Contacts of the helix formed by residues 274 - 296 (chain A) in PDB entry 1V2E
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 GLY 274 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ALA 3.5 5.8 + - - -
271A ARG 4.3 3.6 + - - -
272A ARG 3.4 4.4 + - - -
273A GLU* 1.3 78.9 - - - +
275A PHE* 1.3 65.0 + - - +
276A TYR 3.4 2.9 - - - -
277A GLU* 3.3 19.9 + - - +
278A ALA* 3.3 20.3 + - - +
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Residues in contact with PHE 275 (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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40A PRO* 4.0 30.5 - - + -
42A PHE* 3.9 25.8 - + + -
223A ARG 3.8 21.5 - - - -
224A LEU* 3.9 11.0 - - + -
225A GLU* 4.6 4.5 - - + -
270A ALA* 3.3 24.0 + - + +
273A GLU* 3.3 6.5 - - + -
274A GLY* 1.3 77.2 - - - +
276A TYR* 1.3 72.5 + + - +
278A ALA* 3.3 7.5 + - + +
279A LEU* 3.0 60.8 + - + +
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Residues in contact with TYR 276 (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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73A GLU* 4.2 1.0 + - - -
196A GLU* 3.4 38.7 - - + +
223A ARG* 3.1 53.3 + - - -
224A LEU* 4.1 7.3 - - + +
267A LEU* 3.7 15.9 - - - +
270A ALA* 4.0 22.2 + - + +
271A ARG* 3.5 33.9 - - + -
274A GLY 3.4 0.4 - - - -
275A PHE* 1.3 90.5 - + - +
277A GLU* 1.3 65.6 + - - +
279A LEU* 3.8 8.8 - - + +
280A ARG* 3.1 39.9 + - - +
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Residues in contact with GLU 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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274A GLY* 3.3 19.0 + - - +
275A PHE 3.2 0.2 - - - -
276A TYR* 1.3 80.7 - - - +
278A ALA* 1.3 61.9 + - - +
280A ARG* 3.4 22.3 + - - +
281A GLU* 3.3 28.3 + - + +
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Residues in contact with ALA 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 GLY 3.3 9.9 + - - +
275A PHE* 3.3 11.2 + - + +
277A GLU* 1.3 75.7 - - - +
279A LEU* 1.3 66.7 + - - +
281A GLU* 3.3 8.4 + - - +
282A GLY* 2.9 21.1 + - - -
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Residues in contact with LEU 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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196A GLU* 6.1 2.0 - - + +
197A LEU* 5.1 7.4 - - + -
222A LYS 5.6 2.2 - - - +
223A ARG 3.7 23.3 - - - +
225A GLU* 4.1 29.6 - - + +
275A PHE* 3.0 47.3 + - + +
276A TYR* 3.8 11.2 - - + +
278A ALA* 1.3 75.9 - - - +
280A ARG* 1.3 58.6 + - + +
282A GLY* 3.2 2.8 + - - -
283A TYR* 2.9 49.8 + - + -
286A ARG* 5.2 2.4 + - - +
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Residues in contact with ARG 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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196A GLU* 2.8 54.2 + - - +
197A LEU* 4.4 11.2 - - + -
198A TYR* 3.1 63.3 + - - +
199A TYR* 3.7 4.8 - - - -
202A ARG* 4.5 2.0 - - - +
276A TYR* 3.1 28.3 + - - +
277A GLU* 3.6 30.4 - - - +
278A ALA 3.3 0.2 - - - -
279A LEU* 1.3 76.5 - - + +
281A GLU* 1.3 63.6 + - - +
283A TYR* 3.2 2.4 + - - +
284A ARG* 2.8 31.5 + - - +
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Residues in contact with GLU 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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277A GLU* 3.3 17.1 + - + +
278A ALA* 3.3 10.6 + - - +
280A ARG* 1.3 78.0 - - - +
282A GLY* 1.3 61.0 + - - +
284A ARG* 2.5 43.5 + - - +
285A ARG* 3.0 37.7 + - - +
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Residues in contact with GLY 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 ALA 2.9 14.1 + - - -
279A LEU 3.2 4.9 + - - -
281A GLU* 1.3 77.3 - - - +
283A TYR* 1.3 60.5 + - - +
285A ARG* 3.9 23.2 + - - +
286A ARG* 3.0 38.4 + - - +
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Residues in contact with TYR 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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35A PRO* 4.0 1.7 - - - +
197A LEU* 3.4 23.1 - - + -
199A TYR* 3.3 22.7 - - + +
225A GLU* 2.5 35.8 + - - -
279A LEU* 2.9 38.5 + - + +
280A ARG 3.6 0.7 - - - +
281A GLU 3.1 0.2 - - - -
282A GLY* 1.3 77.8 - - - +
284A ARG* 1.3 61.1 + - - +
286A ARG* 3.1 29.6 + - - +
287A ARG* 2.8 29.3 + - - +
308A TYR* 3.4 42.3 - + + -
350A PHE* 3.9 12.1 - + - -
351A CYS* 3.5 23.0 - - - +
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Residues in contact with ARG 284 (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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198A TYR 4.4 2.4 + - - -
199A TYR* 2.9 55.6 + - + +
200A GLY 5.2 1.2 + - - -
280A ARG* 2.8 14.0 + - - +
281A GLU* 2.5 54.3 + - - +
283A TYR* 1.3 75.6 - - - +
285A ARG* 1.3 63.6 + - - +
287A ARG* 3.1 21.8 + - - +
288A ASP* 3.0 40.1 + - - +
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Residues in contact with ARG 285 (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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281A GLU* 3.0 21.4 + - - +
282A GLY* 3.9 24.2 + - - +
284A ARG* 1.3 78.2 - - - +
286A ARG* 1.3 60.6 + - - +
288A ASP* 3.5 6.1 + - - +
289A LEU* 3.2 23.3 + - + +
354A GLU* 3.3 27.9 + - - +
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Residues in contact with ARG 286 (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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37A ASN* 4.3 16.3 - - - +
225A GLU* 5.2 0.8 + - - -
279A LEU* 5.2 2.2 + - - +
282A GLY* 3.0 24.5 + - - +
283A TYR* 3.1 44.3 + - - +
285A ARG* 1.3 77.7 - - - +
287A ARG* 1.3 65.3 + - - +
289A LEU* 3.6 7.5 - - + +
290A LEU* 3.1 24.9 + - - +
350A PHE* 3.8 14.2 - - + +
351A CYS* 3.7 6.5 - - - +
352A LYS 2.7 49.5 + - - +
353A THR* 5.0 1.0 - - - +
354A GLU* 4.1 27.4 - - + +
357A LEU* 3.8 20.8 - - + +
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Residues in contact with ARG 287 (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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199A TYR* 3.6 29.0 - - + +
283A TYR 2.8 16.6 + - - +
284A ARG* 3.4 23.4 + - - +
286A ARG* 1.3 78.9 - - - +
288A ASP* 1.3 88.4 + - - +
290A LEU* 3.9 1.2 - - - +
291A ALA* 3.0 28.7 + - + +
303A VAL* 3.5 19.1 - - + +
304A PRO* 2.8 49.7 + - + -
305A GLU* 4.7 0.6 - - - +
310A LEU* 4.4 4.1 - - + +
350A PHE* 3.8 29.6 - - + -
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Residues in contact with ASP 288 (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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284A ARG* 3.0 33.2 + - - +
285A ARG* 4.0 6.0 - - - +
287A ARG* 1.3 105.7 + - - +
289A LEU* 1.3 54.4 + - - +
291A ALA* 4.6 2.9 - - - -
292A GLY* 2.7 32.3 + - - +
295A ARG* 5.6 0.7 + - - -
303A VAL* 5.5 0.2 - - - +
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Residues in contact with LEU 289 (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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285A ARG* 3.2 18.0 + - + +
286A ARG* 3.6 6.3 - - - +
287A ARG 3.2 0.2 - - - -
288A ASP* 1.3 76.8 - - - +
290A LEU* 1.3 60.8 + - - +
292A GLY* 3.8 0.2 - - - -
293A GLY* 2.8 27.0 + - - -
354A GLU* 4.4 31.6 - - + +
357A LEU* 4.0 21.1 - - + -
358A HIS* 3.9 33.2 - - + +
361A LEU* 3.8 20.9 - - + +
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Residues in contact with LEU 290 (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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30A LEU* 5.1 3.1 - - + -
286A ARG 3.1 14.6 + - - +
287A ARG 3.9 1.8 - - - +
289A LEU* 1.3 81.5 - - - +
291A ALA* 1.3 65.7 + - - +
293A GLY* 3.0 2.9 + - - -
294A LEU* 2.8 46.9 + - + +
310A LEU* 3.9 16.8 - - + -
348A PHE* 3.7 37.5 - - + -
349A ALA 4.9 0.7 - - - +
350A PHE* 4.0 22.4 - - + -
357A LEU* 4.3 19.1 - - + +
360A ALA* 6.5 0.2 - - + -
361A LEU* 4.1 14.3 - - + +
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Residues in contact with ALA 291 (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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287A ARG* 3.0 17.5 + - + +
288A ASP* 4.3 3.6 - - - +
290A LEU* 1.3 79.1 - - - +
292A GLY* 1.3 56.8 + - - +
294A LEU* 3.4 3.4 + - - +
295A ARG* 2.9 39.6 + - - +
301A VAL* 3.9 16.7 - - + +
303A VAL* 4.4 16.8 - - + -
310A LEU* 3.7 21.5 - - + +
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Residues in contact with GLY 292 (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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288A ASP 2.7 25.4 + - - -
289A LEU 3.8 0.2 - - - -
291A ALA* 1.3 75.3 - - - +
293A GLY* 1.3 60.1 + - - +
295A ARG* 3.1 23.8 + - - +
296A ALA* 3.2 21.1 + - - +
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Residues in contact with GLY 293 (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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289A LEU 2.8 16.2 + - - -
290A LEU 3.6 2.5 - - - -
292A GLY* 1.3 74.3 - - - +
294A LEU* 1.3 64.7 + - - +
296A ALA* 3.7 15.8 + - - +
297A MET* 3.5 18.5 + - - +
361A LEU* 3.9 19.7 - - - -
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Residues in contact with LEU 294 (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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290A LEU* 2.8 37.3 + - + +
291A ALA 3.9 0.2 - - - +
293A GLY* 1.3 74.5 - - - +
295A ARG* 1.3 59.3 + - - +
296A ALA 3.1 0.2 - - - -
297A MET* 2.7 39.3 + - - +
299A LEU* 3.6 25.5 + - + +
301A VAL* 3.7 19.3 - - + -
310A LEU* 4.2 10.3 - - + -
312A ALA* 3.9 23.3 - - + -
348A PHE* 3.9 26.0 - - + -
361A LEU* 3.9 15.7 - - + -
364A LEU* 4.2 10.3 - - + -
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Residues in contact with ARG 295 (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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288A ASP 5.6 0.4 + - - -
291A ALA* 2.9 24.0 + - - +
292A GLY* 3.1 26.9 + - - +
294A LEU* 1.3 74.7 - - - +
296A ALA* 1.3 52.5 + - - +
298A GLY* 2.7 29.6 + - - -
299A LEU 4.4 11.6 - - - +
301A VAL* 4.1 20.8 - - + +
303A VAL* 5.1 12.9 - - - +
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Residues in contact with ALA 296 (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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292A GLY 3.2 9.6 + - - +
293A GLY* 3.7 13.5 - - - +
294A LEU 3.1 0.6 - - - -
295A ARG* 1.3 78.5 - - - +
297A MET* 1.3 56.1 + - + +
298A GLY 3.2 3.6 + - - -
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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
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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