Contacts of the helix formed by residues 291 - 318 (chain D) in PDB entry 2DFD
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 SER 291 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D SER* 4.1 10.5 + - - -
205D LEU* 6.0 0.7 - - - +
290D VAL* 1.3 76.4 - - - +
292D SER* 1.3 57.1 + - - +
293D PHE* 3.4 11.5 + - - +
294D GLU* 2.9 40.3 + - - +
295D GLU* 2.9 27.6 + - - +
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Residues in contact with SER 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D VAL 4.1 0.2 + - - -
291D SER* 1.3 72.3 - - - +
293D PHE* 1.3 62.2 + - - +
295D GLU* 3.4 7.5 + - - +
296D LYS* 3.0 25.6 + - - +
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Residues in contact with PHE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D GLN* 3.7 37.5 - - - +
205D LEU* 4.2 17.0 - - + -
206D THR* 4.3 14.1 - - + -
209D THR* 3.7 23.8 - - + -
291D SER* 3.2 10.9 + - - +
292D SER* 1.3 78.8 - - - +
294D GLU* 1.3 61.2 + - + +
296D LYS* 3.4 7.3 + - + +
297D MET* 3.1 58.8 + - + +
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Residues in contact with GLU 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 4.4 0.7 - - - +
189D PRO 3.9 3.2 - - - +
190D LEU* 3.3 26.9 - - + -
191D ILE* 3.2 13.3 + - - +
192D SER* 2.6 48.2 + - - -
290D VAL* 3.6 11.1 - - + +
291D SER* 2.9 33.4 + - - +
293D PHE* 1.3 76.7 - - + +
295D GLU* 1.3 59.4 + - - +
297D MET* 3.2 23.8 + - + +
298D ILE* 3.0 33.8 + - - +
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Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D VAL* 4.2 20.5 - - + +
291D SER 2.9 17.0 + - - +
292D SER* 3.7 8.5 - - - +
293D PHE 3.4 0.2 - - - -
294D GLU* 1.3 75.9 - - - +
296D LYS* 1.3 56.3 + - - +
298D ILE* 3.2 16.8 + - - +
299D SER* 3.0 28.8 + - - -
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Residues in contact with LYS 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D SER 3.0 17.6 + - - +
293D PHE* 3.7 7.2 - - + +
295D GLU* 1.3 77.4 - - - +
297D MET* 1.3 56.9 + - + +
299D SER* 3.4 6.8 + - - -
300D ASP* 2.8 54.2 + - - +
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Residues in contact with MET 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LYS* 4.6 4.6 - - + +
188D ILE* 3.7 27.2 - - + +
189D PRO* 4.3 7.0 - - - +
209D THR* 3.6 27.4 - - + -
213D GLN* 3.9 14.8 - - - +
293D PHE* 3.1 47.2 + - + +
294D GLU* 3.2 31.6 + - + +
296D LYS* 1.3 75.6 - - + +
298D ILE* 1.3 62.8 + - - +
300D ASP* 3.4 6.5 + - - +
301D ALA* 3.0 26.5 + - - +
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Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ILE* 3.7 25.6 - - + -
188D ILE* 3.6 20.6 - - + -
190D LEU* 5.1 0.7 - - + -
265D THR* 4.9 3.4 - - + -
270D PHE* 4.3 19.9 - - + -
287D ILE* 3.8 27.4 - - + -
290D VAL* 4.6 8.1 - - + -
294D GLU 3.0 21.2 + - - +
295D GLU* 3.2 22.4 + - - +
297D MET* 1.3 75.3 - - - +
299D SER* 1.3 65.5 + - - +
301D ALA* 3.1 12.3 + - - +
302D ILE* 3.3 25.2 + - + +
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Residues in contact with SER 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D GLU* 3.0 17.9 + - - -
296D LYS* 3.6 7.4 - - - -
298D ILE* 1.3 78.6 - - - +
300D ASP* 1.3 67.5 + - - +
301D ALA 3.2 0.7 + - - -
302D ILE* 3.4 20.4 + - - +
303D PRO* 3.6 8.8 - - - +
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Residues in contact with ASP 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LYS* 6.4 2.2 - - + -
296D LYS* 2.8 40.4 + - - +
297D MET* 3.9 6.8 - - - +
299D SER* 1.3 82.2 + - - +
301D ALA* 1.3 58.9 + - - +
303D PRO* 3.6 11.9 - - - +
304D GLU* 5.1 2.8 + - - +
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Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D GLY* 6.1 0.2 - - - -
185D LYS* 3.9 20.4 - - - +
186D THR* 3.9 18.1 - - + +
188D ILE* 4.0 10.3 - - + -
270D PHE* 6.1 1.8 - - + -
297D MET 3.0 16.6 + - - +
298D ILE 3.1 4.9 + - - +
300D ASP* 1.3 77.7 - - - +
302D ILE* 1.3 65.3 + - + +
303D PRO* 3.4 2.1 - - - -
304D GLU* 3.4 6.9 + - - +
305D LEU* 3.1 27.7 + - + +
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Residues in contact with ILE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D THR* 4.8 11.2 - - + +
266D GLU* 3.7 45.3 - - + +
267D CYS* 4.0 22.4 - - - -
270D PHE* 5.2 3.6 - - + -
298D ILE* 3.3 28.2 + - + +
299D SER* 3.4 12.8 + - - +
301D ALA* 1.3 77.4 - - - +
303D PRO* 1.3 67.7 - - + +
305D LEU* 3.2 3.2 + - - +
306D LYS* 2.9 35.9 + - + +
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Residues in contact with PRO 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D SER 3.6 7.6 - - - +
300D ASP* 3.6 13.5 - - - +
301D ALA 3.5 3.8 - - - -
302D ILE* 1.3 97.6 - - + +
304D GLU* 1.3 61.4 + - - +
306D LYS* 3.3 7.1 + - + +
307D ALA* 3.0 24.3 + - - +
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Residues in contact with GLU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ASN* 4.8 1.4 + - - +
183D ALA* 3.9 22.9 - - - +
184D GLY* 5.5 0.6 - - - -
185D LYS* 4.9 7.6 + - - +
186D THR* 3.4 26.4 + - + +
300D ASP 5.1 1.7 + - - +
301D ALA* 3.4 9.1 + - - +
302D ILE 3.4 0.6 - - - -
303D PRO* 1.3 79.0 - - - +
305D LEU* 1.3 64.0 + - - +
307D ALA* 3.4 8.0 + - - +
308D SER* 3.0 29.2 + - - +
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Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ASN* 3.4 37.0 - - + +
180D GLY* 4.0 12.6 - - - +
181D GLY* 3.9 11.7 - - - -
186D THR* 4.1 9.6 - - + -
259D PHE* 4.1 10.3 - - + -
267D CYS* 3.8 13.0 - - - -
269D TYR 4.2 5.8 - - - +
270D PHE* 3.4 37.9 - - + -
301D ALA* 3.1 18.5 + - + +
302D ILE* 3.7 7.0 - - - +
304D GLU* 1.3 75.5 - - - +
306D LYS* 1.3 65.0 + - - +
308D SER* 3.2 4.5 + - - -
309D ILE* 2.9 31.3 + - + +
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Residues in contact with LYS 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D GLU* 3.4 53.6 - - - +
267D CYS* 4.3 12.8 - - - +
268D THR* 6.3 1.8 - - + -
302D ILE* 2.9 26.1 + - + +
303D PRO* 3.7 7.2 - - + +
305D LEU* 1.3 75.0 - - - +
307D ALA* 1.3 57.1 + - - +
309D ILE* 3.2 10.7 + - + +
310D LYS* 2.9 30.2 + - - +
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Residues in contact with ALA 307 (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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303D PRO 3.0 17.0 + - - +
304D GLU* 3.7 7.6 - - - +
306D LYS* 1.3 76.1 - - - +
308D SER* 1.3 56.9 + - - +
310D LYS* 3.3 5.8 + - - +
311D LYS* 2.9 30.5 + - - +
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Residues in contact with SER 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D ASP* 4.6 14.1 + - - -
127D ASN* 3.7 32.2 + - - +
128D SER* 2.7 29.2 + - - -
304D GLU* 3.0 25.9 + - - +
305D LEU* 3.7 4.3 - - - -
307D ALA* 1.3 74.8 - - - +
309D ILE* 1.3 62.7 + - - +
311D LYS* 3.4 6.3 + - - +
312D GLY 3.2 11.3 + - - -
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Residues in contact with ILE 309 (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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127D ASN 4.0 10.5 - - - +
131D PRO* 3.8 10.4 - - + +
259D PHE* 4.6 3.1 - - + -
267D CYS* 4.2 5.6 - - + -
268D THR* 3.5 25.4 - - + +
269D TYR* 3.5 55.0 - - + +
305D LEU* 2.9 26.6 + - + +
306D LYS* 3.5 10.1 - - + +
308D SER* 1.3 77.4 - - - +
310D LYS* 1.3 63.6 + - - +
312D GLY* 3.3 3.1 + - - -
313D GLU* 3.1 44.6 + - - +
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Residues in contact with LYS 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D LYS 2.9 16.0 + - - +
307D ALA* 3.9 6.5 - - - +
309D ILE* 1.3 76.7 - - - +
311D LYS* 1.3 57.3 + - - +
313D GLU* 3.7 13.2 - - - +
314D ASP* 2.7 69.2 + - - +
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Residues in contact with LYS 311 (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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93D ASP* 4.4 25.4 + - - +
96D PHE* 3.4 57.4 - - + -
97D ASN* 5.7 0.6 + - - -
128D SER* 4.2 5.2 - - - +
307D ALA 2.9 18.4 + - - +
308D SER* 3.6 7.4 - - - +
309D ILE 3.2 0.2 - - - -
310D LYS* 1.3 76.3 - - - +
312D GLY* 1.3 62.0 + - - +
314D ASP* 3.6 6.5 + - - +
315D PHE 3.1 17.3 + - - -
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Residues in contact with GLY 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 4.0 8.4 - - - -
128D SER 3.8 11.7 - - - -
131D PRO* 4.6 0.4 - - - -
132D ILE* 3.4 32.2 - - - +
308D SER 3.2 11.1 + - - -
309D ILE 3.3 2.4 + - - -
311D LYS* 1.3 74.7 - - - +
313D GLU* 1.3 64.9 + - - +
315D PHE* 3.1 9.2 + - - +
316D VAL* 3.1 12.5 + - - +
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Residues in contact with GLU 313 (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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131D PRO* 4.4 7.7 - - + +
135D GLU* 4.1 36.6 - - + +
268D THR* 4.3 5.7 + - - +
269D TYR* 3.9 11.3 + - - -
309D ILE* 3.1 36.9 + - - +
310D LYS* 3.7 17.0 - - - +
312D GLY* 1.3 73.0 - - - +
314D ASP* 1.3 67.6 + - - +
316D VAL* 3.3 5.0 + - - +
317D LYS* 3.3 33.6 + - - +
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Residues in contact with ASP 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310D LYS* 2.7 57.4 + - - +
311D LYS* 3.8 6.1 - - - +
313D GLU* 1.3 76.0 - - - +
315D PHE* 1.3 66.3 + - - +
317D LYS* 3.4 33.1 + - - +
318D THR* 3.6 11.3 - - - +
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Residues in contact with PHE 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 3.6 28.7 - + + -
97D ASN* 5.3 1.8 - - - -
100D ALA* 3.5 41.7 - - + -
101D THR* 3.5 28.5 - - - -
104D ALA* 3.8 10.8 - - + -
132D ILE* 4.0 8.3 - - + -
311D LYS 3.1 8.3 + - - +
312D GLY 3.1 4.2 + - - +
314D ASP* 1.3 72.9 - - - +
316D VAL* 1.4 69.6 + - + +
318D THR* 2.7 37.5 + - + -
319D LEU* 3.6 32.5 - - + +
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Residues in contact with VAL 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ILE* 3.5 50.5 - - + +
135D GLU* 3.7 29.6 - - + +
136D VAL* 3.9 19.5 - - + -
139D LYS* 5.5 4.5 - - + -
312D GLY 3.1 7.0 + - - +
313D GLU 3.3 5.3 + - - +
315D PHE* 1.4 75.4 - - + +
317D LYS* 1.3 62.5 + - + +
319D LEU* 3.2 28.3 + - + +
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Residues in contact with LYS 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 5.0 10.1 + - - -
313D GLU* 3.3 20.7 + - - +
314D ASP* 3.6 27.1 - - - +
315D PHE 3.1 0.6 + - - -
316D VAL* 1.3 80.0 - - + +
318D THR* 1.4 58.3 + - + +
319D LEU 3.2 7.0 + - - +
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Residues in contact with THR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D ASP 3.6 14.8 - - - +
315D PHE* 2.7 30.8 + - + +
317D LYS* 1.4 71.9 - - + +
319D LEU* 1.3 67.7 + - - +
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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