - +
284B SER 3.0 4.8 + - - +
286B LYS* 1.3 83.9 - - + +
288B LYS* 1.3 72.8 + - - +
289B PHE* 3.5 17.2 - - + -
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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