Contacts of the helix formed by residues 251 - 277 (chain A) in PDB entry 4M8J
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 LEU 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ILE* 3.8 19.7 - - + +
246A CYS* 3.2 45.8 - - + +
249A PHE* 2.8 25.7 + - + +
250A GLY* 1.3 63.6 - - - -
252A GLN* 1.3 59.2 + - - +
253A LYS* 3.0 41.1 + - - +
254A GLY* 3.3 15.4 + - - -
255A VAL* 3.2 19.3 + - - +
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Residues in contact with GLN 252 (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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250A GLY* 2.7 34.5 + - - +
251A LEU* 1.3 73.6 - - - +
253A LYS* 1.3 62.5 + - - +
255A VAL* 4.3 8.4 - - - +
256A LYS* 3.7 17.2 + - - +
443A ASP* 5.0 17.1 + - - +
449A ARG* 6.3 0.9 - - - +
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Residues in contact with LYS 253 (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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251A LEU* 3.4 40.3 - - - +
252A GLN* 1.3 76.5 - - - +
254A GLY* 1.3 64.2 + - - +
256A LYS* 2.9 24.9 + - - +
257A ILE* 3.2 22.8 + - + +
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Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.3 10.9 + - - -
253A LYS* 1.3 91.8 - - - +
255A VAL* 1.3 55.1 + - - +
257A ILE* 3.3 15.1 + - - +
258A ALA* 3.0 29.5 + - - +
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Residues in contact with VAL 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A CYS* 4.3 28.3 - - + +
251A LEU* 3.2 19.5 - - + +
252A GLN* 4.4 7.4 - - - +
253A LYS 3.1 0.8 + - - -
254A GLY* 1.3 75.4 - - - +
256A LYS* 1.3 57.8 + - - +
258A ALA* 3.4 7.0 + - + +
259A SER* 2.9 28.2 + - - -
420A VAL* 6.0 4.9 - - + -
421A THR* 4.1 18.9 - - + +
424A ASN* 3.3 32.8 - - + +
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Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A GLN 3.7 11.5 + - - +
253A LYS* 2.9 11.4 + - - +
255A VAL* 1.3 77.6 - - - +
257A ILE* 1.3 60.5 + - + +
259A SER* 3.4 11.6 + - - +
260A ASP* 2.9 57.1 + - - +
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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
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253A LYS* 3.2 35.8 + - + +
254A GLY* 3.3 11.4 + - - +
256A LYS* 1.3 76.0 - - + +
258A ALA* 1.3 55.8 + - - +
260A ASP* 2.9 14.8 + - + +
261A VAL* 2.7 37.9 + - + +
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Residues in contact with ALA 258 (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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254A GLY 3.0 16.8 + - - +
255A VAL* 3.6 7.6 - - + +
257A ILE* 1.3 76.3 - - - +
259A SER* 1.3 57.8 + - - +
261A VAL* 3.2 13.1 + - + +
262A GLU* 2.9 30.4 + - - +
417A ILE* 3.8 16.1 - - + +
420A VAL* 6.4 1.8 - - + -
421A THR* 4.9 7.0 - - + -
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Residues in contact with SER 259 (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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255A VAL* 2.9 18.1 + - - -
256A LYS* 3.5 16.3 + - - +
258A ALA* 1.3 75.8 - - - +
260A ASP* 1.3 62.3 + - - +
262A GLU* 3.7 12.9 + - - +
263A THR* 3.2 24.3 + - - -
421A THR* 3.8 22.3 - - - +
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Residues in contact with ASP 260 (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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93A PHE* 5.5 5.2 - - - -
256A LYS* 2.9 42.0 + - - +
257A ILE* 2.9 15.7 + - + +
259A SER* 1.3 74.9 - - - +
261A VAL* 1.3 65.8 + - - +
263A THR* 3.1 7.5 + - - -
264A TYR* 3.0 46.4 + - + -
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Residues in contact with VAL 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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257A ILE* 2.7 18.9 + - + +
258A ALA* 3.2 17.7 - - + +
260A ASP* 1.3 72.3 - - - +
262A GLU* 1.3 56.4 + - - +
264A TYR* 4.5 7.6 - - + +
265A LEU* 2.7 43.1 + - + +
413A ILE* 5.8 2.0 - - + -
417A ILE* 3.7 17.0 - - + -
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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
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100A THR* 2.3 39.8 + - - +
258A ALA 2.9 15.8 + - - +
259A SER* 3.7 15.8 + - - +
260A ASP 3.2 0.2 - - - -
261A VAL* 1.3 76.6 - - - +
263A THR* 1.3 57.4 + - - +
265A LEU* 3.7 6.8 - - - +
266A SER* 2.9 28.4 + - - -
414A LEU* 4.2 18.3 - - + +
417A ILE* 3.8 19.2 - - + +
418A ALA* 3.7 18.8 - - + +
421A THR* 3.1 26.3 + - - +
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Residues in contact with THR 263 (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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93A PHE* 4.0 12.6 - - + -
97A ALA* 3.6 41.4 + - + +
100A THR* 4.5 6.3 + - + -
259A SER* 3.2 12.4 + - - -
260A ASP* 3.1 11.9 + - - -
262A GLU* 1.3 80.4 + - - +
264A TYR* 1.3 65.7 + - + +
266A SER* 3.0 22.6 + - - -
267A PHE* 3.3 33.8 + - + -
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Residues in contact with TYR 264 (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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93A PHE* 3.9 31.6 - + - -
260A ASP* 3.0 48.2 + - + +
261A VAL* 4.0 8.1 - - + +
263A THR* 1.3 81.0 - - - +
265A LEU* 1.3 61.6 + - - +
267A PHE* 3.8 20.0 + + - +
268A LEU* 3.6 16.3 + - - +
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Residues in contact with LEU 265 (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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261A VAL* 2.7 27.4 + - + +
262A GLU* 3.7 5.6 - - - +
264A TYR* 1.3 71.2 - - - +
266A SER* 1.3 57.4 + - - +
268A LEU* 2.7 36.3 + - + +
269A MET* 3.1 32.0 + - + +
410A GLY* 3.6 29.4 - - - +
413A ILE* 3.7 17.5 - - + -
414A LEU* 3.6 33.0 - - + +
417A ILE* 5.1 2.0 - - + -
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Residues in contact with SER 266 (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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100A THR* 3.5 29.5 - - - +
105A LEU* 6.1 0.7 - - - +
262A GLU 2.9 16.4 + - - -
263A THR 3.0 10.5 + - - -
265A LEU* 1.3 75.6 - - - +
267A PHE* 1.3 65.2 + - - +
269A MET* 3.7 1.9 + - - +
270A LEU* 3.1 40.1 + - - +
362A ILE* 5.5 4.2 - - - +
414A LEU* 3.9 19.8 - - - +
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Residues in contact with PHE 267 (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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93A PHE* 3.9 24.0 - + - -
96A PHE* 4.0 48.5 - + - -
100A THR* 5.5 3.4 - - + -
263A THR* 3.3 30.7 + - + -
264A TYR* 3.9 19.5 - + - +
265A LEU 3.1 0.6 - - - -
266A SER* 1.3 82.3 - - - +
268A LEU* 1.3 60.8 + - - +
270A LEU* 3.9 10.6 - - + +
271A GLY* 2.9 27.0 + - - -
361A LEU* 5.4 4.9 - - + -
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Residues in contact with LEU 268 (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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264A TYR 3.6 8.8 + - - +
265A LEU* 2.7 26.0 + - + +
267A PHE* 1.3 73.8 - - - +
269A MET* 1.3 71.9 + - + +
271A GLY* 3.4 1.5 + - - -
272A TRP* 2.7 42.4 + - + +
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Residues in contact with MET 269 (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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265A LEU* 3.1 20.2 + - + +
266A SER 4.2 3.4 - - - +
268A LEU* 1.3 105.9 - - + +
270A LEU* 1.3 63.8 + - + +
272A TRP* 3.4 10.4 - - + +
273A VAL* 2.8 36.8 + - - +
406A ALA 4.8 5.4 - - - +
407A THR* 3.9 17.3 - - - +
410A GLY* 3.5 45.5 - - - +
411A PHE* 4.1 25.8 - - + +
414A LEU* 4.2 10.8 - - + -
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Residues in contact with LEU 270 (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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105A LEU* 5.7 4.5 - - + -
266A SER* 3.1 31.7 + - - +
267A PHE* 3.9 8.7 - - + +
269A MET* 1.3 77.3 - - + +
271A GLY* 1.3 55.7 - - - +
273A VAL 3.4 0.3 + - - -
274A PHE* 2.8 37.4 + - - +
361A LEU* 3.7 32.5 - - + +
362A ILE* 3.9 30.1 - - + -
365A ILE* 3.8 27.8 - - + +
366A LEU* 4.2 22.0 - - + -
411A PHE* 6.1 0.7 - - + -
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Residues in contact with GLY 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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267A PHE 2.9 17.2 + - - -
268A LEU* 3.6 1.3 - - - -
270A LEU* 1.3 76.6 - - - +
272A TRP* 1.3 56.3 + - - +
274A PHE* 3.8 9.4 - - - +
275A ILE* 2.9 37.8 + - - +
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Residues in contact with TRP 272 (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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268A LEU* 2.7 26.4 + - + +
269A MET* 3.4 19.7 - - + +
270A LEU 3.1 0.4 - - - -
271A GLY* 1.3 70.8 - - - +
273A VAL* 1.3 70.4 + - + +
275A ILE* 2.9 22.9 + - + +
276A VAL* 3.0 50.1 + - + +
401A LEU* 4.7 2.5 - - + +
402A PRO* 3.4 22.0 + - + -
403A LEU* 3.7 25.8 - - + -
407A THR* 3.3 39.6 + - + +
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Residues in contact with VAL 273 (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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269A MET 2.8 23.2 + - - +
272A TRP* 1.3 75.2 - - + +
274A PHE* 1.3 56.6 + - - +
277A GLY* 2.8 32.1 + - - +
282A ILE* 4.5 1.2 - - - +
365A ILE* 3.8 20.2 - - + +
366A LEU* 4.5 8.7 - - + -
369A ASN* 3.8 36.1 - - + +
398A TRP* 5.9 0.9 - - + -
401A LEU* 3.9 26.9 - - + -
411A PHE* 4.0 25.8 - - + -
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Residues in contact with PHE 274 (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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270A LEU 2.8 23.5 + - - +
271A GLY* 3.8 9.9 - - - +
273A VAL* 1.3 75.3 - - - +
275A ILE* 1.3 72.8 + - + +
277A GLY 4.1 0.5 + - - -
278A GLY 4.1 0.7 - - - -
279A ALA* 3.4 52.2 + - + +
282A ILE* 4.0 31.0 - - + -
283A VAL* 4.0 19.5 - - + -
365A ILE* 3.6 19.4 - - + +
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Residues in contact with ILE 275 (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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271A GLY* 2.9 24.9 + - - +
272A TRP* 2.9 14.5 + - + +
274A PHE* 1.3 93.7 - - + +
276A VAL* 1.3 75.3 + - + +
277A GLY 3.9 0.2 + - - -
278A GLY* 4.5 0.5 + - - -
279A ALA* 4.5 13.4 + - + +
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TRP* 3.0 46.0 + - + +
275A ILE* 1.3 89.0 - - + +
277A GLY* 1.3 57.2 + - - +
278A GLY 3.2 8.2 + - - -
401A LEU* 3.6 23.7 - - + +
402A PRO* 3.5 30.0 - - + +
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Residues in contact with GLY 277 (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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273A VAL* 2.8 22.9 + - - -
274A PHE 4.6 0.2 - - - -
275A ILE 3.5 0.4 - - - -
276A VAL* 1.3 78.3 - - - +
278A GLY* 1.3 63.3 + - - +
282A ILE* 3.8 7.6 - - - +
369A ASN* 4.9 7.4 - - - -
372A GLN* 2.7 32.0 + - - -
401A LEU* 4.7 8.1 - - - -
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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) + - + + + + + -
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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