Contacts of the helix formed by residues 293 - 326 (chain A) in PDB entry 5V5Z
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 THR 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LYS 4.3 5.8 - - - +
292A MET* 1.3 75.8 - - - +
294A ASP* 1.3 67.0 + - - +
295A GLN* 3.6 5.6 + - - +
296A GLU* 2.9 46.7 + - - +
297A ILE* 3.1 26.4 + - - +
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Residues in contact with ASP 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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258A MET* 3.9 14.0 - - + +
261A ILE* 3.5 19.8 - - + +
262A LYS* 4.1 22.7 - - - +
265A ARG* 2.7 33.2 + - - -
293A THR* 1.3 76.4 - - - +
295A GLN* 1.3 63.9 + - - +
297A ILE* 3.5 11.0 + - - +
298A ALA* 3.2 18.0 + - - +
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Residues in contact with GLN 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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250A GLN* 3.1 30.1 - - - +
251A LYS* 5.3 4.2 - - - +
254A SER* 3.1 14.1 + - - -
258A MET* 3.6 34.9 - - + +
293A THR* 3.3 5.6 + - - +
294A ASP* 1.3 78.7 - - - +
296A GLU* 1.3 54.6 + - + +
298A ALA* 2.6 21.5 + - - -
299A ASN* 2.7 37.5 + - - +
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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
----------------------------------------------------------
128A LYS 4.1 3.8 - - - +
129A GLY* 4.0 31.1 - - - -
130A VAL* 3.3 18.4 - - + +
286A TYR* 5.0 2.5 + - - -
291A LYS 4.2 1.6 - - - +
292A MET* 3.5 19.1 - - + +
293A THR* 2.9 50.5 + - - +
294A ASP 3.4 0.2 - - - -
295A GLN* 1.3 75.1 - - + +
297A ILE* 1.3 63.3 + - - +
299A ASN* 3.3 6.4 + - - +
300A LEU* 3.0 21.0 + - - +
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Residues in contact with ILE 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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261A ILE* 4.3 11.7 - - + -
265A ARG* 5.7 0.7 - - - +
277A ILE* 5.7 2.2 - - + +
280A LEU* 4.1 33.8 - - + +
281A LEU* 5.1 13.5 - - + +
284A SER* 4.0 21.8 - - - +
292A MET* 3.5 28.0 - - + +
293A THR 3.1 18.5 + - - +
294A ASP* 3.7 15.9 - - - +
295A GLN 3.1 0.6 - - - -
296A GLU* 1.3 75.2 - - - +
298A ALA* 1.3 57.7 + - - +
300A LEU* 3.9 1.8 - - - +
301A LEU* 2.9 39.2 + - + +
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Residues in contact with ALA 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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254A SER* 3.6 35.0 - - - +
257A TYR* 3.9 9.2 - - + -
258A MET* 3.7 10.1 - - + +
261A ILE* 4.5 1.3 - - + +
294A ASP 3.2 12.7 + - - +
295A GLN 2.6 17.1 + - - +
297A ILE* 1.3 71.9 - - - +
299A ASN* 1.3 61.0 + - - +
301A LEU* 3.0 16.5 - - - +
302A ILE* 2.9 24.4 + - - +
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Residues in contact with ASN 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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126A PHE* 3.0 25.6 - - - +
127A GLY* 3.1 17.1 - - - -
128A LYS* 2.7 26.6 + - - +
130A VAL* 3.4 16.8 - - + -
250A GLN* 4.4 0.2 - - - -
254A SER* 3.9 4.0 - - - -
295A GLN* 2.7 46.4 + - - +
296A GLU* 3.7 2.2 - - - +
298A ALA* 1.3 71.3 - - - +
300A LEU* 1.3 55.9 + - - +
302A ILE* 2.6 28.7 + - - +
303A GLY* 2.9 10.9 + - - -
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Residues in contact with LEU 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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130A VAL* 3.2 14.4 - - + +
131A ILE* 3.6 24.9 - - + -
142A GLN* 3.6 38.8 - - + +
146A ALA* 6.3 0.2 - - + -
280A LEU* 4.1 24.7 - - + -
292A MET* 4.2 8.5 - - + -
296A GLU 3.0 16.6 + - - +
297A ILE 3.9 3.4 - - - +
299A ASN* 1.3 75.5 - - - +
301A LEU* 1.3 64.2 + - - +
302A ILE 3.2 0.2 + - - -
303A GLY* 3.4 0.3 + - - -
304A ILE* 2.9 49.0 + - + +
601A HEM 6.2 1.3 - - + -
602A 1YN 4.4 2.5 - - + -
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Residues in contact with LEU 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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205A PHE* 3.3 36.6 - - + -
257A TYR* 4.0 25.1 - - + -
261A ILE* 4.4 6.3 - - + -
276A LEU* 4.3 4.9 - - + -
277A ILE* 3.7 27.6 - - + -
280A LEU* 4.2 20.2 - - + -
297A ILE* 2.9 33.5 + - + +
298A ALA* 3.0 19.5 + - - +
300A LEU* 1.3 76.0 - - - +
302A ILE* 1.3 55.5 + - - +
304A ILE* 3.8 5.4 - - - +
305A LEU* 3.0 29.5 + - - +
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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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125A VAL 3.9 5.8 - - - +
126A PHE* 3.5 35.2 - - + +
221A TYR* 4.3 8.5 - - - +
224A LEU* 4.0 14.1 - - + -
250A GLN* 3.9 15.7 - - + +
253A ILE* 4.1 10.8 - - + -
254A SER* 3.7 34.5 - - - +
257A TYR* 3.6 17.9 - - + -
298A ALA 2.9 12.9 + - - +
299A ASN* 2.6 15.2 + - - +
301A LEU* 1.3 68.3 - - - +
303A GLY* 1.3 66.1 + - - +
305A LEU* 3.1 4.0 + - - +
306A MET* 2.8 25.4 + - + +
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Residues in contact with GLY 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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126A PHE* 3.4 34.7 - - - -
131A ILE* 3.6 8.3 - - - -
299A ASN 2.9 9.7 + - - -
302A ILE* 1.3 76.7 - - - +
304A ILE* 1.3 63.2 + - - +
306A MET 3.0 0.7 + - - -
307A GLY 2.8 23.7 + - - -
602A 1YN 3.6 11.2 - - - -
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Residues in contact with ILE 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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146A ALA* 4.6 15.7 - - + -
204A LEU* 4.5 7.4 - - + +
205A PHE* 5.3 1.1 - - + -
276A LEU* 4.0 31.4 - - + -
280A LEU* 4.3 8.1 - - + -
300A LEU* 2.9 51.0 + - + +
301A LEU* 3.8 4.7 - - - +
303A GLY* 1.3 74.4 - - - +
305A LEU* 1.3 65.9 + - - +
308A GLY* 3.1 22.0 + - - -
471A ILE* 5.9 0.9 - - + -
601A HEM 3.4 38.5 - - + +
602A 1YN 3.6 11.5 - - + +
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Residues in contact with LEU 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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197A ILE* 4.1 19.3 - - + -
200A ALA* 3.7 31.6 - - + -
201A SER* 4.3 14.6 - - - +
204A LEU* 5.3 3.8 - - + -
205A PHE* 3.9 20.0 - - + -
213A PHE* 4.9 0.7 - - + -
221A TYR* 3.1 37.0 - - + +
257A TYR* 3.5 11.7 - - - +
301A LEU 3.0 18.1 + - - +
302A ILE 3.6 3.8 - - - +
304A ILE* 1.3 78.9 - - - +
306A MET* 1.3 58.7 + - + +
309A GLN* 2.9 31.4 + - - +
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Residues in contact with MET 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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125A VAL* 3.8 26.7 - - - -
126A PHE* 3.7 14.8 - - + -
197A ILE* 6.2 1.3 - - + -
221A TYR* 3.9 24.5 - - + +
224A LEU* 4.0 13.9 - - + -
225A ASP* 3.7 33.4 - - + +
228A PHE* 4.0 10.8 - - + -
302A ILE 2.8 17.6 + - - +
305A LEU* 1.3 76.4 - - - +
307A GLY* 1.3 65.5 + - - +
309A GLN* 3.6 8.2 - - + +
310A HIS* 3.1 62.2 + - + +
602A 1YN 5.0 0.4 - - - -
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Residues in contact with GLY 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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228A PHE* 5.6 0.9 - - - -
303A GLY 2.8 16.8 + - - -
306A MET* 1.3 74.9 - - - +
308A GLY* 1.3 60.9 + - - +
310A HIS* 3.7 3.2 - - - +
311A THR* 3.1 26.5 + - - +
602A 1YN 3.4 44.6 - - - +
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Residues in contact with GLY 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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196A THR* 4.4 0.4 - - - +
304A ILE 3.1 14.4 + - - -
307A GLY* 1.3 76.8 - - - +
309A GLN* 1.3 62.9 + - - +
311A THR* 4.0 2.9 - - - -
312A SER* 3.0 30.0 + - - -
479A GLN* 4.9 0.6 - - - +
601A HEM 3.4 37.8 - - - +
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Residues in contact with GLN 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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193A PRO* 3.0 37.4 + - - +
196A THR* 3.2 14.8 - - + +
197A ILE* 3.4 37.8 + - + +
221A TYR* 6.1 1.2 - - - +
225A ASP* 4.4 7.3 + - - -
305A LEU* 2.9 23.4 + - + +
306A MET* 3.6 9.2 - - + +
307A GLY 3.2 0.2 - - - -
308A GLY* 1.3 77.9 - - - +
310A HIS* 1.3 87.7 + - + +
313A ALA* 3.0 29.7 + - - +
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Residues in contact with HIS 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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225A ASP* 3.2 31.3 + - - -
228A PHE* 3.3 36.0 - + + -
306A MET* 3.1 30.4 + - + +
307A GLY* 3.7 4.3 - - - +
309A GLN* 1.3 90.8 + - + +
311A THR* 1.3 66.2 + - + +
313A ALA* 3.9 2.0 - - - +
314A SER* 3.0 26.0 + - - -
508A MET* 4.4 12.7 - - + +
509A VAL* 4.1 25.6 - - + +
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Residues in contact with THR 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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307A GLY 3.1 16.3 + - - +
308A GLY 3.7 1.2 + - - -
310A HIS* 1.3 76.1 - - + +
312A SER* 1.3 61.5 + - - +
314A SER* 3.9 2.6 - - - -
315A THR* 3.3 25.8 + - - -
375A PRO* 3.9 16.3 - - + +
376A LEU* 3.9 21.1 - - + -
509A VAL* 4.4 9.4 - - + -
601A HEM 3.0 43.3 - - + +
602A 1YN 3.5 22.4 - - + +
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Residues in contact with SER 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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196A THR* 3.9 6.6 + - - -
308A GLY 3.0 17.2 + - - -
311A THR* 1.3 79.7 + - - +
313A ALA* 1.3 65.0 + - - +
314A SER 3.1 1.6 - - - -
315A THR* 3.3 1.0 + - - -
316A SER* 3.1 20.4 + - - -
476A ALA* 5.0 3.4 + - - +
479A GLN* 2.7 29.9 + - - +
480A LEU* 3.1 34.8 - - - +
601A HEM 4.6 11.4 - - - -
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Residues in contact with ALA 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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192A GLN* 3.5 6.2 - - - +
193A PRO* 3.6 36.1 - - + +
196A THR* 3.3 18.3 + - - +
309A GLN* 3.0 22.5 + - - +
310A HIS* 4.0 2.0 - - - +
312A SER* 1.3 75.9 - - - +
314A SER* 1.3 62.2 + - - +
316A SER* 3.2 5.9 + - - -
317A ALA* 3.0 23.4 + - - +
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Residues in contact with SER 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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189A MET* 6.5 1.1 - - - -
310A HIS 3.0 17.2 + - - -
311A THR* 3.9 7.4 - - - -
313A ALA* 1.3 75.3 - - - +
315A THR* 1.3 62.5 + - - +
317A ALA* 2.8 24.4 + - - +
318A TRP* 2.9 25.4 + - - -
373A HIS 5.1 1.2 + - - -
375A PRO* 4.6 9.6 - - - +
509A VAL* 4.6 9.9 - - - -
510A VAL 3.3 23.4 + - - -
511A LEU* 5.0 4.4 - - - -
512A PRO* 5.9 1.8 - - - -
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Residues in contact with THR 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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311A THR 3.3 16.2 + - - -
312A SER 3.3 4.6 + - - -
314A SER* 1.3 77.8 + - - +
316A SER* 1.3 57.7 + - - +
318A TRP* 4.6 3.1 - - - +
319A PHE* 3.0 37.6 + - + -
366A ILE* 4.4 5.4 - - + -
369A THR* 3.5 17.9 - - + +
370A LEU* 3.8 32.1 - - + +
373A HIS 4.8 3.6 + - - -
375A PRO* 4.0 6.6 - - - +
480A LEU* 3.8 26.2 - - + -
601A HEM 4.3 0.9 - - - +
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Residues in contact with SER 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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192A GLN* 2.9 27.0 + - - +
312A SER 3.1 14.2 + - - -
313A ALA* 3.2 12.0 + - - -
315A THR* 1.3 74.7 - - - +
317A ALA* 1.3 67.3 + - - +
319A PHE* 3.4 26.6 - - - -
320A LEU* 3.0 30.5 + - - +
480A LEU* 3.9 7.4 - - - -
483A ILE* 4.1 12.9 - - - +
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Residues in contact with ALA 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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188A VAL* 3.9 31.9 - - + +
189A MET* 4.8 5.2 - - + -
192A GLN* 3.8 9.4 - - + -
313A ALA 3.0 16.3 + - - +
314A SER* 2.8 12.9 + - - +
316A SER* 1.3 76.5 + - - +
318A TRP* 1.3 62.6 + - - +
320A LEU* 3.1 5.5 + - - +
321A LEU* 3.0 27.1 + - - +
512A PRO* 4.6 11.7 - - + -
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Residues in contact with TRP 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A SER* 2.9 32.6 + - - -
315A THR* 3.9 3.1 - - - +
317A ALA* 1.3 76.5 - - - +
319A PHE* 1.3 58.8 + - - +
321A LEU* 2.8 17.7 + - + +
322A HIS* 2.8 39.4 + + + -
369A THR* 3.6 16.8 - - + -
373A HIS* 3.4 58.1 + + + +
500A VAL* 3.9 9.9 - - + -
501A PRO 3.8 22.7 - - - -
503A PRO* 4.1 16.2 - - + -
510A VAL* 3.7 16.0 + - + +
511A LEU* 3.7 6.3 - - - -
512A PRO* 3.3 49.2 - - + +
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Residues in contact with PHE 319 (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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315A THR* 3.0 24.8 + - + -
316A SER* 3.4 32.8 - - - -
318A TRP* 1.3 76.1 - - - +
320A LEU* 1.3 73.0 + - + +
322A HIS* 4.5 7.2 - - - -
323A LEU* 3.0 33.1 + - - +
365A THR* 4.0 11.0 - - + -
366A ILE* 4.1 7.9 - - + -
369A THR* 3.1 26.8 - - - +
422A PHE* 4.7 0.2 - - + -
480A LEU* 3.6 28.0 - - + -
483A ILE* 4.3 2.7 - - + -
484A LEU* 3.4 59.2 - - + -
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Residues in contact with LEU 320 (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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188A VAL* 4.1 17.0 - - + -
191A THR* 4.7 0.7 - - - +
192A GLN* 3.4 35.9 - - + +
316A SER 3.0 17.5 + - - +
317A ALA 3.2 9.0 - - - +
318A TRP 2.8 1.2 + - - -
319A PHE* 1.3 90.4 - - + +
321A LEU* 1.3 64.1 + - - +
323A LEU 3.5 0.7 + - - -
324A GLY 3.0 5.5 + - - -
487A PHE* 3.5 37.0 - - + -
493A TRP* 2.6 55.4 + - + +
518A ILE* 5.0 7.2 - - + -
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Residues in contact with LEU 321 (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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188A VAL* 4.4 8.5 - - + -
317A ALA 3.0 13.9 + - - +
318A TRP* 2.8 24.2 + - + +
320A LEU* 1.3 71.3 - - - +
322A HIS* 1.3 54.1 + - - +
324A GLY* 2.6 22.9 + - - -
325A GLU* 2.8 12.6 + - - +
495A ILE* 3.7 14.6 - - + +
500A VAL* 4.7 7.6 - - + -
501A PRO* 3.6 37.7 - - + -
512A PRO* 3.6 31.0 - - + -
516A ALA* 4.2 4.9 - - + -
517A GLU 3.6 32.5 - - - +
518A ILE* 5.5 0.7 - - + -
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Residues in contact with HIS 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A TRP* 2.8 37.8 + + + +
319A PHE* 4.5 0.7 - - - -
321A LEU* 1.3 73.0 - - - +
323A LEU* 1.3 60.0 + - - +
325A GLU* 3.1 12.8 + - - +
326A LYS* 2.9 31.9 + - - +
372A MET* 3.5 26.6 - - + +
373A HIS* 3.2 34.8 + + - -
422A PHE* 3.6 47.4 - + + +
500A VAL* 3.9 26.2 - - + +
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Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A PHE 3.0 24.5 + - - +
322A HIS* 1.3 78.0 - - - +
324A GLY* 1.3 53.4 + - - +
326A LYS 4.0 2.2 - - - -
327A PRO* 3.0 18.4 - - - +
329A LEU* 3.4 28.5 - - + +
330A GLN* 2.5 58.4 + - + +
333A ILE* 4.1 8.1 - - + -
365A THR* 4.3 13.5 - - + +
422A PHE* 3.9 19.3 - - + -
484A LEU* 4.1 18.4 - - + -
488A VAL* 4.2 0.9 - - + -
493A TRP* 3.7 13.9 - - + -
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Residues in contact with GLY 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU 3.0 5.9 + - - -
321A LEU 2.6 16.7 + - - -
323A LEU* 1.3 72.5 - - - +
325A GLU* 1.3 60.0 + - - +
327A PRO* 3.5 7.8 - - - +
330A GLN* 3.8 3.1 - - - -
493A TRP* 3.6 20.2 - - - +
494A THR* 3.4 21.0 - - - -
495A ILE* 3.4 18.1 + - - +
498A TYR* 4.1 3.5 - - - -
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Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 2.8 5.6 + - - +
322A HIS* 3.1 14.5 + - - +
324A GLY* 1.3 77.6 - - - +
326A LYS* 1.4 87.9 + - + +
327A PRO* 3.1 10.0 - - - +
495A ILE* 3.6 11.8 - - + +
498A TYR* 3.3 42.7 - - + +
500A VAL* 3.4 35.8 + - + +
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A HIS 2.9 12.5 + - - +
323A LEU 3.5 3.9 - - - +
325A GLU* 1.4 97.2 + - + +
327A PRO* 1.4 51.3 - - - +
328A HIS* 2.6 8.8 + - + -
329A LEU* 2.6 55.4 + - + +
420A GLU 4.7 2.8 + - - -
421A ASP* 3.4 17.2 + - - +
422A PHE* 3.3 47.1 - - + +
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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