Contacts of the helix formed by residues 376 - 400 (chain F) in PDB entry 2AJQ
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 ASP 376 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349F ALA* 5.2 4.1 + - + +
374F VAL* 3.3 5.5 - - + +
375F ASP* 1.3 76.4 - - - +
377F PRO* 1.3 70.7 - - - +
378F GLU* 3.7 12.7 + - - +
379F LYS* 3.0 53.7 + - + +
380F GLN* 2.8 28.4 + - - +
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Residues in contact with PRO 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374F VAL 5.3 0.4 - - - +
375F ASP 3.1 11.6 - - - +
376F ASP* 1.3 90.4 - - - +
378F GLU* 1.3 68.5 + - + +
380F GLN* 3.1 8.5 + - + +
381F ALA* 2.9 26.5 + - - +
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Residues in contact with GLU 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F GLU* 4.7 7.6 - - - +
260F THR* 3.2 40.1 + - + +
376F ASP* 3.3 13.2 - - - +
377F PRO* 1.3 83.8 - - + +
379F LYS* 1.3 64.6 + - - +
381F ALA* 3.2 6.6 + - - +
382F ALA* 3.1 21.4 + - - +
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Residues in contact with LYS 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F THR* 4.3 17.7 - - + -
261F PHE* 3.8 31.4 - - + -
345F LYS 5.6 0.9 - - - -
346F LEU* 5.0 2.4 - - + +
348F GLU* 4.7 15.1 + - - +
349F ALA* 3.8 28.1 - - + +
374F VAL* 4.2 9.9 - - + -
376F ASP* 3.0 35.1 + - + +
378F GLU* 1.3 79.2 - - + +
380F GLN* 1.3 63.5 + - - +
382F ALA* 3.3 18.5 + - - +
383F ILE* 3.5 11.3 + - - +
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Residues in contact with GLN 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372F VAL 3.2 17.4 + - - +
373F ARG* 3.1 24.1 - - - +
374F VAL* 2.9 43.8 + - - +
376F ASP 2.8 13.4 + - - +
377F PRO* 3.1 11.9 + - + +
379F LYS* 1.3 75.9 - - - +
381F ALA* 1.3 63.5 + - - +
383F ILE* 3.1 34.2 + - - +
384F ASP* 4.2 2.1 + - - +
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Residues in contact with ALA 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F PRO 2.9 16.2 + - - +
378F GLU* 3.7 6.1 - - - +
380F GLN* 1.3 78.1 - - - +
382F ALA* 1.3 61.5 + - - +
383F ILE 3.5 0.3 + - - -
384F ASP* 3.6 16.5 + - - +
385F LEU* 3.8 13.8 + - - +
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Residues in contact with ALA 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F LEU* 3.9 18.1 - - + +
260F THR* 4.1 12.6 - - + +
261F PHE* 4.0 16.4 - - + -
378F GLU 3.1 12.2 + - - +
379F LYS 3.4 11.7 - - - +
380F GLN 3.1 0.6 - - - -
381F ALA* 1.3 76.5 - - - +
383F ILE* 1.3 66.0 + - - +
385F LEU* 2.8 25.4 + - + +
386F ILE* 2.9 16.3 + - - +
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Residues in contact with ILE 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F LEU* 4.1 21.3 - - + -
369F LEU* 3.5 38.1 - - + +
370F GLU* 5.5 0.4 - - - +
372F VAL* 3.6 33.2 - - + +
374F VAL* 5.1 2.5 - - + -
379F LYS 3.7 7.0 - - - +
380F GLN* 3.1 39.0 + - - +
382F ALA* 1.3 77.9 - - - +
384F ASP* 1.3 64.9 + - - +
386F ILE* 3.0 14.0 + - + +
387F LYS* 3.0 27.0 + - + +
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Residues in contact with ASP 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F GLU* 4.1 7.1 - - - +
380F GLN 4.2 1.8 + - - +
381F ALA* 3.6 11.5 + - - +
382F ALA 3.2 0.6 - - - -
383F ILE* 1.3 80.3 - - - +
385F LEU* 1.3 61.1 + - + +
387F LYS* 2.7 39.3 + - - +
388F GLU* 3.1 27.7 + - - +
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Residues in contact with LEU 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F ARG* 4.8 9.2 - - - +
253F LEU* 3.8 31.5 - - + +
256F LYS* 4.6 23.8 - - + -
257F LEU* 4.0 18.3 - - + +
260F THR* 5.9 1.6 - - - +
381F ALA 3.8 12.3 + - - +
382F ALA* 2.8 19.8 + - + +
384F ASP* 1.3 79.0 - - + +
386F ILE* 1.3 59.2 + - - +
388F GLU* 4.6 5.2 - - - +
389F TYR* 3.1 27.4 + - - +
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Residues in contact with ILE 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257F LEU* 4.0 17.9 - - + -
261F PHE* 4.0 24.2 - - + -
334F PHE* 4.0 13.0 - - + -
336F PRO* 4.3 8.7 - - + +
342F ILE* 3.6 43.7 - - + -
346F LEU* 5.3 2.2 - - + -
369F LEU* 4.6 8.5 - - + -
382F ALA 2.9 18.0 + - - +
383F ILE* 3.0 18.6 + - + +
385F LEU* 1.3 75.4 - - - +
387F LYS* 1.3 64.6 + - - +
389F TYR* 3.2 6.4 + - - +
390F LEU* 2.9 30.9 + - + +
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Residues in contact with LYS 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366F ASP* 3.1 29.4 - - - +
369F LEU* 3.8 33.2 - - + -
370F GLU* 3.6 32.0 + - - +
383F ILE* 3.0 17.5 + - - +
384F ASP* 2.7 35.5 + - - +
386F ILE* 1.3 76.6 - - - +
388F GLU* 1.3 62.7 + - - +
390F LEU* 3.2 10.5 + - + +
391F MET* 3.1 22.4 + - - +
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Residues in contact with GLU 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F ARG* 2.7 50.2 + - - +
253F LEU* 3.7 10.9 - - + +
384F ASP 3.1 17.5 + - - +
385F LEU* 4.0 9.3 - - - +
387F LYS* 1.3 76.2 - - - +
389F TYR* 1.3 58.9 + - - +
391F MET* 3.3 10.7 + - - +
392F ILE* 2.8 44.5 + - + +
447F TYR* 5.0 3.1 + - - -
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Residues in contact with TYR 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F ARG* 3.7 37.3 - - + +
253F LEU* 3.8 26.2 - - + +
254F LEU* 4.4 15.3 - - + +
257F LEU* 4.5 2.0 - - + -
335F ASN* 4.8 2.4 + - - -
336F PRO* 3.3 46.3 - - + +
337F SER* 3.5 25.4 + - - -
385F LEU 3.1 20.1 + - - +
386F ILE* 3.2 7.6 + - - +
388F GLU* 1.3 77.6 - - - +
390F LEU* 1.3 61.1 + - - +
392F ILE* 3.1 5.3 + - + +
393F GLN* 2.8 40.4 + - + +
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Residues in contact with LEU 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336F PRO 3.6 21.8 - - - +
337F SER* 4.1 17.3 - - - +
339F ARG* 3.5 45.8 - - - +
342F ILE* 4.3 3.6 - - + -
369F LEU* 4.2 11.4 - - + -
386F ILE* 2.9 35.0 + - + +
387F LYS* 3.2 6.3 + - + +
389F TYR* 1.3 77.1 - - + +
391F MET* 1.3 57.0 + - - +
393F GLN* 3.4 5.7 + - + +
394F LYS* 3.0 28.2 + - - +
919X C 6.2 1.8 - - - -
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Residues in contact with MET 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F LEU* 5.0 0.2 - - + -
387F LYS 3.1 13.1 + - - +
388F GLU* 3.5 11.0 - - - +
390F LEU* 1.3 75.5 - - - +
392F ILE* 1.3 79.2 + - + +
394F LYS* 3.2 14.3 + - - +
395F ARG* 3.1 46.7 + - + +
446F PRO* 3.5 29.2 - - + -
447F TYR* 3.3 29.8 - - + -
920X C 4.9 6.3 - - - +
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Residues in contact with ILE 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F LEU* 3.6 35.0 - - + +
249F ARG* 4.3 12.3 - - + -
250F ARG* 4.2 11.4 - - + +
253F LEU* 4.4 6.7 - - + -
388F GLU* 2.8 49.1 + - + +
389F TYR* 3.5 9.2 - - + +
391F MET* 1.3 80.2 - - + +
393F GLN* 1.3 65.5 + - - +
395F ARG* 3.2 2.7 + - - +
396F ILE* 3.0 35.0 + - + +
447F TYR* 4.0 33.2 - - + +
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Residues in contact with GLN 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250F ARG* 3.2 44.2 + - - +
337F SER* 3.8 19.8 + - - +
389F TYR* 2.8 28.8 + - + +
390F LEU* 3.6 9.2 - - + +
392F ILE* 1.3 78.8 - - - +
394F LYS* 1.3 57.8 + - - +
396F ILE* 4.3 6.2 - - - +
397F GLY* 2.8 27.2 + - - -
401F GLU* 4.0 4.4 + - - -
960Z A 5.2 0.7 - - - +
961Z C 2.9 37.4 + - - +
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Residues in contact with LYS 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F LEU 3.0 16.6 + - - +
391F MET* 3.2 7.6 + - - +
393F GLN* 1.3 74.9 - - - +
395F ARG* 1.3 77.6 + - - +
397F GLY* 3.2 1.9 + - - -
398F GLN* 2.9 28.9 + - + +
918X G 4.6 6.5 - - - +
919X C 3.2 69.3 + - - +
920X C 3.7 14.5 + - - +
958Z G 4.4 6.1 - - - +
959Z C 4.8 2.6 + - - -
960Z A 4.8 14.5 + - - +
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Residues in contact with ARG 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242F LEU* 5.9 0.4 - - + -
246F LEU* 4.1 16.4 - - + -
391F MET* 3.1 36.6 + - + +
392F ILE 3.7 5.4 - - - +
394F LYS* 1.3 86.3 - - - +
396F ILE* 1.3 57.7 + - - +
398F GLN* 3.1 6.6 + - - +
399F SER* 2.8 35.3 + - - +
441F PRO* 3.8 29.2 - - - +
445F SER* 3.9 22.4 + - - -
446F PRO* 2.7 35.6 + - - +
447F TYR* 4.3 9.6 - - + -
451F CYS* 4.4 10.8 - - - -
920X C 3.5 39.0 + - - -
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Residues in contact with ILE 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F TYR* 3.8 14.6 - - + -
246F LEU* 3.8 24.9 - - + +
247F ALA* 4.0 11.0 - - - +
250F ARG* 3.8 29.2 - - - +
392F ILE* 3.0 37.7 + - + +
393F GLN* 3.8 5.4 - - - +
395F ARG* 1.3 75.1 - - - +
397F GLY* 1.3 59.0 + - - +
399F SER* 3.8 6.3 - - - -
400F ALA 2.8 26.0 + - - -
401F GLU* 3.0 46.5 + - + +
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Residues in contact with GLY 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393F GLN 2.8 18.5 + - - -
394F LYS* 3.6 2.2 - - - -
396F ILE* 1.3 77.9 - - - +
398F GLN* 1.3 60.8 + - - +
401F GLU* 4.5 0.7 - - - -
402F GLY* 2.8 32.4 + - - -
405F ALA* 3.8 2.3 - - - +
960Z A 3.8 15.6 - - - +
961Z C 3.6 19.3 + - - -
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Residues in contact with GLN 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394F LYS* 2.9 20.7 + - + +
395F ARG* 3.8 5.7 + - - +
397F GLY* 1.3 78.2 - - - +
399F SER* 1.3 57.9 + - - +
404F LYS 4.5 1.3 - - - +
405F ALA* 3.2 21.1 - - - +
406F TRP* 3.3 40.5 + - + +
436F ASN 4.7 0.6 + - - -
439F GLN* 2.8 46.4 + - - +
440F ILE* 4.0 1.4 - - - +
441F PRO* 3.4 21.6 - - - +
920X C 4.8 7.4 - - - +
960Z A 4.7 6.7 - - - -
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Residues in contact with SER 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239F ILE* 4.0 15.5 + - - +
242F LEU* 5.0 6.1 - - - +
243F TYR* 5.3 4.3 - - - +
246F LEU* 4.8 7.6 - - - +
395F ARG* 2.8 29.3 + - - +
396F ILE* 3.8 5.2 + - - -
398F GLN* 1.3 75.2 - - - +
400F ALA* 1.3 63.2 + - - +
405F ALA* 3.6 2.2 - - - -
406F TRP* 3.6 31.5 + - - +
407F LEU* 3.2 30.0 + - - +
451F CYS* 5.6 1.8 - - - -
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Residues in contact with ALA 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243F TYR* 4.0 34.3 - - + -
396F ILE 2.8 14.8 + - - +
399F SER* 1.3 81.2 + - - +
401F GLU* 1.3 60.6 + - + +
405F ALA* 3.4 14.7 - - - +
407F LEU* 3.7 25.8 - - + +
408F ARG* 3.7 16.6 + - - +
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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