Contacts of the helix formed by residues 355 - 382 (chain F) in PDB entry 3IYD
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 ILE 355 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F VAL* 4.0 16.6 - - + -
284F GLU* 3.3 19.1 - - - +
309F ASN 5.1 0.7 - - - +
310F GLU* 3.2 48.0 - - + +
311F THR* 4.3 2.0 - - - +
344F LEU* 3.5 21.8 - - + -
348F GLU* 3.4 41.0 + - + +
353F LEU 4.7 0.2 - - - -
354F THR* 1.3 75.2 - - + +
356F GLU* 1.3 59.0 + - - +
358F VAL* 3.2 21.3 - - + +
359F LYS* 4.2 10.8 + - - +
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Residues in contact with GLU 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F THR* 4.2 29.2 - - - +
308F GLY 5.5 4.7 - - - +
309F ASN 6.1 0.4 - - - +
310F GLU* 3.5 16.9 + - + +
354F THR* 3.0 13.9 - - + +
355F ILE* 1.3 82.1 - - - +
357F GLN* 1.3 60.7 + - - +
359F LYS* 3.9 8.2 + - - +
360F ASP* 3.5 18.3 - - - +
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Residues in contact with GLN 357 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F HIS 4.5 2.2 + - - -
243F ALA* 5.2 5.3 - - - +
246F GLN* 3.0 46.6 + - - +
353F LEU* 4.0 6.9 - - + +
354F THR* 3.1 33.2 + - + +
356F GLU* 1.3 75.6 - - - +
358F VAL* 1.3 63.9 + - - +
359F LYS 3.1 2.7 - - - -
360F ASP* 3.0 31.0 + - + +
361F ILE* 3.1 20.8 - - + +
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Residues in contact with VAL 358 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F TYR* 5.0 13.7 - - + -
277F MET* 3.7 31.7 - - + +
280F VAL* 6.0 1.6 - - + -
351F THR* 5.6 8.7 - - + +
353F LEU* 4.5 24.5 - - + -
354F THR 2.9 15.8 + - - +
355F ILE* 3.2 28.9 - - + +
357F GLN* 1.3 78.7 - - - +
359F LYS* 1.3 64.8 + - + +
361F ILE* 3.6 20.5 + - + +
362F ASN* 3.9 4.2 + - - +
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Residues in contact with LYS 359 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F MET* 3.3 40.1 - - + +
280F VAL* 5.5 5.3 - - - +
281F ARG* 4.5 21.6 - - - +
355F ILE* 4.5 11.8 + - - +
356F GLU* 3.9 11.4 + - - +
357F GLN 3.1 0.8 - - - -
358F VAL* 1.3 79.9 - - - +
360F ASP* 1.3 62.6 + - - +
361F ILE 3.2 0.2 - - - -
362F ASN* 3.4 1.1 + - + -
363F ARG* 3.0 37.2 + - + +
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Residues in contact with ASP 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356F GLU* 3.5 15.9 - - - +
357F GLN* 3.0 22.0 + - + +
359F LYS* 1.3 82.7 - - - +
361F ILE* 1.3 61.7 + - + +
363F ARG* 3.2 29.8 + - - +
364F ARG* 2.9 31.5 + - - +
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Residues in contact with ILE 361 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F SER* 3.5 27.8 - - - +
136F GLU* 4.1 20.4 - - + +
137F TYR* 5.1 4.0 - - + -
273F MET* 3.9 25.6 - - + -
353F LEU* 5.2 8.1 - - + -
357F GLN* 3.1 25.4 - - + +
358F VAL* 3.8 11.4 - - + +
359F LYS 3.2 0.8 - - - -
360F ASP* 1.3 78.6 - - + +
362F ASN* 1.3 59.6 + - + +
364F ARG* 3.3 37.6 - - - +
365F MET* 3.1 18.8 - - - +
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Residues in contact with ASN 362 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F MET* 5.1 4.5 + - + -
274F ARG* 4.4 21.0 + - - +
277F MET* 3.3 22.2 - - + +
281F ARG* 2.8 33.1 - - - +
358F VAL 3.9 3.3 + - - +
359F LYS* 3.4 4.3 + - + +
361F ILE* 1.3 76.4 - - + +
363F ARG* 1.3 66.0 + - - +
364F ARG 3.1 2.5 - - - -
365F MET* 3.0 39.0 + - + +
366F SER* 3.4 16.9 + - - -
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Residues in contact with ARG 363 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359F LYS* 3.0 25.5 + - + +
360F ASP* 3.2 32.6 + - - +
362F ASN* 1.3 77.0 - - - +
364F ARG* 1.3 85.8 + - - +
365F MET 3.8 0.2 + - - -
366F SER* 3.9 9.2 + - - -
367F ILE* 3.4 24.4 - - - +
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Residues in contact with ARG 364 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F GLN* 3.9 15.8 + - + +
132F CYS* 5.1 6.2 - - - -
133F SER* 3.0 23.2 + - - +
136F GLU* 3.9 16.2 + - - +
360F ASP* 2.9 40.1 + - - +
361F ILE* 3.3 40.9 - - - +
363F ARG* 1.3 104.5 - - - +
365F MET* 1.3 63.2 + - - +
366F SER 3.3 1.1 - - - -
367F ILE* 3.6 21.1 + - + +
368F GLY 3.7 4.9 + - - -
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Residues in contact with MET 365 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F GLN 4.7 3.4 - - - +
130F VAL* 4.4 22.0 - - + +
133F SER* 3.5 25.1 - - - +
134F VAL* 4.2 14.8 - - - -
270F VAL* 4.8 15.5 - - + +
273F MET* 3.6 34.5 - - + +
274F ARG* 5.9 4.9 - - + +
361F ILE 3.1 13.0 - - - +
362F ASN* 3.0 36.4 + - - +
364F ARG* 1.3 76.2 - - - +
366F SER* 1.3 57.0 + - - +
367F ILE 3.1 5.4 - - - -
368F GLY* 3.6 1.4 + - - +
369F GLU* 3.2 32.3 + - - +
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Residues in contact with SER 366 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362F ASN* 3.4 16.6 + - - -
363F ARG* 3.9 10.8 + - - -
364F ARG 3.3 0.4 - - - -
365F MET* 1.3 77.3 - - - +
367F ILE* 1.3 63.5 + - - +
369F GLU* 3.4 22.6 + - - +
370F ALA* 3.2 24.8 + - - +
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Residues in contact with ILE 367 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F GLN* 3.9 13.0 + - - +
363F ARG* 3.4 25.4 - - - +
364F ARG* 3.7 13.7 - - + +
365F MET 3.1 0.6 - - - -
366F SER* 1.3 83.8 - - - +
368F GLY* 1.3 62.9 + - - +
369F GLU 3.4 0.2 - - - -
370F ALA* 3.6 3.3 + - - +
371F LYS* 3.3 24.7 + - + +
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Residues in contact with GLY 368 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F GLY* 3.3 38.9 - - - -
127F ILE* 5.6 0.2 - - - +
129F GLN* 3.2 22.9 - - - +
130F VAL* 5.0 2.5 - - - -
364F ARG 3.7 2.2 + - - -
365F MET 3.6 4.7 + - - -
367F ILE* 1.3 79.4 - - - +
369F GLU* 1.3 61.6 + - - +
370F ALA 3.3 0.2 - - - -
371F LYS* 3.8 2.3 + - - +
372F ALA* 3.5 15.2 + - - +
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Residues in contact with GLU 369 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F VAL* 4.9 4.3 - - + +
181F VAL* 3.3 27.8 - - - +
182F GLY* 3.8 10.6 - - - +
274F ARG* 3.5 22.2 + - - -
365F MET* 3.2 20.8 + - - +
366F SER* 3.4 27.1 + - - +
368F GLY* 1.3 75.7 - - - +
370F ALA* 1.3 60.8 + - - +
371F LYS 3.5 0.2 - - - -
372F ALA* 4.0 2.0 - - - -
373F ARG* 3.0 57.4 + - - +
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Residues in contact with ALA 370 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366F SER 3.2 21.0 + - - +
367F ILE* 3.9 5.2 - - + +
368F GLY 3.3 0.4 - - - -
369F GLU* 1.3 79.7 - - - +
371F LYS* 1.3 63.5 + - - +
372F ALA 3.1 1.8 - - - -
373F ARG* 3.4 14.7 - - - +
374F ARG* 3.3 26.5 + - - +
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Residues in contact with LYS 371 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ARG* 3.2 57.6 + - + +
125F ASP* 3.3 24.9 + - - +
126F GLY* 3.2 21.1 - - - +
129F GLN* 4.1 19.3 - - - -
367F ILE* 3.3 14.0 + - + +
368F GLY 4.3 1.8 - - - +
369F GLU 3.5 0.2 - - - -
370F ALA* 1.3 77.8 - - - +
372F ALA* 1.3 57.2 + - - +
374F ARG* 5.1 1.6 - - - +
375F ALA* 3.2 21.9 + - - +
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Residues in contact with ALA 372 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122F ARG 4.0 7.4 - - - +
123F ILE* 3.8 27.4 - - + +
126F GLY* 4.7 0.2 - - - -
127F ILE* 4.6 10.1 - - + -
182F GLY* 5.2 3.1 - - - +
368F GLY 3.5 15.9 + - - +
369F GLU* 4.2 4.0 - - - +
370F ALA 3.1 0.4 - - - -
371F LYS* 1.3 80.5 - - - +
373F ARG* 1.3 64.7 + - - +
374F ARG 3.5 0.2 - - - -
375F ALA* 3.3 3.7 + - - +
376F LYS* 3.0 38.8 + - - +
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Residues in contact with ARG 373 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LEU 5.5 6.1 + - - -
286D ALA* 5.9 0.7 - - - +
182F GLY 4.0 12.1 + - - +
183F SER 4.5 11.1 + - - -
184F GLU* 3.1 42.4 - - + +
369F GLU* 3.0 69.5 + - - +
370F ALA* 3.4 18.8 + - - +
372F ALA* 1.3 76.5 - - - +
374F ARG* 1.3 58.4 + - - +
376F LYS* 3.0 26.0 + - - +
377F LYS* 3.1 23.9 + - - +
----------------------------------------------------------
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Residues in contact with ARG 374 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370F ALA 3.3 14.9 + - - +
371F LYS* 5.1 1.3 - - - +
373F ARG* 1.3 79.6 - - - +
375F ALA* 1.3 61.7 + - - +
377F LYS* 3.4 37.9 + - + +
378F GLU* 4.1 14.6 + - - +
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Residues in contact with ALA 375 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ILE* 3.9 31.0 - - + +
122F ARG* 3.9 34.8 - - + +
123F ILE* 5.1 1.9 - - + +
371F LYS 3.2 21.4 + - - +
372F ALA* 3.3 8.4 + - - +
373F ARG 3.1 0.8 - - - -
374F ARG* 1.3 78.5 - - - +
376F LYS* 1.3 62.2 + - + +
377F LYS 3.4 0.2 - - - -
378F GLU* 4.1 8.9 + - - +
379F MET* 4.4 2.9 - - - +
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Residues in contact with LYS 376 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ILE* 3.9 39.5 - - + +
127F ILE* 6.1 1.6 - - - +
179F THR 5.1 2.2 + - - -
182F GLY* 3.1 34.6 + - - -
183F SER* 3.6 3.2 - - - +
184F GLU* 3.5 12.3 - - - +
372F ALA* 3.1 23.1 - - - +
373F ARG* 3.0 7.9 + - - +
375F ALA* 1.3 76.9 - - - +
377F LYS* 1.3 60.3 + - - +
378F GLU 3.1 6.1 + - - -
379F MET* 3.4 11.1 + - - +
380F VAL* 3.3 22.3 + - - +
416F VAL* 4.3 17.4 - - + +
417F ASP* 3.0 38.2 + - - +
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Residues in contact with LYS 377 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA 4.2 16.2 + - - +
288D PRO* 4.6 24.6 - - + +
184F GLU* 3.2 13.0 - - - +
373F ARG* 3.2 41.5 - - - +
374F ARG* 3.4 32.8 + - + +
376F LYS* 1.3 78.8 - - - +
378F GLU* 1.3 58.8 + - + +
379F MET 3.4 0.4 - - - -
380F VAL* 3.8 9.6 - - - +
381F GLU* 3.4 29.0 - - - +
----------------------------------------------------------
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Residues in contact with GLU 378 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ILE* 3.8 34.0 - - + +
374F ARG* 4.1 16.4 + - - +
375F ALA* 4.4 5.1 - - - +
376F LYS 3.1 0.8 - - - -
377F LYS* 1.3 82.2 - - + +
379F MET* 1.3 60.3 + - - +
381F GLU* 4.2 6.3 - - - +
382F ALA* 3.7 22.7 + - - +
----------------------------------------------------------
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Residues in contact with MET 379 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F GLU* 3.8 45.8 - - + +
119F ILE* 3.7 26.0 - - + -
120F ALA* 5.1 0.7 - - - -
123F ILE* 4.7 13.2 - - - -
375F ALA 4.4 6.7 - - - +
376F LYS* 3.4 3.5 + - - +
377F LYS 3.4 0.2 - - - -
378F GLU* 1.3 78.6 - - - +
380F VAL* 1.3 57.4 + - - +
381F GLU 3.2 4.9 - - - -
383F ASN* 3.1 38.7 + - - +
412F LEU* 4.2 3.1 - - - +
416F VAL* 3.6 26.0 - - + -
419F PHE* 5.1 7.0 - - + -
427F PHE* 3.7 35.7 - - + -
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Residues in contact with VAL 380 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D PRO* 5.4 8.1 - - + +
291D ILE* 6.1 1.0 - - - +
184F GLU* 4.2 14.8 - - - +
376F LYS* 3.3 18.8 - - + +
377F LYS* 3.8 15.3 - - + +
379F MET* 1.3 78.9 - - - +
381F GLU* 1.3 56.5 + - + +
383F ASN 4.7 0.9 - - - -
384F LEU* 3.3 21.9 - - - +
412F LEU* 4.3 13.9 - - + +
413F MET* 3.6 43.8 - - + +
416F VAL* 3.9 22.9 - - + -
----------------------------------------------------------
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Residues in contact with GLU 381 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D PRO* 4.4 7.7 - - + +
290D ILE* 3.4 43.8 - - + +
291D ILE* 6.5 0.2 - - + -
377F LYS 3.4 20.0 - - - +
378F GLU* 4.7 4.7 - - - +
379F MET 3.2 0.2 - - - -
380F VAL* 1.3 81.8 - - + +
382F ALA* 1.3 60.2 + - + +
383F ASN 3.2 4.3 - - - -
384F LEU* 3.3 27.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 382 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F GLU 3.7 18.1 + - - +
381F GLU* 1.3 78.1 - - + +
383F ASN* 1.3 69.5 + - - +
384F LEU 3.5 1.3 + - - -
385F ARG* 5.0 12.7 + - - +
386F LEU* 5.2 1.7 - - - +
----------------------------------------------------------
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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