Contacts of the helix formed by residues 272 - 295 (chain D) in PDB entry 1D2V
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 ASP 272 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D GLN* 3.7 16.6 - - - +
270D ARG 3.2 6.4 + - - +
271D TRP* 1.3 73.8 - - - +
273D GLY* 1.3 67.4 + - - +
274D GLU* 3.7 9.0 + - - +
275D ARG* 3.2 23.7 + - - +
276D LEU* 3.0 23.0 + - - +
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Residues in contact with GLY 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ARG* 4.3 3.6 - - - -
192D ASN 5.5 0.7 - - - -
193D GLN* 2.9 47.1 + - - -
195D GLY* 3.3 15.7 - - - -
272D ASP* 1.3 72.3 - - - +
274D GLU* 1.3 63.0 + - - +
276D LEU 3.1 2.1 + - - -
277D TYR* 2.9 21.5 + - - +
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Residues in contact with GLU 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 6.3 0.4 - - + -
188D ARG* 2.9 34.6 + - - +
190D MET* 5.7 0.5 - - - +
193D GLN* 4.7 0.4 + - - -
272D ASP* 3.4 10.0 + - - +
273D GLY* 1.3 74.6 - - - +
275D ARG* 1.3 57.4 + - - +
277D TYR* 3.5 1.7 + - - +
278D GLN* 2.7 66.3 + - + +
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Residues in contact with ARG 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 5.2 13.1 - - - +
7B TYR* 2.7 25.2 + - - -
271D TRP* 3.1 50.6 - - + +
272D ASP* 3.2 27.0 + - - +
274D GLU* 1.3 79.4 - - - +
276D LEU* 1.3 57.3 + - - +
278D GLN* 3.4 3.4 + - - +
279D GLU* 2.9 53.7 + - - +
577D GLU* 3.0 26.7 + - - +
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Residues in contact with LEU 276 (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 GLN 3.4 21.5 - - - +
194D LEU* 3.6 22.4 - - - +
195D GLY 4.4 1.3 - - - -
261D ALA* 3.6 10.3 - - + +
264D LEU* 3.7 17.1 - - + +
265D LYS* 3.4 45.5 - - + +
271D TRP* 3.8 24.7 - - + +
272D ASP 3.0 20.6 + - - +
273D GLY 3.1 6.0 + - - +
275D ARG* 1.3 76.6 - - - +
277D TYR* 1.3 56.3 - - - +
279D GLU* 3.8 3.3 - - - +
280D ALA* 2.9 34.2 + - - +
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Residues in contact with TYR 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.7 23.5 - - + +
177D TYR* 3.5 36.4 + + - +
184D ALA* 4.5 5.4 + - - +
188D ARG* 3.3 69.6 - - + +
195D GLY* 3.3 21.8 + - - +
196D LEU 5.0 0.7 - - - -
197D LEU* 4.2 5.6 - - + -
257D HIS* 3.4 18.8 - + - -
273D GLY 2.9 9.3 + - - +
274D GLU 3.6 0.9 - - - +
276D LEU* 1.3 75.8 - - - +
278D GLN* 1.3 86.8 + - + +
281D ARG* 2.7 39.2 + - - +
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Residues in contact with GLN 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.5 50.4 - - + +
8B ARG 5.2 1.2 + - - -
10B ILE* 6.1 1.0 - - - +
188D ARG* 4.4 1.6 - - - +
274D GLU* 2.7 48.0 + - + +
275D ARG* 3.9 1.8 - - - +
277D TYR* 1.3 97.4 - - - +
279D GLU* 1.3 58.4 + - - +
281D ARG* 3.2 32.7 + - - +
282D LYS* 2.9 29.6 + - - +
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Residues in contact with GLU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 2.6 31.8 + - - +
264D LEU* 3.9 11.2 - - + -
271D TRP* 3.5 34.7 - - + -
275D ARG* 2.9 35.9 + - - +
276D LEU 3.9 0.2 - - - +
278D GLN* 1.3 75.7 - - - +
280D ALA* 1.3 61.8 + - - +
282D LYS* 3.4 15.1 + - - +
283D ILE* 3.1 27.9 + - - +
524D GLN* 5.0 1.9 + - - -
575D TRP* 3.6 24.5 + - + -
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Residues in contact with ALA 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D HIS* 3.5 39.3 - - + +
260D LEU* 4.1 7.4 - - + +
261D ALA* 4.0 14.6 - - + +
264D LEU* 3.7 8.4 - - + +
276D LEU 2.9 18.3 + - - +
279D GLU* 1.3 74.5 - - - +
281D ARG* 1.4 65.1 + - - +
283D ILE* 3.2 4.8 + - - +
284D VAL* 3.1 27.5 + - - +
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Residues in contact with ARG 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 4.7 0.6 - - - +
8B ARG* 2.8 45.2 + - - +
9B THR 3.0 24.4 + - - -
10B ILE* 3.5 29.2 + - - +
172D ASP* 4.8 12.8 + - - +
177D TYR* 3.3 44.2 - - + +
257D HIS* 3.7 0.4 - - - -
277D TYR* 2.7 40.7 + - - +
278D GLN* 3.2 29.8 + - - +
280D ALA* 1.4 72.3 - - - +
282D LYS* 1.3 57.5 + - - +
284D VAL* 3.6 1.9 + - - +
285D GLY* 3.0 25.5 + - - -
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Residues in contact with LYS 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS 4.5 11.7 + - - -
7B TYR* 4.1 22.5 - - + -
278D GLN 2.9 17.6 + - - +
279D GLU* 3.5 17.7 + - - +
280D ALA 3.2 0.2 - - - -
281D ARG* 1.3 76.0 - - - +
283D ILE* 1.3 63.7 + - - +
285D GLY* 4.0 1.1 - - - -
286D ALA* 3.1 22.3 + - - +
512D PHE* 6.1 4.0 - - - -
518D GLY 5.1 0.6 + - - -
519D VAL* 2.7 50.2 + - + +
520D PHE* 3.6 23.1 - - + -
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Residues in contact with ILE 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D LEU* 3.5 36.1 - - + -
264D LEU* 4.6 8.5 - - + -
279D GLU 3.1 14.1 + - - +
280D ALA 3.2 7.1 + - - +
282D LYS* 1.3 75.8 - - - +
284D VAL* 1.4 52.8 + - - +
286D ALA* 3.0 7.9 + - - +
287D MET* 2.7 39.6 + - - +
520D PHE* 4.6 4.7 - - + -
528D LEU* 4.0 10.8 - - + -
570D LEU* 3.8 17.9 - - + -
572D LEU* 3.7 10.5 - - + -
575D TRP* 3.5 45.3 - - + +
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Residues in contact with VAL 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ALA* 3.9 16.6 - - + -
176D VAL* 4.7 6.7 - - + -
177D TYR* 3.2 26.5 - - + +
253D LEU* 4.5 24.9 - - + +
256D GLU* 4.6 5.4 - - + -
257D HIS* 4.1 17.0 - - + +
260D LEU* 4.0 15.5 - - + -
280D ALA 3.1 15.8 + - - +
281D ARG 3.8 1.3 - - - +
283D ILE* 1.4 71.6 - - - +
285D GLY* 1.4 61.4 + - - +
287D MET* 3.0 12.0 + - + +
288D VAL* 2.8 29.4 + - + +
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Residues in contact with GLY 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 6.0 2.0 - - - -
171D VAL 4.1 0.5 - - - +
172D ASP* 4.2 13.9 - - - -
173D ALA* 4.0 15.9 - - - +
281D ARG 3.0 17.1 + - - -
282D LYS* 4.0 2.0 - - - -
284D VAL* 1.4 76.5 - - - +
286D ALA* 1.3 60.8 + - - +
288D VAL* 3.2 3.9 + - - +
289D GLN* 2.9 31.1 + - - +
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Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D LYS 3.1 13.6 + - - +
283D ILE 3.0 9.6 + - - +
285D GLY* 1.3 73.5 - - - +
287D MET* 1.3 52.5 + - - +
289D GLN* 3.1 14.1 + - - +
290D ILE* 2.7 41.6 + - + +
514D TRP* 3.9 9.9 - - + -
520D PHE* 3.8 11.4 - - + -
528D LEU* 3.8 31.4 - - + -
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Residues in contact with MET 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LEU* 5.8 2.9 - - + -
256D GLU* 3.2 42.4 - - - +
259D ARG* 4.9 0.7 - - - +
260D LEU* 4.4 0.2 - - - -
283D ILE* 2.7 29.0 + - + +
284D VAL* 3.0 12.8 + - + +
286D ALA* 1.3 73.2 - - - +
288D VAL* 1.3 57.9 + - + +
290D ILE* 3.3 0.7 + - - +
291D ILE* 2.8 38.6 + - + +
528D LEU* 4.9 1.3 - - + -
531D ILE* 3.6 48.7 - - + -
536D ILE* 3.8 24.9 - - + -
570D LEU* 3.9 19.1 - - + -
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Residues in contact with VAL 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 3.7 23.1 - - + -
93B LEU* 4.6 4.3 - - + -
96B ASP* 3.6 14.4 - - - +
171D VAL* 3.5 20.4 - - + -
173D ALA* 4.0 18.6 - - + +
175D MET* 4.3 9.0 - - + -
253D LEU* 4.2 25.4 - - + -
284D VAL* 2.8 18.3 + - + +
285D GLY* 3.6 8.1 - - - +
287D MET* 1.3 76.1 - - - +
289D GLN* 1.4 56.1 + - - +
292D THR* 2.6 40.5 + - - +
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Residues in contact with GLN 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ARG* 3.3 9.2 - - - +
171D VAL* 2.9 41.8 + - + +
285D GLY 2.9 16.3 + - - +
286D ALA* 3.5 6.8 - - - +
288D VAL* 1.4 74.6 - - - +
290D ILE* 1.3 59.7 + - - +
292D THR* 3.4 1.2 + - - -
293D TYR* 2.9 38.2 + - - +
510D ASP* 3.2 24.0 + - - -
512D PHE 4.4 0.6 - - - +
513D TRP* 3.4 29.4 - - + +
514D TRP* 3.0 39.9 + - + +
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Residues in contact with ILE 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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286D ALA* 2.7 27.0 + - + +
287D MET 3.8 2.7 - - - +
289D GLN* 1.3 70.1 - - - +
291D ILE* 1.3 66.4 + - - +
293D TYR* 5.5 0.4 - - - -
294D ARG* 2.8 69.4 + - + +
514D TRP* 3.6 40.4 - - + +
528D LEU* 3.5 40.8 - - + +
529D ALA* 4.9 0.9 - - - -
531D ILE* 3.9 16.4 - - + -
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Residues in contact with ILE 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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89B TRP* 3.5 43.3 - - + -
253D LEU* 6.1 0.7 - - + -
287D MET 2.8 23.5 + - - +
290D ILE* 1.3 71.5 - - - +
292D THR* 1.3 57.3 + - - +
294D ARG* 5.2 0.4 - - - +
295D ASP* 3.0 23.4 + - - +
296D TYR* 3.0 23.6 + - - -
531D ILE* 4.1 11.2 - - + -
532D SER* 4.5 1.1 - - - -
533D LEU* 3.8 40.8 - - + +
536D ILE* 4.1 15.7 - - + -
552D PHE* 3.7 22.4 - - + -
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Residues in contact with THR 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 3.0 24.0 + - - +
93B LEU* 3.4 38.2 - - + +
171D VAL* 4.9 0.9 - - + -
288D VAL 2.6 23.7 + - - -
289D GLN* 3.6 4.0 - - - -
290D ILE 3.2 0.2 - - - -
291D ILE* 1.3 75.4 - - - +
293D TYR* 1.3 79.4 + - + +
296D TYR* 3.3 5.3 + - + -
297D LEU* 2.7 44.6 + - + +
503D PHE* 4.2 2.9 - - + -
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Residues in contact with TYR 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D VAL* 4.2 10.4 - - + +
289D GLN* 2.9 24.8 + - - +
290D ILE* 5.5 0.4 - - - -
292D THR* 1.3 91.8 - - + +
294D ARG* 1.3 63.5 + - - +
297D LEU* 3.7 16.4 - - + -
298D PRO* 3.4 17.9 - - - +
306D MET* 4.1 13.0 - - + +
310D LEU* 3.9 17.0 - - + -
503D PHE* 2.6 50.8 + + - -
506D LEU* 3.6 12.1 - - - +
507D ARG* 3.7 23.1 + - + -
513D TRP* 3.5 33.9 - + + -
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Residues in contact with ARG 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ILE* 2.8 41.8 + - + +
291D ILE* 5.2 0.4 - - - +
293D TYR* 1.3 77.7 - - - +
295D ASP* 1.3 93.2 + - - +
298D PRO* 3.5 15.6 - - - +
529D ALA* 3.4 22.4 + - - +
531D ILE* 2.8 30.7 + - - +
532D SER* 3.9 12.5 - - - +
549D ASN* 5.8 2.8 + - - +
550D ASN* 4.6 1.4 + - - -
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Residues in contact with ASP 295 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D ILE* 3.0 24.9 + - - +
294D ARG* 1.3 126.5 + - - +
296D TYR* 1.3 65.6 + - - +
298D PRO* 3.8 1.9 - - - +
299D LEU* 3.7 12.3 - - - +
532D SER* 5.3 1.2 - - - -
533D LEU* 5.3 1.7 + - - +
549D ASN* 5.9 2.8 - - - +
550D ASN* 2.9 43.7 + - - +
551D ILE* 5.6 3.4 - - + +
552D PHE* 3.7 13.2 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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