Contacts of the helix formed by residues 256 - 280 (chain D) in PDB entry 1EGE
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 256 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D MET* 5.9 2.0 - - - +
252D PHE* 2.9 56.0 + - + +
253D ASP* 4.6 7.3 + - - +
255D THR* 1.3 75.0 - - - +
257D PRO* 1.3 65.5 - - + +
259D VAL* 2.8 27.8 + - + +
260D ALA* 2.8 14.7 + - - +
326D THR* 5.3 6.7 + - - +
329D ALA* 4.3 29.2 - - + +
330D SER* 4.1 10.9 + - - -
333D LYS* 4.3 10.8 - - + +
376D GLU* 3.6 19.1 + - + +
377D GLY* 4.7 1.2 - - - -
381D ILE* 4.2 8.1 - - - +
382D GLN* 3.3 31.5 - - - +
385D ILE* 3.6 23.4 - - - +
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Residues in contact with PRO 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D THR* 4.5 6.5 - - + -
81D CYS* 3.5 21.5 - - - -
253D ASP 3.7 7.0 - - - +
254D LYS 4.5 0.4 - - - -
255D THR 3.4 12.8 - - - +
256D ARG* 1.3 95.6 - - + +
258D VAL* 1.3 53.8 + - - +
260D ALA* 3.5 3.2 + - + +
261D ALA* 3.1 21.3 + - - +
312D TYR* 3.6 15.8 - - + +
315D ALA* 3.6 32.1 - - + -
316D ALA 4.3 7.4 - - - +
325D ASN* 3.9 15.0 - - - +
329D ALA* 4.2 7.9 - - + +
332D ALA* 5.1 2.7 - - + -
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D HIS* 4.7 2.9 - - - +
77D THR* 3.7 27.4 - - + -
80D ALA* 3.9 21.5 - - + +
81D CYS* 3.6 11.4 - - - -
84D SER* 3.6 13.9 + - - +
95D GLN* 5.4 1.4 + - - +
99D GLU* 3.3 41.0 - - + +
254D LYS 4.6 1.6 - - - +
255D THR* 2.7 25.0 + - + +
257D PRO* 1.3 70.5 - - - +
259D VAL* 1.3 63.8 + - - +
261D ALA* 3.1 16.8 - - - +
262D GLY* 3.2 5.9 + - - -
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D GLN* 6.4 0.4 - - - +
99D GLU* 5.8 5.8 - - + -
103D LEU* 5.6 3.6 - - + -
255D THR* 2.9 27.9 + - + +
256D ARG* 2.8 21.0 + - - +
258D VAL* 1.3 75.3 - - + +
260D ALA* 1.3 64.3 + - - +
262D GLY* 2.8 14.6 + - - -
263D ALA 3.2 7.4 + - - -
333D LYS* 4.3 21.5 - - + +
372D TYR* 3.5 23.4 - - + -
375D TYR* 4.4 14.8 - - + -
376D GLU* 4.6 19.3 - - + -
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Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D ARG 2.8 14.3 + - - +
257D PRO 3.7 7.9 - - - +
259D VAL* 1.3 73.7 - - - +
261D ALA* 1.3 63.8 + - - +
263D ALA* 2.9 6.6 + - - +
264D VAL* 2.9 26.4 + - - +
311D SER* 5.3 0.2 - - - +
312D TYR* 4.1 6.3 - - + -
332D ALA* 3.8 28.7 - - + +
333D LYS* 4.0 5.8 - - - +
336D ALA* 3.6 24.4 - - + +
372D TYR* 5.4 0.2 - - - -
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Residues in contact with ALA 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D CYS* 3.1 25.8 - - + +
84D SER* 3.0 23.6 - - - +
85D GLU* 3.2 13.5 - - - +
257D PRO 3.1 14.3 + - - +
258D VAL 3.1 8.7 - - - +
259D VAL 3.1 0.2 - - - -
260D ALA* 1.3 76.2 - - - +
262D GLY* 1.3 59.5 + - - +
264D VAL* 3.2 13.2 - - - +
265D GLY 3.1 16.8 + - - -
312D TYR* 3.6 7.8 - - + -
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Residues in contact with GLY 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D SER* 4.3 1.7 + - - -
85D GLU* 4.7 1.1 - - - -
88D ALA* 3.1 25.8 - - - +
95D GLN* 4.5 10.8 - - - -
258D VAL 3.2 4.7 + - - -
259D VAL* 2.8 10.5 + - - -
261D ALA* 1.3 79.5 - - - +
263D ALA* 1.3 62.1 + - - +
266D LEU* 3.1 18.9 + - - +
372D TYR* 3.4 16.2 + - - -
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Residues in contact with ALA 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D VAL 3.2 4.5 + - - +
260D ALA* 2.9 9.9 + - - +
262D GLY* 1.3 74.1 - - - +
264D VAL* 1.3 60.0 + - - +
266D LEU* 3.0 7.5 + - - +
267D ALA 2.9 22.7 + - - -
336D ALA* 3.9 27.8 - - + +
337D GLY 4.3 0.7 - - - +
340D ALA* 3.7 11.5 - - + +
372D TYR* 3.2 39.3 - - + -
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Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D GLU* 3.7 13.0 - - - +
260D ALA 2.9 15.0 + - - +
261D ALA 3.2 15.7 - - - +
263D ALA* 1.3 73.4 - - - +
265D GLY* 1.3 59.7 + - - +
267D ALA* 3.5 6.2 - - - +
268D GLN* 2.9 27.9 + - - +
305D VAL* 3.5 35.7 - - + +
308D ALA* 4.0 15.3 - - + +
309D ARG* 4.0 11.2 - - + +
312D TYR* 3.3 30.1 - - + -
336D ALA* 4.5 1.7 - - + +
339D ILE* 4.8 2.7 - - - -
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Residues in contact with GLY 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D GLU* 3.4 33.0 - - - -
88D ALA* 4.0 0.2 - - - -
89D TYR* 3.6 18.2 - - - -
261D ALA 3.1 9.7 + - - -
262D GLY 3.6 4.5 - - - -
263D ALA 3.1 0.8 - - - -
264D VAL* 1.3 79.1 - - - +
266D LEU* 1.3 59.4 + - - +
268D GLN* 3.4 6.5 + - - +
269D ARG* 3.1 18.4 + - - +
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Residues in contact with LEU 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D ALA* 4.4 7.4 - - - +
92D THR* 3.9 24.0 - - + +
262D GLY 3.1 11.8 + - - +
263D ALA* 3.0 13.1 + - - +
265D GLY* 1.3 74.5 - - - +
267D ALA* 1.3 66.8 + - - +
269D ARG* 3.3 4.4 + - + +
270D ALA* 3.0 23.6 + - - +
340D ALA* 4.1 11.2 - - + +
344D ALA* 4.2 7.0 - - + -
365D LEU* 3.5 41.7 - - + +
368D ASP* 4.8 4.3 - - + -
369D ALA* 3.4 36.6 - - + +
372D TYR* 5.0 1.8 - - + -
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Residues in contact with ALA 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ALA 2.9 10.3 + - - +
264D VAL* 3.5 8.3 - - - +
266D LEU* 1.3 77.9 - - - +
268D GLN* 1.3 56.5 + - - +
270D ALA* 3.2 3.9 + - - +
271D LEU 2.8 24.9 + - - -
305D VAL* 4.0 6.5 - - + -
339D ILE* 3.6 30.7 - - + -
340D ALA* 4.3 8.5 - - - +
343D LEU* 3.3 31.1 - - + +
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Residues in contact with GLN 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 4.5 4.2 + - - -
85D GLU* 4.2 13.5 - - - +
89D TYR* 4.1 12.9 - - + -
264D VAL* 2.9 15.6 + - + +
265D GLY* 3.5 8.1 - - - +
267D ALA* 1.3 73.3 - - - +
269D ARG* 1.3 55.1 + - - +
271D LEU* 3.0 11.2 + - - +
272D ASP* 2.7 66.0 + - - +
305D VAL* 3.4 27.5 - - + +
309D ARG* 2.8 29.6 + - - +
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Residues in contact with ARG 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 3.8 34.6 + - - +
39D ALA* 4.3 10.1 - - - +
89D TYR* 2.7 58.0 + - + +
90D GLY 3.2 18.4 + - - -
265D GLY 3.1 9.3 + - - +
266D LEU* 3.3 10.0 + - + +
268D GLN* 1.3 76.8 - - - +
270D ALA* 1.3 66.3 + - - +
272D ASP* 2.9 2.9 + - - +
273D GLU* 2.8 54.2 + - + +
361D PRO* 4.5 9.4 - - - +
364D LYS* 5.8 2.4 - - - +
365D LEU* 3.4 31.2 - - + +
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Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266D LEU* 3.0 13.7 + - + +
267D ALA* 3.3 10.8 - - - +
269D ARG* 1.3 74.4 - - - +
271D LEU* 1.3 58.2 + - - +
273D GLU* 3.4 2.6 + - - +
274D ALA* 2.8 31.4 + - - +
301D MET* 5.7 0.2 - - - -
343D LEU* 3.9 28.9 - - + +
344D ALA* 4.0 9.6 - - + -
347D ALA* 3.7 11.9 - - + +
362D VAL* 5.1 0.4 - - - -
365D LEU* 3.4 17.6 - - + +
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Residues in contact with LEU 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 3.6 28.3 - - + +
394A TYR* 4.6 3.8 + - - +
267D ALA 2.8 13.6 + - - +
268D GLN* 3.3 16.4 - - - +
270D ALA* 1.3 77.3 - - - +
272D ASP* 1.3 56.7 + - - +
274D ALA* 4.3 3.4 - - - -
275D THR* 2.9 48.5 + - - +
298D LEU* 4.2 10.3 - - + +
301D MET* 4.0 28.3 - - + +
302D ALA* 3.8 9.4 - - + +
305D VAL* 3.6 30.7 - - + -
343D LEU* 3.8 7.8 - - + +
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Residues in contact with ASP 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 2.9 35.8 + - + -
32D ARG* 5.1 1.4 + - - -
89D TYR* 2.7 36.3 + - + +
268D GLN* 2.7 37.4 + - - +
269D ARG 2.9 7.8 + - - +
271D LEU* 1.3 72.5 - - - +
273D GLU* 1.3 64.1 + - + +
276D LYS* 3.0 41.3 + - - +
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Residues in contact with GLU 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D TYR* 5.7 0.4 + - - -
269D ARG* 2.8 57.0 + - + +
270D ALA 4.0 2.7 - - - +
272D ASP* 1.3 73.1 - - + +
274D ALA* 1.3 64.9 + - - +
276D LYS* 3.5 24.5 + - - +
277D TYR* 3.1 24.6 + - - +
351D LEU* 4.3 4.6 - - + +
361D PRO* 4.0 32.2 - - + +
362D VAL* 4.4 11.0 - - + -
365D LEU* 5.2 1.8 - - + -
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Residues in contact with ALA 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D ALA 2.8 19.6 + - - +
271D LEU* 3.9 6.3 - - - +
273D GLU* 1.3 78.5 - - - +
275D THR* 1.3 61.7 + - - +
277D TYR* 3.8 1.9 - - - +
278D ALA* 3.0 23.6 + - - +
298D LEU* 4.3 2.5 - - + -
301D MET* 4.3 16.8 - - + -
347D ALA* 3.9 24.2 - - + +
350D ILE* 4.2 10.4 - - + +
351D LEU* 4.1 11.2 - - - +
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Residues in contact with THR 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 2.8 36.1 + - + +
391A ILE* 4.5 11.7 - - + -
394A TYR* 3.9 27.8 - - + -
271D LEU* 2.9 20.8 + - - +
274D ALA* 1.3 72.9 - - - +
276D LYS* 1.3 66.2 + - - +
278D ALA* 3.3 4.4 + - - +
279D LEU* 3.0 33.3 + - + +
289D VAL* 4.9 0.2 - - - +
298D LEU* 3.4 20.9 - - + +
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Residues in contact with LYS 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A TYR* 4.4 18.4 - - + -
89D TYR* 4.3 15.0 + - - -
272D ASP* 3.0 31.8 + - - +
273D GLU* 3.8 23.9 + - - +
274D ALA 3.4 0.6 - - - -
275D THR* 1.3 76.1 - - - +
277D TYR* 1.3 63.8 + - - +
279D LEU* 3.2 23.0 + - - +
280D GLU* 3.6 11.6 + - - +
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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
----------------------------------------------------------
399C FAD 4.0 3.4 + - - -
273D GLU 3.1 15.5 + - - +
274D ALA 3.8 3.4 - - - +
276D LYS* 1.3 79.5 - - - +
278D ALA* 1.3 58.5 + - - +
279D LEU 3.0 0.2 - - - -
280D GLU* 3.0 5.0 + - + +
281D ARG* 2.9 81.9 + - + +
288D LEU* 4.4 2.5 - - + -
350D ILE* 3.7 19.5 - - + -
351D LEU* 3.4 46.5 + - + -
354D ASN* 3.4 19.9 + - + -
360D TYR* 5.0 11.0 - + - -
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Residues in contact with ALA 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D ALA 3.0 18.5 + - - +
275D THR 3.3 4.9 + - - +
277D TYR* 1.3 75.7 - - - +
279D LEU* 1.3 59.6 + - - +
280D GLU 3.3 0.6 + - - -
281D ARG 4.2 0.8 - - - +
288D LEU* 3.3 31.6 + - + -
289D VAL* 3.2 38.1 + - + +
294D ILE* 4.2 9.2 - - + -
298D LEU* 4.2 6.7 - - + -
350D ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ILE* 3.6 29.2 - - + +
394A TYR* 3.8 36.6 - - + +
395A LYS* 4.0 21.1 - - + +
275D THR* 3.0 23.1 + - + +
276D LYS* 3.4 13.5 - - - +
277D TYR 3.0 1.0 - - - -
278D ALA* 1.3 79.1 - - - +
280D GLU* 1.3 78.9 + - + +
287D LEU* 2.9 27.9 - - + +
289D VAL* 4.1 14.8 - - + -
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Residues in contact with GLU 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D LYS 3.6 10.0 + - - +
277D TYR* 3.0 5.5 + - + +
279D LEU* 1.3 101.9 - - + +
281D ARG* 1.3 65.1 + - - +
282D LYS* 3.2 15.1 + - - +
287D LEU* 3.8 10.2 - - - +
----------------------------------------------------------
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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