Contacts of the strand formed by residues 289 - 321 (chain A) in PDB entry 3C0M
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 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 3.5 1.9 - - - +
206A ASN 2.8 32.7 + - - -
285A VAL* 3.4 7.3 - - - +
286A PRO* 2.9 37.4 + - - +
287A ALA 3.4 3.5 + - - -
288A ARG* 1.3 81.0 + - - +
290A LYS* 1.3 63.6 + - - +
419A PRO* 4.8 0.8 - - - +
420A VAL 3.3 22.7 + - - -
421A PRO* 4.0 2.6 - - - +
422A LEU* 3.3 8.6 - - - +
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Residues in contact with LYS 290 (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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203A TRP* 3.5 57.8 - - + +
204A ALA 3.0 16.8 - - - +
205A VAL* 3.5 18.4 - - + -
285A VAL* 4.2 1.8 - - - -
289A SER* 1.3 80.2 - - - +
291A ILE* 1.3 61.6 + - - +
418A ALA 4.1 0.7 - - - +
419A PRO* 3.6 0.4 - - - +
420A VAL* 2.9 48.2 + - - +
421A PRO 5.2 6.3 + - - -
422A LEU* 4.8 10.5 - - + +
444A GLU* 5.2 4.7 - - - +
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Residues in contact with ILE 291 (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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203A TRP* 3.3 5.1 - - - -
204A ALA* 3.0 37.5 + - + -
283A PRO* 3.4 39.7 - - + -
284A THR 4.5 6.7 - - - +
285A VAL* 3.8 19.9 - - + +
290A LYS* 1.3 73.3 - - - +
292A PRO* 1.3 70.3 - - + +
293A VAL* 3.4 4.1 - - + +
416A ILE* 3.8 19.3 - - + -
417A GLY 3.7 18.2 - - - +
419A PRO* 3.8 23.1 - - + -
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Residues in contact with PRO 292 (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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202A GLY 3.3 10.5 - - - +
203A TRP* 3.6 24.0 - - + -
291A ILE* 1.3 83.9 - - - +
293A VAL* 1.3 57.8 - - - +
416A ILE* 3.4 2.6 - - - -
417A GLY* 2.8 45.1 + - - -
418A ALA 3.2 22.4 - - - +
420A VAL* 5.4 0.4 - - + -
134B GLN* 4.0 26.5 - - + +
135B TYR* 3.4 19.6 + - + +
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Residues in contact with VAL 293 (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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200A VAL 3.6 0.7 - - - +
201A VAL* 3.4 4.9 - - - -
202A GLY 3.0 24.3 + - - -
203A TRP 4.2 2.5 - - - -
204A ALA* 4.1 17.5 - - + +
217A VAL* 6.1 5.4 - - + -
291A ILE* 3.4 22.9 - - + +
292A PRO* 1.3 79.9 - - - +
294A LYS* 1.3 62.0 + - - +
295A ILE* 5.2 5.4 - - + -
414A ILE* 4.9 12.6 - - + -
415A GLU 3.2 7.6 - - - +
416A ILE* 4.6 10.3 - - + -
443A LEU* 5.6 3.8 - - + -
445A ILE* 4.5 28.0 - - + -
462A LEU* 6.5 0.2 - - + -
135B TYR* 3.6 2.6 + - - -
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Residues in contact with LYS 294 (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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199A THR* 3.4 26.9 - - + +
200A VAL 3.5 2.9 - - - -
201A VAL* 3.8 7.2 - - + -
293A VAL* 1.3 73.9 - - - +
295A ILE* 1.3 74.0 + - - +
296A GLU* 3.1 24.1 + - - +
413A ASN 3.5 2.4 - - - +
414A ILE* 3.6 0.2 - - - -
415A GLU* 2.8 46.7 + - + +
135B TYR* 3.5 36.3 + - + +
138B GLU* 2.6 40.5 + - - -
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Residues in contact with ILE 295 (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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198A LYS 3.9 0.2 - - - +
199A THR* 3.5 0.7 - - - -
200A VAL* 2.7 55.4 + - + +
219A LEU* 3.9 31.4 - - + -
293A VAL* 5.2 7.2 - - + -
294A LYS* 1.3 82.5 - - - +
296A GLU* 1.3 65.5 + - - +
297A LEU* 3.9 19.5 + - + -
411A ALA* 4.5 5.6 - - + -
412A GLY 4.9 2.0 - - - +
413A ASN 4.0 9.2 - - - +
414A ILE* 4.1 25.1 - - + -
462A LEU* 4.2 26.0 - - + -
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Residues in contact with GLU 296 (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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196A LEU* 3.9 11.6 - - + +
198A LYS 3.7 2.7 - - - -
199A THR* 3.8 21.8 - - + +
294A LYS* 3.1 33.1 + - - +
295A ILE* 1.3 75.3 - - - +
297A LEU* 1.3 61.6 + - - +
298A TYR* 2.3 44.5 + - + +
411A ALA* 3.4 1.9 - - - -
412A GLY* 2.7 36.2 + - - +
413A ASN 4.5 3.8 + - - -
415A GLU* 4.5 7.1 - - - +
138B GLU* 4.3 3.3 - - - +
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Residues in contact with LEU 297 (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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196A LEU* 3.7 5.7 - - - +
197A VAL* 3.1 30.7 + - + +
198A LYS* 2.7 27.6 + - + +
200A VAL* 4.3 11.4 - - + -
219A LEU* 5.9 0.9 - - + -
277A LEU* 5.2 1.8 - - + -
295A ILE* 4.2 14.1 - - + +
296A GLU* 1.3 81.7 - - - +
298A TYR* 1.3 62.4 + - - +
410A PHE 3.8 0.2 - - - -
411A ALA* 3.6 23.1 - - + -
452A LEU* 4.0 27.8 - - + -
455A LEU* 6.2 0.4 - - + -
457A PHE* 3.5 41.1 - - + -
460A VAL* 6.1 2.7 - - + -
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Residues in contact with TYR 298 (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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194A ARG* 3.4 37.9 + - + +
195A GLN 3.6 15.3 - - - +
196A LEU* 4.0 20.4 - - + -
197A VAL* 4.5 1.8 - - - -
296A GLU* 2.3 50.8 + - + +
297A LEU* 1.3 74.8 - - - +
299A LYS* 1.3 63.8 + - - +
300A ALA 4.3 0.2 - - - -
409A GLN* 3.1 9.5 - - - +
410A PHE* 2.7 77.9 + + + +
412A GLY* 4.0 13.9 - - - -
457A PHE* 3.7 4.0 - - - -
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Residues in contact with LYS 299 (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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193A ASP* 4.8 11.7 + - - +
194A ARG* 3.9 0.3 - - - -
195A GLN* 3.0 59.2 + - + +
197A VAL* 3.5 22.2 - - + -
298A TYR* 1.3 78.5 - - - +
300A ALA* 1.3 61.7 + - - +
301A ASP* 5.2 5.9 + - - -
407A GLU* 5.2 15.1 + - + +
408A SER 3.4 9.6 - - - +
409A GLN* 4.2 20.4 - - + +
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Residues in contact with ALA 300 (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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193A ASP* 3.3 16.8 - - - +
194A ARG* 3.8 15.7 - - + -
253A THR* 3.4 30.7 - - - +
255A LEU* 5.8 0.2 - - - +
299A LYS* 1.3 76.1 - - - +
301A ASP* 1.3 64.5 + - - +
407A GLU* 3.8 2.3 - - - +
408A SER* 3.1 33.1 + - - +
410A PHE* 4.6 10.4 - - + -
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Residues in contact with ASP 301 (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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191A GLN* 3.5 26.8 + - - +
192A SER* 3.4 17.7 - - - -
193A ASP* 2.7 38.1 + - - +
253A THR* 4.5 5.0 + - - +
255A LEU* 6.2 0.4 - - - -
299A LYS* 5.2 6.3 + - - -
300A ALA* 1.3 79.4 - - - +
302A ILE* 1.3 62.4 + - - +
406A ALA 3.1 18.6 - - - +
407A GLU* 3.9 20.1 - - + +
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Residues in contact with ILE 302 (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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189A VAL* 4.2 11.9 - - + -
191A GLN* 3.2 10.6 - - - +
192A SER* 4.3 5.2 - - - +
250A VAL* 3.0 46.9 - - + +
251A GLY* 4.6 2.0 - - - +
253A THR* 3.5 25.7 + - + +
255A LEU* 5.6 6.0 - - + +
301A ASP* 1.3 74.3 - - - +
303A SER* 1.3 71.6 + - - +
304A TYR* 3.2 30.1 - - + -
404A PHE* 4.4 10.8 - - + -
405A SER* 3.1 2.6 - - - -
406A ALA* 3.0 34.3 + - + +
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Residues in contact with SER 303 (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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189A VAL* 3.2 6.4 - - - +
190A THR* 2.8 33.9 + - - -
191A GLN* 2.8 47.6 + - - +
302A ILE* 1.3 76.5 + - - +
304A TYR* 1.3 65.8 + - - +
404A PHE 3.2 9.6 - - - -
405A SER* 3.7 10.6 - - - -
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Residues in contact with TYR 304 (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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184A PHE* 3.7 14.3 - + - -
186A HIS* 3.7 15.7 - - + -
187A GLY 4.6 3.4 - - - +
188A ASP 3.9 2.2 - - - +
189A VAL* 3.9 17.0 - - + -
190A THR* 4.2 2.0 + - - -
247A TRP* 2.6 32.8 + - - -
248A PRO 3.9 1.0 + - - -
250A VAL* 3.7 37.6 - - + +
255A LEU* 6.3 0.2 - - + -
302A ILE* 3.2 35.9 - - + -
303A SER* 1.3 75.1 - - - +
305A PRO* 1.3 83.2 - - + +
306A TYR* 3.6 8.2 + - + -
403A ASP* 4.5 2.5 - - - -
404A PHE* 3.0 45.3 + + + -
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Residues in contact with PRO 305 (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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186A HIS* 3.1 5.9 - - - +
187A GLY* 2.8 37.8 + - - +
188A ASP 3.4 17.9 - - - +
190A THR* 4.1 8.5 - - - +
304A TYR* 1.3 84.6 - - + +
306A TYR* 1.3 60.8 + - - +
402A GLY 3.6 11.9 - - - +
403A ASP* 3.7 15.7 - - - +
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Residues in contact with TYR 306 (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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184A PHE* 4.1 9.4 - - + -
185A LYS 3.3 9.6 - - - +
186A HIS* 4.2 1.1 - - - +
229A LYS* 3.7 13.3 - - + +
230A THR 2.9 19.4 + - - -
231A ASN* 3.1 13.2 + - - -
247A TRP* 4.1 7.9 - + + -
265A TRP* 3.2 19.1 + + - -
304A TYR* 3.6 16.8 + - + -
305A PRO* 1.3 76.6 - - - +
307A GLU* 1.3 70.2 + - - +
308A PHE* 3.6 21.8 - + - -
400A ILE 3.8 9.2 - - - -
401A THR* 3.7 12.7 + - - +
402A GLY* 3.3 50.1 + - - +
403A ASP 3.5 17.7 - - - -
404A PHE* 4.0 9.0 - - + -
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Residues in contact with GLU 307 (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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183A SER 3.4 4.7 - - - +
184A PHE* 3.6 0.5 - - - -
185A LYS* 2.8 60.0 + - + +
306A TYR* 1.3 80.9 - - - +
308A PHE* 1.3 70.0 + - - +
309A LYS* 3.4 30.5 + - - -
399A GLY* 4.7 2.3 - - - -
400A ILE 3.4 7.9 - - - +
401A THR* 3.2 24.8 - - + +
188B ASP* 5.7 0.5 - - - +
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Residues in contact with PHE 308 (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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179A LEU* 3.7 34.5 - - + -
180A ASP 4.1 1.8 - - - -
181A PRO* 4.0 15.3 - - + -
183A SER* 3.9 5.8 - - - +
184A PHE* 3.6 38.8 - + + -
245A PHE* 3.7 26.0 - + - -
247A TRP* 3.7 35.4 - + - -
248A PRO* 4.4 4.0 - - + -
265A TRP* 3.9 13.2 - + - -
306A TYR* 3.6 21.3 - + - -
307A GLU* 1.3 78.5 - - - +
309A LYS* 1.3 65.5 + - - +
399A GLY* 3.7 3.3 - - - -
400A ILE* 2.8 32.7 + - - +
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Residues in contact with LYS 309 (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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92A ASP* 3.3 36.8 + - - +
93A ILE 5.4 2.0 + - - -
179A LEU* 3.7 2.6 - - - +
180A ASP* 2.7 36.7 + - + +
183A SER* 2.8 30.0 + - - +
307A GLU* 3.4 26.9 + - - -
308A PHE* 1.3 74.6 - - - +
310A ALA* 1.3 54.6 + - - +
397A ARG* 4.2 29.2 - - + +
398A ALA 3.5 12.5 - - - +
399A GLY* 3.9 12.3 - - - +
400A ILE* 4.5 0.9 - - - -
186B HIS* 5.3 5.3 - - - -
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Residues in contact with ALA 310 (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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177A TYR* 4.4 18.4 - - + +
178A ASN 3.4 15.0 - - - +
179A LEU* 4.0 6.3 - - + +
239A VAL* 4.9 3.1 - - + -
309A LYS* 1.3 73.9 - - - +
311A ASP* 1.3 64.5 + - - +
312A VAL* 3.5 1.6 + - - +
397A ARG* 3.4 3.9 - - - -
398A ALA* 2.7 37.1 + - + +
400A ILE* 3.2 26.6 - - + +
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Residues in contact with ASP 311 (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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176A ALA 3.6 1.0 - - - +
177A TYR* 3.3 5.1 - - - -
178A ASN* 2.8 48.9 + - + +
180A ASP* 3.8 20.6 - - - +
310A ALA* 1.3 72.3 - - - +
312A VAL* 1.3 62.3 + - - +
313A SER* 3.8 3.2 + - - -
395A PRO* 5.8 1.4 - - - +
396A VAL 3.9 4.3 - - - +
397A ARG* 3.4 26.0 - - - +
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Residues in contact with VAL 312 (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 ILE* 5.5 0.4 - - + -
101A VAL* 5.1 9.2 - - + -
105A LEU* 5.1 3.1 - - + -
175A PHE* 4.2 13.5 - - + -
176A ALA 3.6 3.6 - - - +
177A TYR* 3.9 28.3 - - + -
310A ALA 3.9 1.3 - - - +
311A ASP* 1.3 74.8 - - - +
313A SER* 1.3 67.0 + - - +
314A TYR* 4.4 11.8 - - + -
345A ILE* 4.6 2.1 - - - +
396A VAL* 2.9 50.3 + - + +
397A ARG 4.1 0.2 - - - -
398A ALA* 3.8 27.1 - - + +
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Residues in contact with SER 313 (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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174A ASN 4.6 0.4 - - - -
175A PHE* 3.5 3.5 - - - -
176A ALA* 3.1 48.3 + - - +
178A ASN* 5.8 0.9 + - - +
311A ASP* 3.8 3.8 + - - -
312A VAL* 1.3 74.1 - - - +
314A TYR* 1.3 69.2 + - - +
344A VAL* 6.2 1.1 - - - -
345A ILE 3.4 14.8 - - - -
346A GLY* 4.1 12.6 - - - -
347A PRO* 4.2 11.8 - - - +
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Residues in contact with TYR 314 (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* 3.8 16.6 - - + -
112A PHE* 3.6 30.8 - + - -
172A VAL* 4.1 6.5 - - + -
173A SER 3.5 10.1 - - - +
174A ASN 3.6 9.2 - - - -
175A PHE* 3.7 31.6 - + + -
312A VAL* 4.4 12.8 - - + -
313A SER* 1.3 81.8 - - - +
315A ASP* 1.3 77.4 + - - +
316A LEU* 4.2 8.5 - - + +
344A VAL* 4.4 2.0 - - - +
345A ILE* 2.9 64.1 + - + +
392A VAL 4.3 8.5 + - - -
394A ARG 5.4 0.2 + - - -
396A VAL* 4.6 16.2 - - + +
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Residues in contact with ASP 315 (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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171A LYS 3.6 0.7 - - - +
172A VAL* 3.5 6.9 - - - -
173A SER* 2.9 40.8 + - - +
174A ASN* 3.0 33.9 + - + +
314A TYR* 1.3 82.7 - - - +
316A LEU* 1.3 60.9 + - - +
317A THR* 4.1 3.8 - - - +
342A THR* 4.2 12.7 + - - +
343A PHE 3.7 3.8 - - - +
344A VAL* 4.1 24.9 - - - +
349A LYS* 5.7 2.8 - - - -
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Residues in contact with LEU 316 (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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112A PHE* 4.0 26.9 - - + -
116A THR* 4.0 24.2 - - + -
119A LEU* 4.5 12.3 - - + -
170A ILE* 4.3 9.4 - - + -
171A LYS 3.6 0.4 - - - +
172A VAL* 4.0 12.6 - - + -
314A TYR* 4.0 8.9 + - + -
315A ASP* 1.3 72.8 - - - +
317A THR* 1.3 60.9 + - - +
318A LEU* 4.2 13.6 + - + -
341A HIS 3.9 0.5 - - - +
342A THR* 3.0 2.4 - - - -
343A PHE* 2.7 50.2 + - + +
345A ILE* 4.1 27.8 - - + -
392A VAL* 4.3 11.4 - - + -
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Residues in contact with THR 317 (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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169A ALA 3.7 0.7 - - - +
170A ILE* 3.5 3.1 - - - -
171A LYS* 2.8 61.1 + - + +
173A SER* 5.2 3.1 + - - -
315A ASP* 4.9 4.7 - - - +
316A LEU* 1.3 73.7 + - - +
318A LEU* 1.3 70.4 + - - +
319A SER* 4.0 4.2 + - - +
340A ASN* 4.5 19.3 - - - +
341A HIS 3.3 14.1 - - - +
342A THR* 3.2 20.5 + - + +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR 4.9 4.0 - - - +
119A LEU* 4.6 5.8 - - + -
120A ALA* 3.8 29.4 - - + +
123A LEU* 4.1 15.3 - - + -
125A TYR* 2.9 32.1 + - + +
169A ALA 3.6 3.4 - - - -
170A ILE* 3.4 33.9 - - + -
316A LEU* 4.4 16.2 - - + -
317A THR* 1.3 77.8 - - - +
319A SER* 1.3 62.0 + - - +
341A HIS 2.6 37.7 + - - +
343A PHE* 4.2 15.9 - - + -
371A TRP* 5.9 0.2 - - + -
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 3.6 6.1 - - - -
167A LYS 4.5 0.7 - - - +
168A THR* 3.5 0.7 - - - +
169A ALA* 2.9 51.0 + - - +
171A LYS* 5.9 1.7 - - - +
317A THR* 4.0 6.0 + - - +
318A LEU* 1.3 73.8 - - - +
320A GLY* 1.3 58.3 + - - +
339A TRP 3.4 6.1 - - - -
340A ASN* 2.7 30.7 + - - -
----------------------------------------------------------
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 3.5 11.6 - - - -
166A ASP* 5.5 2.0 - - - -
167A LYS 5.0 3.4 - - - -
168A THR* 4.5 10.8 - - - -
319A SER* 1.3 74.1 - - - +
321A PHE* 1.3 62.0 + - - -
338A ASN* 3.3 8.5 - - - +
339A TRP* 2.9 28.8 + - - +
----------------------------------------------------------
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TYR* 3.7 2.4 - - - -
126A ALA* 3.1 42.5 + - + +
127A TRP* 3.4 35.9 - + - -
162A TYR* 4.0 5.4 - + - -
163A ARG* 3.3 52.7 - - + +
166A ASP* 4.1 11.6 + - + -
168A THR* 5.2 0.4 + - - -
320A GLY* 1.3 73.7 - - - -
322A LEU* 1.3 76.3 + - - +
323A ARG* 4.6 3.1 - - - -
336A ARG* 3.7 25.6 - - + +
337A PRO 3.1 9.0 - - - +
338A ASN* 3.1 21.5 - - - +
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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