Contacts of the helix formed by residues 354 - 382 (chain L) in PDB entry 6PSU
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 354 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L HIS* 5.9 5.8 - - + -
310L GLU* 4.5 6.7 - - - -
311L THR* 5.1 11.4 - - + -
348L GLU* 4.7 6.1 - - - -
353L LEU* 1.3 80.2 - - + +
355L ILE* 1.3 59.4 + - - +
356L GLU* 3.7 6.3 + - - +
357L GLN* 2.9 47.7 + - - +
358L VAL* 3.3 5.4 + - - +
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Residues in contact with ILE 355 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L MET* 5.5 0.4 - - - -
280L VAL* 3.3 31.4 - - + -
306L PHE* 6.5 0.2 - - + -
310L GLU* 4.1 8.3 + - + +
311L THR* 5.6 1.0 - - + +
344L LEU* 4.4 11.0 - - + -
347L ILE* 3.3 17.0 - - + +
348L GLU* 3.2 40.0 + - + +
351L THR* 3.0 31.2 - - + +
354L THR* 1.3 73.7 - - - +
356L GLU* 1.3 51.3 + - - +
357L GLN 3.3 0.2 - - - -
358L VAL* 3.3 7.4 + - + -
359L LYS* 2.6 45.3 + - + +
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Residues in contact with GLU 356 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306L PHE* 5.7 1.7 - - - -
307L THR* 5.5 9.1 - - + +
310L GLU* 2.9 35.7 + - - +
354L THR* 3.1 4.9 - - - +
355L ILE* 1.3 75.8 - - - +
357L GLN* 1.3 63.7 + - - +
359L LYS* 3.0 47.2 + - - +
360L ASP* 3.2 29.9 + - + +
363L ARG* 5.8 1.6 - - - -
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Residues in contact with GLN 357 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242L HIS* 3.7 26.1 + - - -
246L GLN* 4.2 9.7 + - - +
353L LEU* 3.0 41.4 - - - +
354L THR* 2.9 25.3 + - - +
356L GLU* 1.3 77.8 - - - +
358L VAL* 1.3 62.6 + - + +
359L LYS 3.2 0.2 + - - -
360L ASP* 3.5 1.6 + - - +
361L ILE* 2.9 38.8 + - + +
364L ARG* 4.8 0.3 + - - -
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Residues in contact with VAL 358 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137L TYR* 5.0 9.6 - - + -
138L PRO* 6.3 0.4 - - + -
276L MET* 4.2 27.6 - - + -
277L MET* 5.2 5.4 - - - -
280L VAL* 6.4 1.1 - - + -
351L THR* 3.3 46.9 - - + +
353L LEU* 4.7 2.9 - - + +
354L THR 3.6 11.9 - - - +
355L ILE* 3.3 8.4 + - + +
357L GLN* 1.3 76.1 - - + +
359L LYS* 1.3 53.4 + - - +
361L ILE* 3.4 15.4 - - + +
362L ASN* 2.7 38.9 + - + +
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Residues in contact with LYS 359 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277L MET* 3.3 30.5 - - + +
280L VAL* 6.0 0.4 - - + -
284L GLU* 5.5 6.0 + - - +
306L PHE* 5.5 11.2 - - + -
307L THR* 6.1 2.0 - - - +
310L GLU* 5.8 0.2 - - - +
355L ILE* 2.6 34.9 + - + +
356L GLU* 3.0 36.6 + - - +
357L GLN 3.1 0.2 - - - -
358L VAL* 1.3 72.0 - - - +
360L ASP* 1.3 53.4 + - - +
361L ILE 3.0 0.5 + - - -
362L ASN* 2.7 9.2 - - - +
363L ARG* 2.6 43.6 + - - +
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Residues in contact with ASP 360 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356L GLU* 3.2 20.1 + - + +
357L GLN* 3.8 1.8 - - - +
359L LYS* 1.3 77.1 - - - +
361L ILE* 1.3 56.5 + - - +
363L ARG* 3.0 41.2 + - - +
364L ARG* 2.9 42.9 + - - +
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Residues in contact with ILE 361 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133L SER* 2.9 39.7 + - - +
136L GLU* 2.9 48.9 - - + +
137L TYR* 3.9 9.4 - - + +
138L PRO* 5.4 0.9 - - + -
273L MET* 4.9 3.4 - - - -
357L GLN* 2.9 38.7 + - + +
358L VAL* 3.4 16.2 - - + +
359L LYS 3.0 0.4 - - - -
360L ASP* 1.3 78.5 - - - +
362L ASN* 1.3 62.6 + - + +
364L ARG* 3.1 18.0 + - - +
365L MET 2.9 21.7 + - - -
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Residues in contact with ASN 362 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273L MET* 3.9 15.8 + - + -
274L ARG* 3.3 14.3 - - - +
277L MET* 3.1 42.0 - - - +
281L ARG* 4.9 1.2 - - - +
358L VAL* 2.7 16.3 + - + +
359L LYS* 2.7 29.1 - - - +
361L ILE* 1.3 77.6 - - + +
363L ARG* 1.3 65.5 + - - +
365L MET* 3.4 24.6 - - + +
366L SER* 3.0 28.6 + - - -
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Residues in contact with ARG 363 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356L GLU* 5.8 1.8 - - - -
359L LYS* 2.6 29.6 + - - +
360L ASP* 3.0 34.1 + - - +
362L ASN* 1.3 74.5 + - - +
364L ARG* 1.3 52.2 + - - +
366L SER* 4.1 1.9 - - - -
367L ILE* 2.8 74.0 + - + +
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Residues in contact with ARG 364 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L GLN* 4.5 19.9 + - + +
132L CYS* 4.7 8.0 - - - -
133L SER* 4.0 9.4 + - - +
136L GLU* 3.6 26.7 + - - +
357L GLN 4.8 0.2 + - - -
360L ASP* 2.9 46.3 + - - +
361L ILE* 3.1 43.0 + - - +
363L ARG* 1.3 79.8 - - - +
365L MET* 1.3 65.1 + - - +
367L ILE* 3.2 14.3 + - + +
368L GLY* 3.0 19.9 + - - -
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Residues in contact with MET 365 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L GLN* 4.4 4.1 - - - +
130L VAL* 3.3 41.1 - - + +
133L SER* 3.0 23.3 - - - +
270L VAL* 5.1 6.5 - - - -
273L MET* 3.4 37.7 - - + +
274L ARG* 4.4 11.7 - - - +
361L ILE 2.9 7.1 + - - +
362L ASN* 3.4 36.1 - - + +
363L ARG 3.2 0.6 - - - -
364L ARG* 1.3 79.0 - - - +
366L SER* 1.3 61.3 + - - +
368L GLY* 3.1 1.0 + - - -
369L GLU* 2.4 38.0 + - + +
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Residues in contact with SER 366 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274L ARG* 4.9 11.6 + - - -
362L ASN* 3.0 15.5 + - - -
363L ARG* 4.4 1.6 - - - -
365L MET* 1.3 85.0 - - - +
367L ILE* 1.3 60.5 + - - +
369L GLU* 3.3 18.1 - - - +
370L ALA* 2.9 29.7 + - - +
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Residues in contact with ILE 367 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L GLN* 5.0 4.0 - - - +
363L ARG* 2.8 76.4 + - + +
364L ARG* 3.3 10.8 - - + +
365L MET 3.1 0.2 - - - -
366L SER* 1.3 79.0 - - - +
368L GLY* 1.3 62.7 + - - +
370L ALA* 4.3 1.9 - - - +
371L LYS* 3.5 16.5 + - - +
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Residues in contact with GLY 368 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126L GLY* 4.5 1.1 - - - -
129L GLN* 3.2 34.1 - - - +
364L ARG 3.0 11.3 + - - -
365L MET 3.6 1.1 - - - -
367L ILE* 1.3 76.7 - - - +
369L GLU* 1.3 53.0 - - - +
371L LYS* 3.0 10.1 + - - +
372L ALA* 2.2 41.8 + - - +
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Residues in contact with GLU 369 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L VAL* 3.8 21.4 - - + +
365L MET* 2.4 26.0 + - + +
366L SER* 3.3 18.0 - - - +
367L ILE 3.3 0.2 - - - -
368L GLY* 1.3 71.5 - - - +
370L ALA* 1.3 53.4 + - - +
372L ALA* 3.0 9.1 + - + +
373L ARG* 2.4 82.7 + - + +
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Residues in contact with ALA 370 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366L SER 2.9 17.2 + - - +
367L ILE* 4.3 2.5 - - - +
369L GLU* 1.3 76.8 + - - +
371L LYS* 1.3 52.4 + - - +
373L ARG* 3.3 30.9 + - - +
374L ARG* 2.3 46.0 + - + +
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Residues in contact with LYS 371 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L ARG* 3.4 52.8 + - + +
125L ASP* 3.7 9.7 + - - +
126L GLY 3.7 2.6 - - - +
129L GLN* 3.1 33.9 + - - +
367L ILE 3.5 13.1 + - - +
368L GLY* 3.0 8.2 + - - +
370L ALA* 1.3 76.6 - - - +
372L ALA* 1.3 53.0 + - - +
374L ARG* 3.0 10.9 + - + +
375L ALA* 2.6 31.7 + - - +
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Residues in contact with ALA 372 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L ILE* 3.8 12.7 - - + +
126L GLY* 3.3 31.9 - - - -
127L ILE* 4.3 3.1 - - + +
130L VAL* 5.9 0.2 - - + -
368L GLY 2.2 31.3 + - - +
369L GLU* 3.2 10.3 - - + +
371L LYS* 1.3 70.6 - - - +
373L ARG* 1.3 62.5 + - + +
375L ALA* 3.0 17.3 + - - +
376L LYS* 3.2 18.5 + - - +
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Residues in contact with ARG 373 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286J ALA* 4.9 13.7 + - - +
369L GLU* 2.4 63.2 + - + +
370L ALA* 3.4 26.0 + - - +
372L ALA* 1.3 68.0 - - + +
374L ARG* 1.3 64.6 + - - +
376L LYS* 3.0 27.5 + - - +
377L LYS* 2.9 70.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 374 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122L ARG* 4.8 2.0 - - - +
370L ALA* 2.3 40.9 + - + +
371L LYS* 3.1 14.1 - - + +
373L ARG* 1.3 68.3 - - - +
375L ALA* 1.3 59.6 + - - +
377L LYS* 3.4 21.5 + - + +
378L GLU* 2.9 55.7 + - - +
381L GLU* 4.5 4.2 + - - -
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Residues in contact with ALA 375 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L ILE* 3.0 28.0 - - + +
122L ARG* 4.0 13.7 - - + +
123L ILE* 3.2 35.0 - - + +
371L LYS* 2.6 14.8 + - + +
372L ALA 3.0 5.4 + - - +
374L ARG* 1.3 74.0 - - - +
376L LYS* 1.3 62.2 + - - +
378L GLU* 3.0 23.3 + - - +
379L MET 3.3 2.3 + - - -
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Residues in contact with LYS 376 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123L ILE* 3.6 32.3 - - + -
372L ALA 3.6 3.1 - - - +
373L ARG* 3.0 35.1 + - - +
375L ALA* 1.3 77.0 - - - +
377L LYS* 1.3 64.8 + - + +
379L MET* 2.9 14.2 + - - +
380L VAL* 3.0 15.6 + - - +
416L VAL* 3.4 36.7 - - + +
417L ASP* 4.7 17.3 + - - +
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Residues in contact with LYS 377 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286J ALA 4.6 12.7 + - - -
287J ALA 5.2 0.9 - - - -
288J PRO* 4.5 26.5 - - + -
373L ARG* 2.9 64.0 + - - +
374L ARG* 3.7 26.0 - - - +
376L LYS* 1.3 77.3 - - + +
378L GLU* 1.3 56.8 + - - +
380L VAL* 2.9 23.9 - - + +
381L GLU* 2.6 29.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 378 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L LEU* 3.9 11.9 - - + +
119L ILE* 3.8 16.5 - - + +
122L ARG* 3.1 33.2 + - - -
374L ARG* 2.9 53.1 + - - +
375L ALA* 3.0 20.8 - - - +
376L LYS 3.1 0.2 - - - -
377L LYS* 1.3 78.4 - - - +
379L MET* 1.3 60.9 + - - +
381L GLU* 3.3 29.0 - - - +
382L ALA* 3.7 3.5 + - - +
----------------------------------------------------------
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Residues in contact with MET 379 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L LEU* 4.5 8.3 - - + -
116L GLU* 4.9 16.6 - - + +
119L ILE* 3.9 20.8 - - + +
120L ALA* 4.6 8.1 - - + +
123L ILE* 3.3 33.9 - - + -
375L ALA 3.3 3.6 + - - +
376L LYS 2.9 6.0 + - - +
378L GLU* 1.3 78.3 - - - +
380L VAL* 1.3 65.5 + - - +
382L ALA* 3.1 21.5 + - - +
383L ASN* 3.6 3.5 + - + +
416L VAL* 4.4 24.5 - - + +
419L PHE* 4.7 20.6 - - + -
427L PHE* 4.8 19.1 - - + -
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Residues in contact with VAL 380 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288J PRO* 4.1 20.4 - - + -
291J ILE* 4.4 16.6 - - + -
376L LYS 3.0 11.9 + - - +
377L LYS* 2.9 27.8 - - - +
379L MET* 1.3 77.3 - - - +
381L GLU* 1.3 64.3 + - + +
383L ASN 3.2 5.8 + - - +
384L LEU* 3.0 31.9 - - + +
412L LEU* 3.9 27.7 - - + +
413L MET* 4.8 11.2 - - + -
416L VAL* 4.4 15.4 - - + +
----------------------------------------------------------
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Residues in contact with GLU 381 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288J PRO* 5.8 3.1 - - + +
290J ILE* 5.3 15.7 - - + +
108L VAL* 3.0 33.9 - - + +
374L ARG* 4.5 5.7 + - - -
377L LYS* 2.6 31.9 - - - +
378L GLU* 3.3 18.5 - - - +
379L MET 3.1 0.4 - - - -
380L VAL* 1.3 80.7 - - + +
382L ALA* 1.3 58.5 + - - +
383L ASN 3.0 5.9 + - - -
384L LEU* 3.6 17.2 + - - +
----------------------------------------------------------
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Residues in contact with ALA 382 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L VAL* 4.1 4.9 - - + -
109L GLU 3.0 29.8 - - - +
110L LEU* 4.3 7.8 - - - +
111L LEU* 3.5 42.6 + - + +
116L GLU* 6.1 1.0 - - - +
378L GLU 3.7 1.4 + - - +
379L MET* 3.1 9.6 + - - +
381L GLU* 1.3 78.7 - - + +
383L ASN* 1.3 63.9 + - - +
384L LEU 3.9 0.2 - - - -
385L ARG* 6.2 1.8 - - - -
54O T 5.0 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