Contacts of the helix formed by residues 282 - 303 (chain D) in PDB entry 7CAL
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 MET 282 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 4.0 12.8 - - - -
209A ILE* 4.5 11.2 - - + -
255A ILE* 3.8 18.8 - - + -
701A 3PE 5.8 0.4 - - - -
278D ILE* 3.1 20.5 + - - +
279D PHE* 3.8 19.1 - - + +
280D PHE 3.2 0.4 - - - -
281D MET* 1.3 75.7 - - - +
283D PHE* 1.3 64.2 + - - +
284D ASN 3.3 0.2 - - - -
285D LEU* 3.6 10.3 + - + +
286D GLY 3.6 12.6 + - - -
701D 3PE 1.5 107.2 - - + +
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Residues in contact with PHE 283 (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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204D VAL* 6.0 1.3 - - + -
208D ALA* 4.0 26.5 - - + -
279D PHE 3.7 12.5 + - - +
280D PHE* 3.1 22.8 + + + +
282D MET* 1.3 78.7 - - - +
284D ASN* 1.3 70.3 + - - +
286D GLY* 3.2 3.7 + - - +
287D LEU* 2.9 50.2 + - + +
701D 3PE 3.6 42.3 - - + +
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Residues in contact with ASN 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A THR* 6.3 1.3 - - - -
257D THR* 3.7 16.1 + - - +
258D LEU* 3.7 35.6 - - - +
260D THR* 5.1 5.4 - - + -
280D PHE* 2.9 54.6 + - - +
281D MET* 3.9 9.6 - - + +
282D MET 3.3 0.4 - - - -
283D PHE* 1.3 83.6 - - - +
285D LEU* 1.3 64.2 + - - +
287D LEU* 3.7 5.9 - - - +
288D THR* 3.2 28.5 + - + +
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Residues in contact with LEU 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A THR* 5.1 8.7 - - + +
209A ILE* 5.7 2.0 - - + -
255A ILE* 4.9 4.5 - - + -
258A LEU* 3.8 20.0 - - + -
259A THR* 3.8 34.7 - - + +
288A THR* 4.6 18.4 - - + -
291A LEU* 4.0 27.7 - - + +
281D MET 3.7 5.9 + - - +
282D MET* 3.6 12.5 + - + +
283D PHE 3.3 0.6 - - - -
284D ASN* 1.3 78.8 - - - +
286D GLY* 1.3 59.7 + - - +
288D THR* 4.0 3.7 + - - +
289D ALA* 3.3 26.6 + - + +
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Residues in contact with GLY 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A MET* 4.7 13.2 - - - +
282D MET 3.6 4.9 + - - -
283D PHE 3.2 7.1 + - - -
285D LEU* 1.3 79.3 - - - +
287D LEU* 1.3 61.0 + - - +
289D ALA* 4.1 4.4 - - - +
290D TYR* 3.3 20.8 + - - +
701D 3PE 3.6 32.5 - - - +
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D VAL* 4.0 25.1 - - + -
205D THR* 4.4 12.3 - - + -
208D ALA* 4.3 7.0 - - + -
258D LEU* 3.9 39.7 - - + -
283D PHE* 2.9 44.3 + - + +
284D ASN* 4.1 6.3 - - - +
285D LEU 3.3 0.4 - - - -
286D GLY* 1.3 77.6 - - - +
288D THR* 1.3 62.6 + - + +
289D ALA 3.2 0.2 - - - -
290D TYR* 3.0 9.9 + - + +
291D LEU* 3.0 37.6 + - + +
701D 3PE 4.2 12.5 - - + +
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Residues in contact with THR 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 5.4 3.4 - - - +
285C LEU* 4.5 18.8 - - + -
258D LEU* 3.6 23.8 - - + +
259D THR* 5.4 0.9 - - - -
260D THR* 5.4 6.4 - - + +
284D ASN 3.2 19.7 + - - +
285D LEU* 4.0 5.0 + - - +
287D LEU* 1.3 81.0 - - + +
289D ALA* 1.3 58.7 + - - +
290D TYR 3.2 0.4 - - - -
291D LEU* 4.0 9.6 - - + +
292D ILE* 3.3 39.7 + - - +
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Residues in contact with ALA 289 (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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291A LEU* 4.4 11.4 - - + +
292A ILE* 4.1 26.4 - - + +
295A MET* 3.3 36.0 - - + +
296A THR 4.8 0.2 + - - -
285D LEU* 3.3 18.4 + - + +
286D GLY* 4.3 4.3 - - - +
287D LEU 3.2 0.8 - - - -
288D THR* 1.3 80.3 + - - +
290D TYR* 1.3 57.3 + - - +
292D ILE* 4.8 0.9 - - - -
293D GLY* 3.6 15.8 + - - -
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Residues in contact with TYR 290 (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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295A MET* 4.5 11.0 - - + -
299A VAL* 4.7 10.0 - - + +
197D ARG* 4.5 2.4 + - - -
200D LYS* 4.7 5.9 - - - +
201D LEU* 3.7 24.5 - - + +
204D VAL* 4.7 12.0 - - + +
286D GLY 3.3 18.7 + - - +
287D LEU* 3.0 7.9 + - + +
289D ALA* 1.3 79.1 - - - +
291D LEU* 1.3 72.9 + - + +
293D GLY* 4.0 1.1 - - - -
294D ASN* 2.9 57.9 + - - +
701D 3PE 3.5 75.3 + - + -
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Residues in contact with LEU 291 (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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285C LEU* 4.0 31.2 - - + +
289C ALA* 4.4 8.4 - - + +
201D LEU* 4.0 26.9 - - + +
204D VAL* 5.5 1.1 - - + -
205D THR* 3.7 33.0 - - + -
287D LEU* 3.0 27.3 + - + +
288D THR* 4.5 7.2 - - + +
290D TYR* 1.3 93.2 - - + +
292D ILE* 1.3 62.1 + - + +
294D ASN* 3.8 3.3 - - - +
295D MET* 2.9 31.4 + - - +
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Residues in contact with ILE 292 (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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292A ILE* 3.7 37.0 - - + -
296A THR* 5.0 0.7 - - - +
288C THR* 5.0 4.3 - - - +
289C ALA* 4.1 27.0 - - + +
292C ILE* 3.7 44.6 - - + -
288D THR* 3.3 26.0 + - - +
289D ALA* 4.8 0.4 - - - -
291D LEU* 1.3 78.0 - - + +
293D GLY* 1.3 54.2 + - - +
295D MET* 3.5 1.1 + - - +
296D THR* 2.5 42.3 + - - +
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Residues in contact with GLY 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ILE* 5.5 0.2 - - - +
295A MET 4.6 1.6 - - - -
296A THR* 3.6 36.0 + - - +
299A VAL* 3.5 19.5 - - - +
289D ALA 3.6 15.9 + - - -
290D TYR 3.8 1.1 + - - -
291D LEU 3.3 0.2 - - - -
292D ILE* 1.3 79.5 - - - +
294D ASN* 1.3 59.8 + - - +
296D THR* 3.9 2.6 + - - -
297D ASN* 3.4 14.4 + - - +
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Residues in contact with ASN 294 (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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299A VAL* 3.4 23.4 - - - +
303A THR* 4.9 2.0 - - - +
197D ARG* 3.0 31.6 - - - +
201D LEU* 3.8 25.3 - - + +
290D TYR* 2.9 49.1 + - - +
291D LEU 3.9 0.2 - - - +
292D ILE 3.2 0.2 - - - -
293D GLY* 1.3 77.4 - - - +
295D MET* 1.3 58.5 + - - +
296D THR 3.2 0.2 - - - -
297D ASN* 3.2 10.4 + - - +
298D LEU* 3.0 32.0 + - + +
701D 3PE 4.7 1.1 + - - -
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Residues in contact with MET 295 (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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286C GLY* 4.8 17.9 - - - +
289C ALA* 3.3 37.0 - - + +
290C TYR* 4.5 9.0 - - + -
701C 3PE 6.2 2.9 - - + -
198D CYS* 4.6 13.5 - - + -
201D LEU* 4.6 14.1 - - + +
291D LEU 2.9 19.1 + - - +
292D ILE 4.2 0.9 - - - +
294D ASN* 1.3 74.5 - - - +
296D THR* 1.3 60.3 + - - +
298D LEU* 3.8 22.6 - - - +
299D VAL* 2.9 40.9 + - + +
302D TRP* 6.0 2.9 - - - -
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Residues in contact with THR 296 (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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296A THR* 3.8 25.1 + - + +
300A VAL* 6.1 0.4 - - - -
292C ILE 4.8 0.2 - - - -
293C GLY* 3.6 22.4 + - - +
296C THR* 3.8 37.1 + - + -
292D ILE* 2.5 30.9 + - - +
293D GLY* 4.0 1.2 - - - -
295D MET* 1.3 77.8 - - - +
297D ASN* 1.3 60.9 + - - +
299D VAL* 4.2 1.0 - - - +
300D VAL* 3.3 30.7 + - + +
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Residues in contact with ASN 297 (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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296A THR* 5.4 0.6 - - - +
299A VAL* 4.2 9.6 - - + +
300A VAL* 4.1 20.9 - - + +
303A THR* 2.9 28.2 + - - -
307A ARG* 2.9 37.7 + - - +
193D TYR* 5.1 4.4 + - - -
197D ARG* 6.0 1.0 - - - +
293D GLY 3.4 12.9 + - - +
294D ASN* 3.2 14.5 + - - +
296D THR* 1.3 79.1 - - - +
298D LEU* 1.3 63.6 + - - +
300D VAL* 4.0 5.6 - - - +
301D HIS* 3.2 23.4 + - - +
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Residues in contact with LEU 298 (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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193D TYR* 4.6 13.0 - - + +
194D PHE* 4.0 24.8 - - + +
197D ARG* 4.1 32.3 - - + +
198D CYS* 3.7 30.1 - - - -
201D LEU* 4.8 5.8 - - + -
294D ASN* 3.0 22.1 + - + +
295D MET* 3.8 18.8 - - - +
296D THR 3.2 0.4 - - - -
297D ASN* 1.3 83.5 - - - +
299D VAL* 1.3 54.4 + - - +
301D HIS* 3.2 5.5 + - + +
302D TRP* 2.6 47.2 + - + +
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Residues in contact with VAL 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C TYR* 4.7 10.8 - - + +
293C GLY* 3.5 26.2 - - - +
294C ASN* 3.4 40.2 - - - +
297C ASN* 4.2 8.7 - - + -
701C 3PE 6.1 0.4 - - - +
295D MET* 2.9 31.3 + - + +
296D THR 4.2 0.9 - - - +
298D LEU* 1.3 73.6 - - + +
300D VAL* 1.3 61.5 + - - +
302D TRP* 3.3 15.4 - - + +
303D THR* 2.9 40.6 + - + +
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Residues in contact with VAL 300 (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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307A ARG* 5.0 12.3 - - - +
293C GLY 5.4 0.2 - - - +
296C THR 6.1 0.2 - - - -
297C ASN* 4.1 28.3 - - + +
296D THR* 3.3 24.6 + - + +
297D ASN* 4.0 8.1 - - - +
299D VAL* 1.3 77.9 - - + +
301D HIS* 1.3 60.9 + - - +
303D THR* 4.8 0.7 - - - -
304D SER* 3.2 28.2 + - - -
307D ARG* 4.3 13.9 - - - +
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Residues in contact with HIS 301 (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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307A ARG* 3.6 36.7 + - + +
310A ARG* 4.5 9.6 - - + -
311A ASP* 2.6 39.3 + - - -
314A ARG* 3.8 15.9 + - - -
193D TYR* 3.8 27.5 - + + -
194D PHE* 3.2 38.6 - + + -
297D ASN 3.2 17.7 + - - +
298D LEU* 3.2 8.8 + - + +
300D VAL* 1.3 75.0 - - - +
302D TRP* 1.3 65.1 + - - +
304D SER* 4.2 6.2 + - - -
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Residues in contact with TRP 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ARG* 5.0 4.2 + - - -
701C 3PE 3.9 42.8 - - - +
194D PHE* 4.1 45.1 - + + +
195D TRP* 4.4 26.5 - + - -
295D MET* 6.0 3.3 - - - -
298D LEU* 2.6 34.9 + - + +
299D VAL* 3.3 20.9 - - + +
301D HIS* 1.3 76.7 - - - +
303D THR* 1.3 68.8 + - + +
304D SER* 3.6 2.8 + - - -
305D ARG* 4.7 5.5 + - - +
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Residues in contact with THR 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C TYR* 4.5 10.8 - - - +
197C ARG* 4.4 19.1 - - - +
294C ASN* 4.9 0.2 - - - +
297C ASN* 2.9 26.9 + - - +
701C 3PE 4.2 24.7 - - - +
299D VAL* 2.9 20.1 + - + +
300D VAL* 4.0 2.4 - - - -
302D TRP* 1.3 84.1 - - + +
304D SER* 1.3 58.9 + - - +
305D ARG 3.4 2.2 - - - +
306D THR* 4.4 9.0 - - - +
307D ARG* 3.3 25.9 + - - +
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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