Contacts of the helix formed by residues 253 - 280 (chain A) in PDB entry 4LML
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 TYR 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG 3.5 21.1 + - - +
117A ARG* 5.0 2.7 - - - -
118A TYR 4.3 14.3 + - - +
119A PRO* 5.6 0.2 - - + -
120A PHE* 4.4 17.9 - + - -
252A THR* 1.3 70.8 - - - +
254A THR* 1.3 65.5 + - - +
256A ALA* 3.1 4.7 + - - +
257A ILE* 3.0 56.7 + - + +
306A ASN* 4.9 9.0 + - - -
309A LEU* 4.3 7.2 - - + -
310A ALA* 4.2 31.2 - - - +
313A PHE* 3.5 35.8 - + + -
314A PHE* 4.3 22.5 - + - -
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Residues in contact with THR 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 2.9 34.4 + - + -
119A PRO* 3.8 10.5 - - + +
200A ILE* 6.2 3.4 - - + -
201A ILE* 5.5 8.7 - - + -
204A MET* 6.0 3.6 - - + -
241A VAL* 4.9 19.7 - - + -
252A THR* 3.6 3.2 - - - -
253A TYR* 1.3 81.7 - - - +
255A GLY* 1.3 57.6 + - - +
257A ILE* 3.5 16.9 + - + +
258A ILE* 3.0 40.5 + - + +
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Residues in contact with GLY 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A MET* 5.0 4.7 - - - +
252A THR* 3.5 20.4 + - - -
253A TYR 3.3 0.6 - - - -
254A THR* 1.3 76.9 - - - +
256A ALA* 1.3 62.9 + - - +
258A ILE* 3.5 13.5 - - - +
259A PHE* 3.4 18.9 + - - +
198D PRO* 4.3 11.1 - - - +
199D ASN* 5.4 6.5 - - - -
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A MET* 4.6 15.7 - - + -
252A THR 3.3 16.5 + - - +
253A TYR* 3.1 12.9 + - - +
255A GLY* 1.3 74.0 - - - +
257A ILE* 1.3 56.9 + - - +
258A ILE 3.0 0.9 - - - -
259A PHE* 2.7 29.8 + - - +
260A MET* 2.9 12.0 + - - +
309A LEU* 4.4 16.8 - - + -
313A PHE* 4.9 6.3 - - + -
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 5.2 11.4 - - + -
204A MET* 4.6 15.9 - - + -
205A LEU* 6.5 1.6 - - + -
253A TYR* 3.0 38.8 + - + +
254A THR* 3.7 19.5 - - + +
256A ALA* 1.3 74.6 - - - +
258A ILE* 1.3 62.0 + - - +
260A MET* 3.5 15.4 - - + +
261A ILE* 2.9 41.7 + - + +
302A PHE* 6.4 1.3 - - + -
306A ASN* 4.7 17.7 - - - +
309A LEU* 3.7 21.8 - - + -
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Residues in contact with ILE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MET* 4.0 17.7 - - + -
234A HIS* 3.1 34.5 + - + +
237A PHE 4.7 2.5 - - - +
238A ASN* 3.2 50.3 - - - +
241A VAL* 5.0 11.0 - - + -
254A THR* 3.0 25.1 + - + +
255A GLY* 3.5 17.9 - - - +
256A ALA 2.9 0.2 + - - -
257A ILE* 1.3 78.0 - - - +
259A PHE* 1.3 63.4 + - + +
261A ILE* 3.4 1.9 + - - -
262A TYR* 2.9 25.7 + - + -
198D PRO 4.9 4.7 - - - +
199D ASN* 5.4 2.2 - - - +
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A MET* 6.0 6.1 - - + -
255A GLY 3.4 11.9 - - - +
256A ALA* 2.7 10.4 + - - +
258A ILE* 1.3 81.9 - - + +
260A MET* 1.3 60.4 + - - +
262A TYR* 3.2 14.3 - + + +
263A LEU* 2.9 58.8 + - + +
197D ILE* 5.7 2.0 - - + -
198D PRO* 4.4 25.6 - - + +
202D LEU* 3.5 49.6 - - + -
203D PRO* 5.2 0.7 - - + -
206D PHE* 3.8 5.6 - + - -
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Residues in contact with MET 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ALA 2.9 11.0 + - - +
257A ILE* 3.5 12.8 - - + +
259A PHE* 1.3 78.5 - - - +
261A ILE* 1.3 56.6 + - - +
263A LEU* 2.9 34.2 + - + +
264A PHE* 2.9 40.7 + - + -
302A PHE* 4.2 7.2 - - + -
305A ALA* 3.8 31.6 - - + +
306A ASN* 3.5 25.8 - - - +
309A LEU* 3.8 27.1 - - + -
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Residues in contact with ILE 261 (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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204A MET* 3.6 34.8 - - + +
205A LEU* 5.6 3.4 - - + -
208A LEU* 3.9 20.2 - - + -
234A HIS* 3.2 24.0 - - + +
257A ILE* 2.9 31.3 + - + +
258A ILE* 3.5 0.4 - - - +
259A PHE 3.3 0.2 - - - -
260A MET* 1.3 73.0 - - + +
262A TYR* 1.3 63.8 + - - +
264A PHE* 3.1 7.9 + - - +
265A TYR* 2.9 52.3 + - + -
302A PHE* 4.2 24.2 - - + -
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Residues in contact with TYR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 4.2 11.3 - - + +
234A HIS* 3.4 20.6 - + - -
235A ILE* 3.6 30.7 - - + +
238A ASN* 3.2 45.6 + - - +
258A ILE* 2.9 27.9 + - + -
259A PHE* 3.2 14.8 - + + +
261A ILE* 1.3 74.1 - - - +
263A LEU* 1.3 63.6 + - - +
265A TYR* 3.3 6.5 + - - +
266A PHE* 3.0 22.2 + - - +
198D PRO 4.6 1.8 - - - -
203D PRO* 3.4 47.4 - - + +
206D PHE* 4.1 19.5 - + + +
207D ILE* 5.4 1.8 - - + -
237D PHE* 3.8 4.9 - - - -
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 2.9 40.7 + - + +
260A MET* 2.9 28.2 + - + +
262A TYR* 1.3 76.2 - - - +
264A PHE* 1.3 61.8 + - + +
266A PHE* 3.1 10.5 + - - +
267A VAL* 2.9 35.4 + - + +
206D PHE* 3.3 33.0 - - + -
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Residues in contact with PHE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 4.4 11.7 - - + -
211A SER* 5.8 0.4 - - - -
212A TRP* 3.7 20.6 - + + -
260A MET* 2.9 33.6 + - + +
261A ILE* 3.1 10.3 + - - +
263A LEU* 1.3 82.3 - - + +
265A TYR* 1.3 60.2 + - - +
267A VAL* 3.2 16.7 - - + +
268A ALA* 2.9 28.8 + - - +
298A PHE* 4.1 7.8 - + + -
301A VAL* 3.7 31.0 - - + -
302A PHE* 3.2 50.7 - + + -
305A ALA* 5.0 1.1 - - + -
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Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 3.0 35.7 + - - +
208A LEU* 3.2 20.4 + - + +
211A SER* 3.5 16.8 - - - -
227A VAL* 3.4 26.0 - - + +
230A THR* 3.1 26.5 - - - -
231A LEU* 3.2 42.2 - - + -
234A HIS* 4.1 8.7 - + + -
261A ILE* 2.9 50.6 + - + -
262A TYR 3.7 4.9 - - - +
264A PHE* 1.3 75.2 - - - +
266A PHE* 1.3 63.1 + - - +
268A ALA* 3.3 3.9 + - - -
269A VAL* 3.0 21.8 + - - +
210D ILE* 4.6 2.7 - - - -
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Residues in contact with PHE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR 3.0 12.9 + - - +
263A LEU* 3.2 11.9 - - - +
265A TYR* 1.3 78.0 - - - +
267A VAL* 1.3 66.3 + - + +
269A VAL* 3.3 4.9 + - - +
270A ILE* 2.9 52.3 + - + +
206D PHE* 3.8 33.9 - + + -
209D PHE* 3.5 42.4 - + + -
210D ILE* 3.5 30.2 - - + +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 2.9 20.7 + - + +
264A PHE* 3.2 30.1 - - + +
266A PHE* 1.3 82.7 - - + +
268A ALA* 1.3 64.0 + - - +
270A ILE* 3.6 11.5 - - + +
271A GLU* 2.9 29.8 + - - +
298A PHE* 3.7 20.4 - - + -
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER* 4.5 7.0 - - - +
212A TRP* 5.4 3.4 - - + -
215A PHE* 5.0 7.1 - - + -
227A VAL* 3.6 21.3 - - + -
264A PHE 2.9 21.1 + - - +
265A TYR* 3.4 6.7 - - - +
266A PHE 3.2 0.2 - - - -
267A VAL* 1.3 74.0 - - - +
269A VAL* 1.3 65.6 + - - +
271A GLU* 3.1 6.2 + - - +
272A VAL* 3.0 27.3 + - + +
298A PHE* 4.0 19.5 - - + -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 6.1 2.0 - - - -
227A VAL* 3.5 25.7 - - + +
228A VAL* 4.7 10.3 - - + -
265A TYR 3.0 8.4 + - - +
266A PHE 3.6 7.2 - - - +
268A ALA* 1.3 74.8 - - - +
270A ILE* 1.3 67.0 + - + +
272A VAL* 3.2 10.7 - - + +
273A THR* 3.0 24.5 + - - +
210D ILE* 3.6 49.8 - - + -
213D THR* 4.0 24.5 - - + +
226D LEU* 5.3 1.6 - - + -
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A PHE* 2.9 47.6 + - + +
267A VAL* 3.6 10.8 - - + +
269A VAL* 1.3 77.4 - - + +
271A GLU* 1.3 59.4 + - - +
273A THR* 3.4 5.3 + - + +
274A VAL* 3.0 37.2 + - + +
209D PHE 6.6 0.2 - - - -
210D ILE* 6.5 0.4 - - - -
213D THR* 4.2 16.2 - - - +
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Residues in contact with GLU 271 (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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215A PHE* 3.3 23.5 - - + -
267A VAL 2.9 18.4 + - - +
268A ALA* 3.1 7.6 + - - +
270A ILE* 1.3 79.7 - - - +
272A VAL* 1.3 86.0 + - - +
274A VAL* 3.2 10.4 + - - +
275A GLN* 2.9 29.4 + - - +
290A ILE* 4.5 15.2 - - + +
291A THR* 3.6 18.7 + - - +
294A SER* 2.9 29.6 + - - +
298A PHE* 4.7 5.2 - - + -
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ALA* 4.9 7.4 - - + +
215A PHE* 5.1 5.6 - - + -
220A TYR* 3.4 18.0 - - + -
223A ASN* 3.5 54.5 - - + +
224A VAL* 5.2 3.4 - - + +
227A VAL* 4.5 4.9 - - + -
268A ALA 3.0 12.8 + - - +
269A VAL* 3.2 25.8 - - + +
271A GLU* 1.3 88.1 + - - +
273A THR* 1.3 57.0 + - - +
275A GLN* 3.1 9.7 + - - +
276A HIS 2.9 24.1 + - - -
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Residues in contact with THR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 2.9 26.1 + - - +
269A VAL* 3.0 19.2 + - - +
270A ILE* 3.6 7.2 - - + +
272A VAL* 1.3 76.3 - - - +
274A VAL* 1.3 65.3 + - + +
276A HIS* 3.2 4.7 + - - +
277A TYR* 3.0 22.0 + - - +
213D THR* 3.0 37.1 + - - +
216D TRP* 3.6 33.2 - - + +
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 3.0 20.9 + - + +
271A GLU* 3.4 13.2 - - - +
273A THR* 1.3 79.2 - - + +
275A GLN* 1.3 63.9 + - - +
277A TYR* 3.5 4.3 + - - +
278A LEU* 3.0 27.9 + - + +
290A ILE* 4.0 31.4 - - + -
216D TRP* 6.1 6.1 - - + -
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER 3.9 7.3 + - - +
218A THR* 3.7 25.4 + - + -
219A SER 4.9 2.2 - - - -
220A TYR* 5.1 3.2 - - - +
223A ASN* 3.5 25.9 + - - +
271A GLU* 2.9 19.6 + - - +
272A VAL* 3.3 14.8 + - - +
274A VAL* 1.3 80.2 - - - +
276A HIS* 1.3 58.2 + - - +
278A LEU* 3.8 4.9 - - - +
279A LYS* 2.9 39.4 + - + +
287A ALA* 4.7 16.2 - - + +
290A ILE* 5.8 4.5 - - + -
291A THR* 2.5 39.1 + - - +
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Residues in contact with HIS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 3.4 42.7 - + + +
272A VAL 2.9 5.7 + - - -
273A THR 3.2 8.3 + - - +
275A GLN* 1.3 75.3 - - - +
277A TYR* 1.3 68.0 + - - +
279A LYS* 3.1 11.6 + - - +
280A VAL* 3.0 52.5 + - + +
216D TRP 3.8 2.5 - - - -
217D SER* 3.0 43.6 + - - -
218D THR* 3.6 10.9 + - - -
219D SER* 3.8 16.5 + - - -
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Residues in contact with TYR 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A THR 3.0 10.9 + - - +
274A VAL* 4.2 3.8 - - - +
276A HIS* 1.3 79.4 - - - +
278A LEU* 1.3 61.6 + - + +
280A VAL* 3.3 18.1 - - + +
281A GLU* 3.1 50.7 + - + +
216D TRP* 3.3 45.3 - + + +
218D THR* 5.7 4.0 - - - -
295D ARG* 3.4 38.2 + - - -
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A VAL* 3.0 19.8 + - + +
275A GLN* 3.8 4.7 - - - +
277A TYR* 1.3 80.4 - - + +
279A LYS* 1.3 59.2 + - - +
281A GLU* 3.3 16.1 + - + +
283A GLN* 3.5 42.0 + - + +
286A ARG* 3.6 37.2 - - + +
287A ALA* 3.7 19.5 - - + +
290A ILE* 4.1 15.5 - - + -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR* 3.4 46.9 - - + -
220A TYR* 5.6 2.9 - - - +
275A GLN* 2.9 25.4 + - + +
276A HIS* 3.1 13.1 + - - +
278A LEU* 1.3 77.8 - - - +
280A VAL* 1.3 68.7 + - - +
281A GLU 3.2 0.2 - - - -
282A SER* 3.5 12.2 + - - +
283A GLN 4.9 2.9 - - - +
284A PRO* 5.1 14.2 - - + +
287A ALA* 4.8 15.9 - - + +
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A HIS* 3.0 47.2 + - + +
277A TYR* 3.3 25.6 - - + +
279A LYS* 1.3 82.6 - - - +
281A GLU* 1.3 65.8 + - + +
282A SER* 3.2 9.5 + - - -
218D THR* 5.0 12.1 - - - +
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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