Contacts of the helix formed by residues 252 - 283 (chain A) in PDB entry 3PM0
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 ASN 252 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 2.6 47.6 + - + +
250A PHE* 3.0 25.1 + - + -
251A PRO* 1.3 73.6 - - - +
253A PRO* 1.3 76.6 - - + +
254A VAL* 2.6 36.1 + - + +
255A ARG* 2.7 13.5 + - - +
256A THR* 2.9 25.5 + - - -
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Residues in contact with PRO 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 4.7 13.5 + - - +
252A ASN* 1.3 88.6 - - + +
254A VAL* 1.3 61.0 + - + +
256A THR* 3.2 8.5 + - - +
257A VAL* 2.8 32.3 + - - +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 4.0 17.3 - - + +
241A VAL* 3.6 39.5 - - + +
247A LEU* 3.8 27.6 - - + -
248A GLN* 3.1 15.1 + - - +
252A ASN* 2.6 19.4 + - + +
253A PRO* 1.3 74.0 - - + +
255A ARG* 1.3 60.5 + - - +
257A VAL* 3.4 8.3 - - + +
258A PHE* 3.4 15.6 + - - +
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Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU 3.5 5.8 - - - +
248A GLN* 3.4 39.8 + - - +
249A TYR 5.6 0.6 - - - -
250A PHE* 3.3 24.3 - - - +
251A PRO* 3.8 36.7 - - - +
252A ASN* 2.7 19.7 + - - +
254A VAL* 1.3 72.5 - - - +
256A THR* 1.3 68.0 + - - +
258A PHE 3.6 0.2 + - - -
259A ARG* 2.7 79.9 + - - +
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Residues in contact with THR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 5.8 1.3 - - - +
252A ASN 2.9 17.1 + - - -
253A PRO* 3.3 12.8 - - - +
255A ARG* 1.3 83.8 + - - +
257A VAL* 1.3 63.2 + - - +
259A ARG* 3.4 5.8 + - - +
260A GLU* 3.1 48.3 + - + +
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLU* 3.6 28.7 - - + +
233A ARG* 3.6 42.6 - - + +
234A THR* 3.7 5.4 - - - +
241A VAL* 3.7 21.1 - - + -
253A PRO 2.8 19.0 + - - +
254A VAL* 3.4 16.4 - - - +
256A THR* 1.3 72.5 - - - +
258A PHE* 1.3 56.3 + - - +
260A GLU* 3.2 10.6 + - - +
261A PHE* 2.7 34.6 + - - +
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Residues in contact with PHE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 5.5 5.6 - - + -
122A SER* 4.0 26.9 - - - -
125A VAL* 4.6 6.5 - - + -
234A THR* 4.3 1.8 - - + -
241A VAL* 3.4 27.8 - - + -
248A GLN* 3.6 28.9 - - + +
254A VAL 3.4 14.1 + - - +
255A ARG 4.1 0.2 - - - +
256A THR 3.4 0.8 - - - -
257A VAL* 1.3 82.1 - - - +
259A ARG* 1.3 61.2 + - + +
261A PHE* 3.0 18.5 - + - +
262A GLU* 2.8 63.3 + - + +
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Residues in contact with ARG 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLN* 4.9 5.5 + - - +
255A ARG* 2.7 75.6 + - - +
256A THR* 3.8 5.8 - - - +
258A PHE* 1.3 80.3 - - + +
260A GLU* 1.3 62.7 + - + +
262A GLU* 3.4 15.2 + - - +
263A GLN* 3.1 23.4 + - - +
266A ARG* 5.5 0.5 + - - -
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A HIS* 5.8 3.0 - - + +
230A GLU* 3.1 40.8 - - + +
233A ARG* 3.9 6.4 + - - -
256A THR* 3.1 29.5 + - + +
257A VAL* 3.5 16.1 - - - +
259A ARG* 1.3 76.7 - - + +
261A PHE* 1.3 52.3 - - - +
263A GLN* 3.0 11.4 - - - +
264A LEU* 2.8 38.1 + - + +
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Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER* 3.6 21.3 - - - -
125A VAL* 4.1 8.1 - - + -
126A VAL* 3.9 18.2 - - + -
230A GLU* 3.8 9.4 - - - +
231A PHE* 3.7 28.0 - + - -
234A THR* 3.3 43.3 - - + +
235A VAL* 4.0 10.1 - - + -
257A VAL 2.7 14.8 + - - +
258A PHE* 3.0 22.0 - + - +
260A GLU* 1.3 76.9 - - - +
262A GLU* 1.3 66.6 + - - +
264A LEU* 3.3 10.2 + - + +
265A ASN* 2.9 50.2 + - - -
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.2 28.5 - - + +
258A PHE* 2.8 56.8 + - + +
259A ARG* 3.8 14.6 - - - +
261A PHE* 1.3 73.2 - - - +
263A GLN* 1.3 57.7 + - - +
265A ASN* 3.9 1.4 - - - +
266A ARG* 2.9 51.6 + - - +
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Residues in contact with GLN 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG 3.1 14.2 + - - +
260A GLU* 3.0 17.7 - - - +
262A GLU* 1.3 78.4 - - - +
264A LEU* 1.3 55.5 + - - +
266A ARG* 3.3 28.9 + - - +
267A ASN* 3.0 53.0 + - - +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 4.9 1.3 - - - +
227A HIS* 3.5 48.5 - - + +
230A GLU* 3.9 12.8 - - + -
231A PHE* 4.0 13.5 - - + +
260A GLU* 2.8 12.9 + - + +
261A PHE* 3.4 24.0 - - + +
263A GLN* 1.3 71.6 - - - +
265A ASN* 1.3 74.0 + - - +
267A ASN* 3.1 12.5 + - - +
268A PHE* 2.9 35.6 + - + +
800A BHF 3.7 33.4 - - + -
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Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.1 22.0 - - + +
126A VAL* 4.0 15.6 - - - +
127A SER 4.9 2.1 + - - +
231A PHE* 3.5 21.0 - - - -
261A PHE* 2.9 64.0 + - - +
262A GLU 4.0 2.7 - - - +
264A LEU* 1.3 78.7 - - - +
266A ARG* 1.3 65.8 + - - +
268A PHE* 3.8 4.7 - - - +
269A SER* 3.0 30.3 + - - -
800A BHF 4.2 5.9 - - - -
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Residues in contact with ARG 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG 5.5 0.4 + - - -
262A GLU* 2.9 44.3 + - - +
263A GLN* 3.3 43.1 + - - +
265A ASN* 1.3 78.1 - - - +
267A ASN* 1.3 61.8 + - - +
269A SER* 3.7 4.4 + - - -
270A ASN* 2.8 41.9 + - - +
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Residues in contact with ASN 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLU* 4.7 13.3 + - - +
224A LEU* 4.0 16.2 - - + +
227A HIS* 5.3 5.1 + - - -
263A GLN* 3.0 40.6 + - - +
264A LEU* 3.1 10.7 + - - +
266A ARG* 1.3 80.7 - - - +
268A PHE* 1.3 59.5 + - - +
270A ASN* 3.5 8.5 + - - +
271A PHE* 3.0 28.8 + - - +
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Residues in contact with PHE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 3.2 45.3 - - + -
225A LEU* 3.9 22.0 - - + -
228A ASN* 5.2 0.2 - - - -
264A LEU* 2.9 21.0 + - + +
265A ASN* 3.8 8.5 - - - +
266A ARG 3.4 0.2 - - - -
267A ASN* 1.3 74.7 - - - +
269A SER* 1.3 65.9 + - - +
271A PHE* 3.3 5.5 + + - +
272A ILE* 3.0 28.6 + - + +
325A THR* 4.2 23.1 - - + -
328A PHE* 3.5 28.7 - + - -
329A GLY* 3.9 13.9 - - - -
332A GLN* 4.0 6.3 - - - -
800A BHF 3.8 33.7 - + + -
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 4.1 9.2 + - - -
128A GLY* 3.9 22.3 + - - -
265A ASN* 3.0 16.1 + - - +
266A ARG* 4.0 5.6 - - - -
268A PHE* 1.3 79.4 - - - +
270A ASN* 1.3 53.0 + - - +
272A ILE* 3.4 1.4 + - - +
273A LEU* 2.7 46.7 + - - +
325A THR* 4.8 12.5 + - - +
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Residues in contact with ASN 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ARG* 2.8 34.4 + - - +
267A ASN* 3.9 8.5 + - - +
268A PHE 3.3 0.4 - - - -
269A SER* 1.3 77.8 - - - +
271A PHE* 1.3 57.2 + - - +
273A LEU* 3.6 14.1 - - - +
274A ASP* 2.9 32.9 + - - +
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Residues in contact with PHE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PHE* 3.7 31.2 - + - -
214A TYR* 3.5 37.7 - + - -
220A GLU* 6.1 0.9 - - - -
221A PHE* 4.3 18.2 - + - -
224A LEU* 3.9 21.5 - - + -
267A ASN 3.0 19.1 + - - +
268A PHE* 3.3 8.7 - + - +
270A ASN* 1.3 77.7 - - - +
272A ILE* 1.3 69.2 + - + +
274A ASP* 3.9 4.6 - - - +
275A LYS* 3.4 31.8 + - + +
328A PHE* 3.8 17.0 - + - -
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PHE* 4.1 11.9 - - + -
268A PHE* 3.0 16.8 + - + +
269A SER 4.1 2.2 - - - +
271A PHE* 1.3 88.5 - - + +
273A LEU* 1.3 57.1 + - - +
274A ASP 3.3 0.2 - - - -
275A LYS* 3.4 6.3 + - - +
276A PHE* 2.7 31.5 + - - +
293A MET* 3.8 5.1 - - + +
321A PRO* 3.7 16.4 - - + +
324A ILE* 3.1 34.5 - - + +
325A THR* 3.3 39.9 - - + +
328A PHE* 4.2 17.7 - - + -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A SER* 2.7 27.4 + - - +
270A ASN* 3.6 15.7 - - - +
272A ILE* 1.3 76.1 - - - +
274A ASP* 1.3 66.4 + - - +
276A PHE* 3.0 15.2 + - + +
277A LEU* 2.9 49.3 + - + +
321A PRO* 4.9 13.2 - - + -
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Residues in contact with ASP 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN 2.9 17.7 + - - +
271A PHE* 3.9 5.6 - - - +
273A LEU* 1.3 78.2 - - - +
275A LYS* 1.3 63.5 + - - +
277A LEU* 3.4 8.0 + - - +
278A ARG* 2.5 67.6 + - - +
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PHE* 3.4 50.9 + - + +
212A CYS* 4.2 14.7 - - - +
214A TYR* 3.4 27.9 + - - -
271A PHE* 3.4 23.5 + - + +
272A ILE* 3.4 7.7 + - - +
273A LEU 3.2 0.4 - - - -
274A ASP* 1.3 80.0 - - - +
276A PHE* 1.3 62.6 + - - +
278A ARG* 3.2 24.4 + - - +
279A HIS* 2.9 40.3 + - + +
293A MET* 4.0 10.1 - - + -
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE 2.7 22.3 + - - +
273A LEU* 3.0 12.8 + - + +
275A LYS* 1.3 73.3 - - - +
277A LEU* 1.3 84.7 + - + +
279A HIS* 3.3 2.4 + - - +
280A CYS* 2.9 52.2 + - - +
293A MET* 3.6 22.9 - - + +
297A ILE* 3.9 17.9 - - + -
317A LEU* 3.9 24.7 - - + -
320A VAL* 3.9 12.8 - - + -
321A PRO* 3.5 33.2 - - + -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 2.9 37.5 + - + +
274A ASP* 3.9 6.5 - - - +
275A LYS 3.4 0.2 - - - -
276A PHE* 1.3 93.4 - - + +
278A ARG* 1.3 57.9 + - + +
280A CYS* 3.6 6.1 + - + +
281A GLU* 3.0 43.6 + - - +
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Residues in contact with ARG 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP* 2.5 48.1 + - - +
275A LYS* 3.2 31.8 + - - +
276A PHE 3.1 0.6 - - - -
277A LEU* 1.3 77.3 - - + +
279A HIS* 1.3 69.8 + - - +
281A GLU* 3.2 16.8 + - - +
282A SER* 3.0 29.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A PHE* 3.3 21.9 + - + -
275A LYS* 2.9 38.9 + - + +
276A PHE 3.9 0.4 - - - +
278A ARG* 1.3 79.6 - - + +
280A CYS* 1.3 63.1 + - - +
282A SER* 3.8 4.1 - - - +
283A LEU* 2.9 29.1 + - - +
290A ARG* 5.6 0.6 + - - -
291A ASP* 2.5 30.2 + - - -
293A MET* 3.3 35.8 - - + +
294A ASP* 3.5 25.1 - - - +
297A ILE* 3.7 7.6 - - + -
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Residues in contact with CYS 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PHE* 2.9 45.3 + - + +
277A LEU* 3.7 9.0 - - + +
279A HIS* 1.3 79.6 - - - +
281A GLU* 1.3 60.6 + - + +
283A LEU* 3.5 15.8 + - - +
297A ILE* 3.1 40.2 - - + -
301A GLU* 4.9 6.9 - - - +
317A LEU* 4.7 9.2 - - - -
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 3.0 37.6 + - - +
278A ARG* 3.2 16.6 + - - +
280A CYS* 1.3 77.3 - - + +
282A SER* 1.3 60.7 + - - +
283A LEU 3.7 1.4 + - - -
284A ARG* 4.1 16.3 + - - -
----------------------------------------------------------
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG* 3.0 18.2 + - - +
279A HIS* 4.2 4.0 - - - -
281A GLU* 1.3 75.4 - - - +
283A LEU* 1.3 60.4 + - - +
284A ARG* 3.0 30.9 + - - +
287A ALA* 4.3 5.0 - - - +
----------------------------------------------------------
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A HIS 2.9 13.1 + - - +
280A CYS* 3.7 13.0 - - - +
281A GLU 3.4 2.5 - - - -
282A SER* 1.3 75.2 - - - +
284A ARG* 1.3 62.1 + - - +
287A ALA* 3.8 22.9 - - + +
288A ALA 4.5 1.8 - - - +
289A PRO* 4.3 11.7 - - + -
294A ASP* 3.3 55.2 - - + +
297A ILE* 4.1 12.3 - - + -
298A LEU* 4.0 27.8 - - + +
301A GLU* 4.6 13.8 - - - +
----------------------------------------------------------
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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