Contacts of the helix formed by residues 261 - 283 (chain A) in PDB entry 1F7V
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 GLU 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A TYR* 5.3 2.9 + - - -
254A ARG* 3.6 16.6 + - - +
259A ASP* 2.6 22.8 + - - +
260A GLU* 1.3 72.5 - - - +
262A ALA* 1.3 61.6 + - - +
264A LYS* 3.5 16.4 + - - +
265A ILE* 3.6 12.6 + - - +
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Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A TYR* 3.5 37.8 - - + +
254A ARG* 4.2 9.4 - - + +
255A MET* 3.8 14.8 - - + -
259A ASP* 2.8 24.8 + - + +
261A GLU* 1.3 73.8 - - - +
263A LEU* 1.3 53.1 + - + +
264A LYS 2.6 16.5 + - - -
265A ILE* 3.0 5.0 + - - +
266A TRP* 2.9 24.3 + - - +
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TRP* 3.6 35.2 - - + -
255A MET* 3.4 37.7 - - + +
258A GLY* 3.8 12.6 - - - +
259A ASP 3.0 17.8 + - - +
260A GLU* 4.3 9.0 - - - +
261A GLU 3.5 0.2 - - - -
262A ALA* 1.3 73.1 - - - +
264A LYS* 1.3 57.0 + - - +
266A TRP* 4.2 16.3 - - + -
267A LYS* 3.5 35.1 + - - +
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLU 3.6 14.9 + - - +
261A GLU* 3.5 13.5 - - - +
262A ALA 2.6 6.9 + - - -
263A LEU* 1.3 78.0 - - - +
265A ILE* 1.3 59.2 + - - +
266A TRP 3.1 1.3 - - - -
267A LYS* 3.5 20.2 + - + +
268A ARG* 3.0 28.6 + - - +
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PHE* 4.2 10.4 - - + -
200A ALA* 4.9 8.1 - - + +
203A PHE* 4.9 20.0 - - + -
204A GLU* 6.2 3.1 - - + -
251A TYR* 2.9 37.9 - - + +
261A GLU* 3.6 11.7 + - - +
262A ALA 3.0 6.1 + - - +
264A LYS* 1.3 79.4 - - - +
266A TRP* 1.3 65.9 + - - +
268A ARG* 3.5 22.0 - - - +
269A PHE* 3.2 21.5 + - - +
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Residues in contact with TRP 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 5.3 2.0 - - - +
191A ASP* 3.0 27.0 + - - +
192A TRP* 3.5 34.0 - + - +
196A PHE* 3.2 48.6 - + + -
255A MET* 4.1 9.8 - - - -
262A ALA 2.9 16.3 + - - +
263A LEU* 4.2 20.6 - - + -
265A ILE* 1.3 74.6 - - - +
267A LYS* 1.3 88.0 + - + +
268A ARG 3.0 1.1 - - - -
269A PHE* 2.8 7.1 + + - +
270A ARG* 2.7 63.0 + - + +
295A SER* 4.0 16.4 - - - -
296A GLN* 5.4 2.2 - - - -
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.5 22.8 + - - +
264A LYS* 3.5 24.0 + - + +
266A TRP* 1.3 103.2 - - + +
268A ARG* 1.3 62.3 + - - +
270A ARG* 3.5 6.4 - - + +
271A GLU* 3.0 48.5 + - + +
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Residues in contact with ARG 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A PHE* 5.2 6.3 - - - -
209A GLU* 2.9 38.7 + - - -
212A LEU* 3.3 25.8 - - - +
213A VAL* 5.6 2.0 - - - +
264A LYS 3.0 17.7 + - - +
265A ILE* 3.5 22.0 - - - +
266A TRP 3.0 0.8 + - - -
267A LYS* 1.3 78.2 - - - +
269A PHE* 1.3 62.5 + - - +
271A GLU* 3.9 6.8 - - - +
272A PHE* 3.2 22.3 + - + +
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Residues in contact with PHE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.1 53.2 - - + -
196A PHE* 3.7 25.4 - + + -
199A LEU* 3.5 29.8 - - + -
220A LEU* 4.1 28.0 - - + -
265A ILE 3.2 10.1 + - - +
266A TRP* 2.8 8.2 + + - +
268A ARG* 1.3 79.6 - - - +
270A ARG* 1.3 55.8 + - - +
272A PHE* 3.0 16.3 + + - +
273A SER* 2.7 40.5 + - - -
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 4.1 10.3 - - - -
189A LEU* 4.4 4.0 - - - +
191A ASP* 2.5 39.1 + - - -
266A TRP* 2.7 46.7 + - + +
267A LYS* 3.5 12.3 - - + +
269A PHE* 1.3 72.5 - - - +
271A GLU* 1.3 64.3 + - + +
273A SER* 3.0 19.2 + - - -
274A ILE* 2.9 47.9 + - - +
291A TYR 3.7 19.0 + - - -
292A SER 4.0 4.6 + - - -
295A SER* 4.1 0.2 + - - -
296A GLN* 3.6 24.9 - - - +
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LYS* 3.0 46.4 + - + +
268A ARG* 3.9 5.9 - - - +
270A ARG* 1.3 78.8 - - + +
272A PHE* 1.3 63.6 + - - +
274A ILE* 3.4 8.0 + - - +
275A GLU* 3.1 33.2 + - - +
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Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PRO* 3.4 39.0 - - + -
217A ILE* 4.4 5.2 - - + -
220A LEU* 4.0 15.9 - - + -
268A ARG* 3.2 11.9 + - + +
269A PHE* 3.0 23.0 + + - +
271A GLU* 1.3 76.1 - - - +
273A SER* 1.3 70.6 + - - +
275A GLU* 2.9 27.3 + - + +
276A LYS* 3.0 51.7 + - + +
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ILE* 3.7 36.8 - - - +
269A PHE* 2.7 29.1 + - - -
270A ARG 3.0 14.2 + - - -
272A PHE* 1.3 79.2 - - - +
274A ILE* 1.3 66.6 + - - +
276A LYS* 3.0 8.7 + - - +
277A TYR* 2.8 41.4 + - - -
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 3.7 28.7 - - + -
270A ARG* 2.9 46.3 + - - +
271A GLU* 3.7 6.5 - - - +
272A PHE 3.3 0.2 - - - -
273A SER* 1.3 85.2 + - - +
275A GLU* 1.3 58.6 + - + +
277A TYR* 3.3 8.5 + - - +
278A ILE* 2.9 48.8 + - + +
291A TYR* 3.9 30.5 - - + +
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLU* 3.1 24.1 + - - +
272A PHE* 2.9 20.3 + - + +
274A ILE* 1.3 76.3 - - + +
276A LYS* 1.3 69.4 + - + +
278A ILE* 3.3 18.6 + - + +
279A ASP* 3.4 18.2 + - - +
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Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A ILE* 3.3 34.3 - - + -
272A PHE* 3.0 50.4 + - + +
273A SER* 3.4 9.0 - - - +
275A GLU* 1.3 78.7 - - - +
277A TYR* 1.3 63.4 + - + +
279A ASP* 3.6 18.6 + - - +
280A THR* 3.3 21.9 + - - -
419A ASP* 5.4 2.1 - - - +
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PRO* 3.7 23.5 - - + +
153A ASN 4.2 2.4 + - - -
154A ILE* 3.5 41.0 + - + -
156A LYS 4.5 4.3 + - - -
158A PHE* 3.6 45.2 - + + +
189A LEU* 5.0 5.6 - - + -
273A SER* 2.8 33.4 + - - +
274A ILE* 3.6 9.2 - - - +
276A LYS* 1.3 74.5 - - + +
278A ILE* 1.3 65.9 + - - +
279A ASP 3.1 1.8 - - - -
280A THR* 3.0 7.7 + - - -
281A TYR* 2.9 56.4 + + + -
291A TYR* 4.4 5.6 - + + -
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Residues in contact with ILE 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A ILE* 2.9 36.0 + - + +
275A GLU* 3.3 10.7 + - + +
277A TYR* 1.3 74.9 - - - +
279A ASP* 1.3 66.0 + - - +
281A TYR* 3.8 1.7 + - - +
282A ALA* 3.1 24.6 + - + +
286A ILE 4.9 0.7 - - - +
291A TYR* 3.2 36.6 - - + +
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Residues in contact with ASP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A GLU 3.4 14.9 + - - +
276A LYS* 3.8 22.4 + - - +
277A TYR 3.1 0.8 - - - -
278A ILE* 1.3 81.5 - - - +
280A THR* 1.3 60.1 + - - +
282A ALA* 3.1 7.3 + - - +
283A ARG* 2.8 29.6 + - - +
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Residues in contact with THR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PHE* 4.2 27.3 - - + -
276A LYS 3.3 12.4 + - - -
277A TYR* 3.0 12.9 + - - -
279A ASP* 1.3 78.8 - - - +
281A TYR* 1.3 65.9 + - + +
283A ARG* 3.0 18.2 + - - +
284A LEU* 3.3 17.5 + - + +
418A LEU* 4.5 12.8 - - + -
419A ASP* 2.9 34.6 + - - +
422A LEU* 5.2 4.5 - - + -
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Residues in contact with TYR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A SER* 2.8 24.8 + - - -
152A PRO* 3.5 15.2 - - - +
158A PHE* 3.8 9.3 - + - -
166A THR* 3.8 23.1 - - + -
187A ASN* 2.9 28.0 + - - -
277A TYR* 2.9 48.9 + + + +
278A ILE 4.2 2.7 - - - +
280A THR* 1.3 79.3 - - + +
282A ALA* 1.3 54.3 + - - +
284A LEU* 2.9 17.9 + - + +
286A ILE* 2.7 45.0 + - + +
288A TYR* 3.2 32.1 - + + -
291A TYR* 3.5 13.5 - + - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A ILE* 3.1 22.1 + - + +
279A ASP* 3.1 7.7 + - - +
281A TYR* 1.3 73.1 - - - +
283A ARG* 1.3 55.0 + - - +
284A LEU 2.8 5.4 - - - -
285A ASN* 2.7 26.3 + - - +
286A ILE 3.4 12.7 + - - +
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ASP 2.8 12.9 + - - +
280A THR* 3.0 14.1 + - - +
282A ALA* 1.3 75.8 - - - +
284A LEU* 1.3 58.6 + - - +
285A ASN* 3.4 3.3 + - - -
419A ASP* 3.4 23.1 + - - +
422A LEU* 3.4 34.8 - - + +
423A GLU* 3.3 40.0 + - - +
426A LYS* 4.2 2.8 - - - +
451A ASP* 2.5 45.7 + - - +
452A LEU* 6.0 0.2 - - - +
455A ILE* 3.3 23.3 - - + +
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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