Contacts of the helix formed by residues 365 - 401 (chain A) in PDB entry 2R7D
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 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A PRO* 4.1 3.1 - - - -
363A PRO 3.6 2.3 + - - -
364A LEU* 1.3 75.7 - - - +
366A SER* 1.3 64.1 + - - +
367A LYS* 3.5 10.1 + - - +
368A VAL* 2.9 44.7 + - - +
369A MSE 3.1 8.0 + - - +
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Residues in contact with SER 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PRO* 3.6 18.8 - - - +
322A PRO* 3.5 30.8 + - - +
365A SER* 1.3 75.3 - - - +
367A LYS* 1.3 58.2 + - - +
369A MSE 3.2 3.8 - - - +
370A ALA* 2.8 31.2 + - - +
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Residues in contact with LYS 367 (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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365A SER* 3.2 9.1 + - - +
366A SER* 1.3 77.1 - - - +
368A VAL* 1.3 78.8 + - + +
370A ALA* 3.2 7.6 + - - +
371A ALA* 3.1 23.6 + - + +
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Residues in contact with VAL 368 (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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364A LEU* 3.2 25.4 - - + -
365A SER* 2.9 47.8 + - - +
367A LYS* 1.3 85.5 - - + +
369A MSE 1.3 51.1 + - - +
371A ALA* 3.1 9.4 + - - +
372A HIS* 2.8 50.8 + - + +
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Residues in contact with MSE 369 (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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287A PRO* 3.7 8.5 - - + +
288A LEU* 4.0 9.2 - - - +
289A PRO* 3.9 14.6 - - - -
322A PRO* 4.0 14.6 - - + -
349A VAL* 3.6 25.6 - - + -
353A GLN* 3.3 44.4 - - + +
364A LEU* 4.4 9.2 - - + -
365A SER 3.1 9.6 + - - +
366A SER* 3.2 13.5 - - - +
368A VAL* 1.3 80.0 - - - +
370A ALA* 1.3 65.9 + - - +
372A HIS* 3.3 5.6 + - - +
373A ILE* 3.0 47.1 + - + +
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Residues in contact with ALA 370 (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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322A PRO* 4.4 15.2 - - + +
366A SER 2.8 19.4 + - - +
367A LYS* 3.7 7.2 - - - +
369A MSE 1.3 74.3 - - - +
371A ALA* 1.3 60.1 + - - +
373A ILE* 3.5 11.0 + - - +
374A ALA* 3.1 23.6 + - - +
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Residues in contact with ALA 371 (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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367A LYS* 3.1 18.5 + - + +
368A VAL* 3.1 13.4 + - - +
370A ALA* 1.3 75.8 - - - +
372A HIS* 1.3 65.4 + - + +
374A ALA* 3.3 6.4 + - - +
375A GLU* 3.0 29.6 + - - +
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Residues in contact with HIS 372 (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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129A PRO* 6.2 1.6 - - + -
130A ASP* 4.4 8.7 + - - -
138A ARG* 3.2 49.8 + - - +
345A TYR* 4.5 12.3 + - + -
346A LEU* 5.7 0.2 - - - -
349A VAL* 5.5 5.6 - - + +
364A LEU* 3.9 30.1 - - + +
368A VAL* 2.8 30.4 + - + +
369A MSE 4.1 7.4 - - - +
371A ALA* 1.3 77.9 - - + +
373A ILE* 1.3 63.2 + - + +
375A GLU* 4.1 8.2 - - - +
376A SER* 2.9 30.1 + - - -
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Residues in contact with ILE 373 (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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289A PRO* 3.8 35.2 - - + -
320A PHE* 3.8 40.2 - - + +
321A GLN* 4.2 6.1 - - - +
322A PRO* 4.5 0.2 - - + -
346A LEU* 4.3 8.7 - - + -
369A MSE 3.0 40.1 + - + +
370A ALA* 3.7 9.0 - - - +
371A ALA 3.2 0.2 - - - -
372A HIS* 1.3 77.7 - - + +
374A ALA* 1.3 62.6 + - - +
376A SER* 3.3 4.8 + - - -
377A GLN* 3.0 41.8 + - + +
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Residues in contact with ALA 374 (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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370A ALA 3.1 15.3 + - - +
371A ALA* 3.6 6.5 - - - +
372A HIS 3.3 0.2 - - - -
373A ILE* 1.3 83.4 - - - +
375A GLU* 1.3 62.8 + - - +
377A GLN* 3.7 3.6 + - - +
378A MSE 3.2 29.2 + - + +
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Residues in contact with GLU 375 (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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138A ARG* 3.3 40.7 + - + -
371A ALA 3.0 16.2 + - - +
372A HIS* 4.1 9.7 - - - +
374A ALA* 1.3 78.0 - - - +
376A SER* 1.3 61.7 + - - +
378A MSE 3.2 29.3 + - + +
379A ASN* 3.1 23.0 + - - +
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Residues in contact with SER 376 (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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138A ARG* 3.7 17.5 - - - -
141A GLY* 3.9 2.4 - - - -
345A TYR* 3.4 37.7 - - - -
346A LEU* 3.8 14.2 - - - +
372A HIS 2.9 22.1 + - - -
373A ILE 3.3 4.3 + - - -
375A GLU* 1.3 75.1 - - - +
377A GLN* 1.3 63.3 + - - +
379A ASN* 3.0 6.1 + - - +
380A ALA* 2.8 28.9 + - - +
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Residues in contact with GLN 377 (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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318A THR 5.5 0.3 - - - +
320A PHE* 3.6 27.6 - - + -
346A LEU* 3.7 21.7 - - + +
373A ILE* 3.0 35.5 + - + +
374A ALA* 4.0 5.4 - - - +
375A GLU 3.4 0.2 - - - -
376A SER* 1.3 81.5 + - - +
378A MSE 1.3 59.5 + - + +
380A ALA* 3.8 14.5 - - - +
381A ASP* 2.8 45.7 + - - +
384A ARG* 4.7 5.9 - - - +
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Residues in contact with MSE 378 (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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374A ALA* 3.2 10.8 - - + +
375A GLU* 3.2 40.8 - - + +
376A SER 3.3 0.4 - - - -
377A GLN* 1.3 77.5 - - + +
379A ASN* 1.3 67.0 + - - +
381A ASP* 3.5 9.6 + - - +
382A ALA* 3.3 21.5 + - - +
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Residues in contact with ASN 379 (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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138A ARG 3.0 20.1 + - - +
139A ALA* 3.1 31.1 + - - +
140A ARG 3.5 11.4 - - - +
375A GLU* 3.1 22.8 + - - +
376A SER 3.0 5.7 + - - +
378A MSE 1.3 80.5 - - - +
380A ALA* 1.3 63.5 + - - +
382A ALA* 3.3 6.7 + - - +
383A THR* 2.9 27.6 + - - +
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Residues in contact with ALA 380 (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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140A ARG 3.8 8.7 + - - -
141A GLY* 4.0 17.3 - - - +
142A ALA* 4.9 0.4 - - - -
376A SER 2.8 16.1 + - - +
377A GLN* 3.8 16.8 - - - +
379A ASN* 1.3 76.5 - - - +
381A ASP* 1.3 56.8 + - - +
383A THR* 3.2 2.9 + - - -
384A ARG* 2.9 62.4 + - - +
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Residues in contact with ASP 381 (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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317A ARG* 5.5 5.7 + - - -
377A GLN* 2.8 37.7 + - - +
378A MSE 3.6 9.6 - - - +
380A ALA* 1.3 77.4 - - - +
382A ALA* 1.3 57.2 + - - +
384A ARG* 3.5 9.2 + - - +
385A GLN* 3.0 29.5 + - - +
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Residues in contact with ALA 382 (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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61A LEU* 3.8 33.2 - - + +
63A ALA* 4.7 3.5 - - + +
378A MSE 3.3 11.8 + - - +
379A ASN* 3.8 8.3 - - - +
380A ALA 3.3 0.2 - - - -
381A ASP* 1.3 75.5 - - - +
383A THR* 1.3 65.7 + - - +
385A GLN* 4.5 4.9 - - - -
386A ALA* 3.1 23.7 + - - +
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Residues in contact with THR 383 (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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63A ALA* 4.5 11.9 - - + +
64A ALA 5.7 0.5 + - - -
140A ARG* 2.8 25.1 + - + +
142A ALA* 3.7 24.7 - - + +
143A THR 4.1 4.0 - - - +
144A LEU* 3.4 36.3 - - + +
379A ASN 2.9 11.3 + - - -
380A ALA* 3.2 5.8 + - - -
382A ALA* 1.3 77.8 - - - +
384A ARG* 1.3 57.4 + - - +
386A ALA* 3.1 6.0 + - - +
387A GLU* 3.0 23.7 + - - +
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Residues in contact with ARG 384 (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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141A GLY 4.9 1.2 + - - -
142A ALA* 4.0 18.4 - - + +
344A ARG* 3.7 34.4 - - - +
377A GLN* 4.7 7.5 - - - +
380A ALA* 2.9 57.0 + - - +
381A ASP* 3.9 8.2 + - - +
383A THR* 1.3 77.4 - - + +
385A GLN* 1.3 58.5 + - - +
387A GLU* 3.2 12.8 + - - +
388A ARG* 2.9 38.6 + - + +
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Residues in contact with GLN 385 (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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61A LEU* 3.7 20.9 - - + -
381A ASP 3.0 19.3 + - - +
382A ALA* 3.9 6.3 - - - +
383A THR 3.2 0.2 - - - -
384A ARG* 1.3 73.4 - - - +
386A ALA* 1.3 67.0 + - - +
388A ARG* 3.1 29.3 + - - +
389A LEU* 3.0 49.9 + - + +
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Residues in contact with ALA 386 (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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57A TYR* 4.2 5.5 - - - +
58A ALA* 3.9 25.6 - - + -
61A LEU* 3.5 16.3 - - + +
63A ALA* 4.2 10.3 - - + -
144A LEU* 4.3 7.2 - - + -
146A LEU* 4.8 0.7 - - + -
382A ALA 3.1 14.1 + - - +
383A THR 3.1 9.4 + - - +
385A GLN* 1.3 76.8 - - - +
387A GLU* 1.3 60.8 + - - +
389A LEU* 4.0 1.6 - - - +
390A SER* 2.8 31.5 + - - -
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Residues in contact with GLU 387 (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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143A THR 3.8 9.5 - - - +
144A LEU* 3.9 11.2 - - + +
145A TYR* 3.0 56.2 + - - +
146A LEU* 4.4 5.4 - - - -
147A PRO* 5.3 0.2 - - - +
383A THR* 3.0 12.4 + - - +
384A ARG* 3.4 16.5 - - - +
385A GLN 3.1 0.2 - - - -
386A ALA* 1.3 78.4 - - - +
388A ARG* 1.3 56.2 - - + +
390A SER* 3.3 2.8 + - - -
391A ARG* 2.9 47.5 + - - +
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Residues in contact with ARG 388 (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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384A ARG* 2.9 24.9 + - + +
385A GLN* 3.1 32.3 + - - +
387A GLU* 1.3 75.9 - - + +
389A LEU* 1.3 65.6 + - - +
391A ARG* 3.4 10.5 + - - +
392A ARG* 3.1 22.2 + - - +
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Residues in contact with LEU 389 (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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57A TYR* 3.6 37.5 - - + -
61A LEU* 4.0 14.1 - - + -
385A GLN* 3.0 50.2 + - + +
388A ARG* 1.3 75.3 - - - +
390A SER* 1.3 67.0 + - - +
392A ARG* 3.2 4.4 + - - -
393A HIS* 3.0 19.4 + - - +
454A MSE 3.4 32.8 - - + +
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Residues in contact with SER 390 (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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55A THR* 4.1 17.1 + - - -
57A TYR* 4.1 14.0 - - - +
58A ALA* 4.9 2.9 + - - +
146A LEU* 3.5 24.8 - - - +
147A PRO* 4.1 8.7 - - - -
386A ALA 2.8 22.1 + - - -
387A GLU 3.7 4.0 - - - -
389A LEU* 1.3 78.7 - - - +
391A ARG* 1.3 61.5 + - - +
393A HIS* 3.3 7.0 + - - +
394A HIS* 3.2 31.4 + - - -
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Residues in contact with ARG 391 (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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145A TYR 4.9 3.8 + - - +
147A PRO* 4.1 20.4 - - + +
243A VAL* 2.9 34.4 + - - +
244A ARG* 4.7 0.8 - - - +
245A VAL* 3.6 42.5 + - + +
387A GLU* 2.9 43.3 + - + +
388A ARG* 3.7 9.4 - - - +
389A LEU 3.2 0.2 - - - -
390A SER* 1.3 74.1 - - - +
392A ARG* 1.3 65.3 + - - +
394A HIS 3.5 0.2 + - - -
395A THR* 2.8 29.9 + - - -
427A ALA* 5.9 0.8 - - - +
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Residues in contact with ARG 392 (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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388A ARG 3.1 13.4 + - - +
389A LEU* 3.2 10.7 + - - +
391A ARG* 1.3 77.6 - - - +
393A HIS* 1.3 63.6 + - - +
395A THR* 3.2 7.6 + - - -
396A LEU* 2.9 31.6 + - + +
428A PHE* 3.4 43.1 - - + -
429A ASP* 4.1 15.8 + - - +
430A VAL* 5.8 0.4 - - - +
454A MSE 3.6 46.1 + - - -
455A ARG* 5.2 1.6 - - - +
456A VAL* 5.5 1.8 - - - +
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Residues in contact with HIS 393 (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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41A HIS* 4.3 13.9 + + - -
52A GLU* 2.9 29.5 + - - -
53A ALA 4.2 1.6 - - - -
54A ARG 3.5 19.1 + - - -
55A THR* 3.4 23.8 - - + +
57A TYR* 4.1 15.5 - + + -
389A LEU 3.0 13.2 + - - +
390A SER* 3.4 9.2 - - - +
392A ARG* 1.3 78.6 - - - +
394A HIS* 1.3 65.5 + - - +
396A LEU* 3.2 14.0 + - - +
397A ARG* 3.2 24.8 + - + +
451A LEU* 3.8 29.9 - - + +
454A MSE 3.6 11.4 - - - -
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Residues in contact with HIS 394 (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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53A ALA* 3.2 25.9 + - + -
55A THR* 3.5 17.4 + - + +
147A PRO* 3.5 21.6 - - + +
148A ASP* 4.3 14.0 + - + -
245A VAL* 3.8 20.0 - - + -
246A LYS 4.8 0.2 - - - +
247A ALA* 3.5 17.5 - - + +
252A ALA* 3.3 16.0 - - + +
254A VAL* 4.8 0.3 - - - +
390A SER* 3.2 22.3 + - - +
393A HIS* 1.3 82.6 - - - +
395A THR* 1.3 65.2 + - - +
397A ARG* 2.8 35.2 + - - +
398A PHE* 3.0 19.8 + - - +
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Residues in contact with THR 395 (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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245A VAL* 3.8 17.4 - - - +
254A VAL* 4.0 18.0 - - + +
391A ARG* 2.8 24.1 + - - +
392A ARG* 3.2 8.9 + - - -
394A HIS* 1.3 76.2 - - - +
396A LEU* 1.3 58.2 + - - +
398A PHE* 3.2 4.0 + - - +
399A ILE* 2.9 35.3 + - + +
426A LEU* 4.4 19.8 + - + +
428A PHE* 3.9 28.3 - - + -
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Residues in contact with LEU 396 (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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392A ARG* 2.9 24.6 + - + +
393A HIS 3.2 6.9 + - - +
395A THR* 1.3 74.7 - - - +
397A ARG* 1.3 60.1 + - - +
399A ILE* 3.3 9.1 + - + +
400A ALA* 2.8 30.8 + - - +
428A PHE* 3.7 26.2 - - + -
449A ILE* 4.0 9.1 - - + +
450A ASP 4.6 1.3 - - - +
451A LEU* 3.9 15.0 - - + -
454A MSE 3.4 49.1 - - + +
455A ARG 4.2 1.3 - - - +
456A VAL* 3.2 31.0 - - + -
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Residues in contact with ARG 397 (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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51A ASP* 5.4 0.6 + - - -
52A GLU* 3.2 35.2 + - + +
53A ALA* 3.7 25.9 - - - +
247A ALA* 3.8 12.5 - - - +
248A ASP 5.1 3.0 + - - +
251A GLY* 3.9 20.2 - - - -
252A ALA* 3.8 16.8 - - + +
393A HIS* 3.2 14.6 + - - +
394A HIS* 2.8 45.0 + - - +
396A LEU* 1.3 76.3 - - - +
398A PHE* 1.3 64.4 + - - +
400A ALA* 3.3 7.1 + - - +
401A ALA* 3.0 24.1 + - - +
451A LEU* 4.1 18.2 - - + -
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Residues in contact with PHE 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA* 3.3 26.6 - - + +
253A SER* 3.7 9.0 - - - -
254A VAL* 3.5 52.0 - - + -
255A PHE* 6.5 0.7 - + - -
394A HIS 3.0 11.9 + - - +
395A THR 3.2 8.7 + - - +
397A ARG* 1.3 77.8 - - - +
399A ILE* 1.3 61.3 + - - +
401A ALA* 3.3 13.3 + - + +
402A GLN* 3.0 53.3 + - + +
405A ARG* 4.2 8.7 - - - -
407A TRP* 3.8 16.2 - + - -
425A ASP 5.7 0.2 - - - -
426A LEU* 3.8 12.3 - - + -
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A THR* 2.9 24.2 + - + +
396A LEU* 3.5 14.6 - - + +
398A PHE* 1.3 76.6 - - - +
400A ALA* 1.3 63.4 + - - +
402A GLN* 3.1 23.7 + - - +
403A PRO* 4.0 1.7 - - - +
407A TRP* 4.7 11.5 + - + +
426A LEU* 3.9 30.3 - - + -
428A PHE* 4.0 31.2 - - + -
446A PHE* 3.4 43.5 - - + -
449A ILE* 4.3 11.4 - - + -
456A VAL* 5.4 0.4 - - + -
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 5.7 4.3 - - - +
396A LEU 2.8 20.2 + - - +
397A ARG* 3.3 7.8 + - - +
399A ILE* 1.3 73.5 - - - +
401A ALA* 1.3 60.2 + - - +
402A GLN 3.4 0.7 + - - -
403A PRO* 3.5 14.5 - - - +
449A ILE* 4.0 31.2 - - + -
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA 6.0 0.7 - - - +
397A ARG 3.0 16.4 + - - +
398A PHE* 3.6 11.2 - - + +
399A ILE 3.1 0.8 - - - -
400A ALA* 1.3 77.8 - - - +
402A GLN* 1.3 65.6 + - + +
403A PRO* 3.4 7.9 - - - +
404A GLU* 4.7 0.9 - - - +
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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