Contacts of the helix formed by residues 273 - 296 (chain A) in PDB entry 1EF1
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 ARG 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 5.5 6.0 - - + -
253A LYS* 2.8 29.0 - - - +
271A ALA* 3.2 18.3 - - - +
272A PRO* 1.3 86.4 - - + +
274A LEU* 1.3 101.0 + - - +
275A ARG* 3.2 55.9 - - + +
276A ILE* 3.5 23.4 + - + +
277A ASN* 3.6 2.8 + - - -
278A LYS* 6.1 0.2 - - - +
273B ARG* 5.5 13.2 - - + +
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Residues in contact with LEU 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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250A PHE* 3.1 40.2 - - + -
252A ASP* 3.9 29.8 - - - +
253A LYS* 3.0 10.6 - - - +
273A ARG* 1.3 91.2 - - - +
275A ARG* 1.3 65.3 - - - +
277A ASN* 3.0 4.9 + - - +
278A LYS* 3.0 46.3 + - + +
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 3.3 24.4 + - - -
53A LYS* 3.4 35.0 - - - +
55A PHE* 3.4 50.4 - - - +
57A THR* 4.9 2.4 + - - -
273A ARG* 3.2 39.2 - - + +
274A LEU* 1.3 78.6 - - - +
276A ILE* 1.3 62.7 + - + +
278A LYS* 3.3 14.3 + - - +
279A ARG* 3.2 43.6 + - + +
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Residues in contact with ILE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PHE* 6.5 0.2 - - + -
206A PHE* 3.5 33.0 - - + -
207A SER 4.8 2.0 - - - +
271A ALA* 4.1 12.1 - - + -
272A PRO* 4.4 15.5 - - + -
273A ARG* 3.5 26.2 + - + +
274A LEU 3.2 0.2 - - - -
275A ARG* 1.3 81.3 - - + +
277A ASN* 1.3 60.5 + - - +
279A ARG* 3.2 17.0 + - - +
280A ILE* 2.9 41.9 + - + +
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Residues in contact with ASN 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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250A PHE* 3.7 22.5 - - + +
252A ASP 3.0 22.0 + - - +
253A LYS* 3.1 23.8 + - - +
254A LYS 4.1 0.8 + - - +
255A PHE* 3.0 34.1 - - + +
269A PHE* 4.1 0.9 - - - -
271A ALA* 3.4 21.1 - - - +
273A ARG 3.6 3.4 + - - -
274A LEU 3.0 8.4 + - - +
276A ILE* 1.3 74.5 - - - +
278A LYS* 1.3 61.2 + - - +
280A ILE* 4.0 8.9 - - - +
281A LEU* 2.9 29.8 + - - +
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE* 3.8 25.4 - - + -
273A ARG* 6.1 0.2 - - - +
274A LEU* 3.0 46.8 + - + +
275A ARG* 3.4 12.8 - - - +
276A ILE 3.2 0.2 - - - -
277A ASN* 1.3 76.7 - - - +
279A ARG* 1.3 58.9 + - + +
281A LEU* 3.4 2.1 + - - +
282A ALA* 3.0 29.1 + - - +
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Residues in contact with ARG 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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48A GLN* 3.4 16.6 + - - -
56A SER* 3.1 25.0 + - - -
57A THR* 3.7 15.8 + - - +
58A TRP* 3.3 35.7 - - + +
206A PHE* 4.2 18.2 - - + -
275A ARG* 3.2 26.3 + - + +
276A ILE* 3.6 17.7 - - - +
278A LYS* 1.3 75.2 - - + +
280A ILE* 1.3 63.7 - - - +
282A ALA* 3.4 6.5 + - - +
283A LEU* 3.0 35.3 + - + +
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Residues in contact with ILE 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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206A PHE* 3.7 42.4 - - + -
208A ILE* 4.8 2.9 - - + -
218A LEU* 3.8 29.8 - - + -
220A VAL* 4.2 3.6 - - + -
225A LEU* 6.3 0.2 - - + -
255A PHE* 3.9 20.4 - - + -
269A PHE* 4.2 9.0 - - + -
271A ALA* 5.1 0.4 - - + -
276A ILE* 2.9 28.4 + - + +
277A ASN* 3.7 18.6 - - - +
278A LYS 3.3 0.2 - - - -
279A ARG* 1.3 74.4 - - - +
281A LEU* 1.3 58.6 + - - +
283A LEU* 3.4 3.3 + - - +
284A CYS* 2.9 44.8 + - - -
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 3.7 29.2 - - + +
249A SER* 3.8 16.2 - - - +
250A PHE* 3.7 31.2 - - + -
255A PHE* 4.1 9.6 - - + -
277A ASN 2.9 16.9 + - - +
278A LYS 3.8 4.3 - - - +
279A ARG 3.2 0.2 - - - -
280A ILE* 1.3 78.4 - - - +
282A ALA* 1.3 63.4 + - - +
284A CYS* 3.3 3.3 + - - +
285A MSE 3.0 55.3 + - + +
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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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58A TRP* 6.4 0.4 - - + -
60A LYS* 5.9 7.2 - - - -
83A LYS* 4.5 17.7 - - - +
84A PHE* 4.4 4.2 - - - -
278A LYS 3.0 17.6 + - - +
279A ARG* 3.7 6.1 - - - +
281A LEU* 1.3 77.8 - - - +
283A LEU* 1.3 62.7 + - + +
285A MSE 3.4 10.1 + - - +
286A GLY* 3.0 20.8 + - - -
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Residues in contact with LEU 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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58A TRP* 5.1 4.5 - - + +
83A LYS* 3.9 40.4 - - + +
84A PHE* 3.8 10.3 - - + -
204A ASN* 3.5 30.3 - - + +
206A PHE* 3.5 33.0 - - + -
220A VAL* 4.0 13.2 - - + -
279A ARG* 3.0 22.3 + - + +
280A ILE 3.8 3.1 - - - +
282A ALA* 1.3 72.0 - - + +
284A CYS* 1.3 64.9 + - - +
287A ASN* 2.9 33.3 + - - +
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Residues in contact with CYS 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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220A VAL* 4.2 2.7 - - - -
225A LEU* 3.7 35.9 - - - -
242A TRP* 3.8 19.3 - - + -
248A ILE* 3.8 24.2 - - + -
255A PHE* 4.9 5.2 - - - -
280A ILE* 2.9 42.5 + - - +
281A LEU 3.7 3.1 - - - +
283A LEU* 1.3 71.6 - - - +
285A MSE 1.3 58.8 + - - +
288A HIS* 2.8 36.3 + - - +
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Residues in contact with MSE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ILE* 4.2 16.4 - - + -
281A LEU* 3.0 43.5 + - + +
282A ALA* 3.6 7.9 - - - +
284A CYS* 1.3 77.5 - - - +
286A GLY* 1.3 57.5 + - - +
288A HIS* 3.6 5.1 - - - +
289A GLU* 3.0 33.2 + - - +
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Residues in contact with GLY 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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84A PHE* 3.6 27.6 - - - -
282A ALA 3.0 12.2 + - - -
285A MSE 1.3 77.8 - - - +
287A ASN* 1.3 60.4 + - - +
289A GLU* 3.8 9.3 - - - +
290A LEU* 3.2 29.9 + - - +
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Residues in contact with ASN 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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83A LYS 5.1 0.2 + - - -
84A PHE* 3.3 31.7 - - - +
85A TYR 4.9 1.4 + - - +
204A ASN* 4.5 8.1 - - - +
220A VAL* 4.2 8.7 - - - +
221A ASP 3.5 24.7 + - - +
222A ALA* 3.3 25.8 + - - +
242A TRP* 3.6 10.9 + - + -
283A LEU* 2.9 32.5 + - - +
286A GLY* 1.3 71.8 - - - +
288A HIS* 1.3 67.1 + - - +
290A LEU* 3.9 4.4 - - - +
291A TYR* 2.9 25.8 + - - +
294A ARG* 5.0 1.1 + - - +
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Residues in contact with HIS 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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242A TRP* 3.7 49.9 + + + -
243A SER* 5.7 0.2 - - - -
245A ILE* 4.8 9.9 + - + -
284A CYS 2.8 24.0 + - - +
285A MSE 3.6 4.9 + - - +
287A ASN* 1.3 74.6 - - - +
289A GLU* 1.3 65.1 + - - +
291A TYR* 3.2 3.5 + - - +
292A MSE 3.1 56.9 + - + +
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Residues in contact with GLU 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 MSE 3.0 18.4 + - - +
286A GLY* 3.8 9.0 - - - +
288A HIS* 1.3 78.7 + - - +
290A LEU* 1.3 64.8 + - + +
292A MSE 3.4 4.7 + - - +
293A ARG* 2.9 37.1 + - + +
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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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43A TRP* 3.9 40.8 - - + +
44A PHE* 4.7 5.8 - - + -
84A PHE* 3.6 39.9 - - + -
286A GLY 3.2 14.0 + - - +
287A ASN* 4.1 4.7 - - - +
289A GLU* 1.3 83.9 - - + +
291A TYR* 1.3 63.6 + - - +
293A ARG* 3.9 24.5 + - - +
294A ARG* 3.0 52.3 + - - +
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Residues in contact with TYR 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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87A GLU* 3.2 16.2 - - - -
222A ALA 3.4 16.2 - - - +
223A LEU* 3.9 8.1 - - + -
241A PRO* 6.6 0.2 - - + -
242A TRP* 3.4 23.6 - + + -
243A SER 5.5 0.2 - - - -
287A ASN 2.9 19.3 + - - +
288A HIS 3.4 4.3 - - - +
289A GLU 3.2 0.2 - - - -
290A LEU* 1.3 78.5 - - - +
292A MSE 1.3 85.2 + - + +
294A ARG* 3.3 15.0 + - - +
295A ARG* 2.9 58.4 + - - +
502C ASP* 3.7 14.9 + - - -
503C ARG* 2.8 31.6 + - + +
505C GLU* 2.9 24.5 + - - -
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Residues in contact with MSE 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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242A TRP* 3.7 14.4 - - + -
243A SER* 4.1 14.1 - - - +
288A HIS* 3.1 48.8 + - + +
289A GLU* 3.7 5.4 - - - +
291A TYR* 1.3 106.0 - - + +
293A ARG* 1.3 59.6 + - - +
295A ARG* 2.9 25.9 + - - +
296A LYS* 2.9 22.5 + - - +
502C ASP* 4.6 5.6 - - - +
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Residues in contact with ARG 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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43A TRP* 3.3 53.6 - - - +
289A GLU* 2.9 24.5 + - + +
290A LEU* 3.9 23.6 + - - +
292A MSE 1.3 76.3 - - - +
294A ARG* 1.3 60.2 + - - +
296A LYS 4.1 7.9 - - - -
297A PRO* 3.6 29.8 - - + +
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Residues in contact with ARG 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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44A PHE* 3.8 11.9 - - - -
85A TYR 3.7 18.8 + - - -
86A PRO* 3.7 2.6 - - - +
87A GLU* 2.9 39.0 + - - +
91A GLU* 6.0 0.4 - - - -
92A GLU* 2.6 40.7 + - - +
222A ALA* 4.6 7.9 + - - +
287A ASN 5.0 0.4 + - - -
290A LEU* 3.0 54.2 + - - +
291A TYR* 3.6 10.4 - - - +
292A MSE 3.0 1.0 + - - -
293A ARG* 1.3 77.2 - - - +
295A ARG* 1.3 66.6 + - + +
297A PRO* 4.9 3.4 - - - +
500C ALA* 4.6 8.1 - - - +
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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
----------------------------------------------------------
87A GLU* 2.7 43.9 + - - -
291A TYR* 2.9 50.2 + - - +
292A MSE 2.9 11.6 + - - +
294A ARG* 1.3 86.2 - - + +
296A LYS* 1.3 76.4 + - + +
297A PRO* 3.7 6.1 - - - +
500C ALA* 4.3 17.8 - - + +
501C LYS* 3.2 29.4 + - - +
502C ASP* 4.0 11.4 - - - +
504C SER* 3.4 15.7 + - - -
505C GLU* 3.3 19.4 + - - -
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A MSE 2.9 18.9 + - + +
293A ARG* 4.1 3.8 - - - -
295A ARG* 1.3 87.4 + - + +
297A PRO* 1.4 67.7 - - - +
501C LYS* 6.1 2.6 - - - +
502C ASP 5.9 3.2 - - - +
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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
------------------------------------------------------------
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