Contacts of the helix formed by residues 320 - 342 (chain B) in PDB entry 1QI9
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 320 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASP 4.9 1.6 - - - +
279A ASN* 3.5 24.0 - - - +
280A ILE* 3.4 18.4 - - + +
292B LEU* 3.8 34.8 - - + -
297B PHE* 4.1 5.8 - - + -
298B ASN 5.3 0.2 + - - -
299B ARG* 4.0 33.2 + - + +
315B PHE* 3.8 22.8 + - + -
319B GLY* 1.3 68.0 - - - -
321B SER* 1.3 61.6 + - - +
322B HIS 3.4 0.2 - - - -
323B TYR* 3.8 5.6 - - + -
324B PHE* 2.8 42.0 + - + -
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.6 10.8 - - - -
331A GLU* 2.6 30.5 + - - +
334A GLN* 3.9 6.8 - - - +
315B PHE* 3.4 32.9 + - - -
316B VAL* 3.7 11.8 + - - +
319B GLY 3.3 0.8 + - - -
320B ILE* 1.3 79.4 - - - +
322B HIS* 1.3 59.3 + - - +
325B ARG* 2.8 37.2 + - - +
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Residues in contact with HIS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B PHE 3.3 2.0 + - - +
316B VAL 3.3 16.1 + - - +
317B ASN* 3.6 2.4 - - - -
318B PHE* 2.9 31.1 + + - +
319B GLY 3.2 10.7 + - - +
321B SER* 1.3 80.3 + - - +
323B TYR* 1.3 62.0 + - - +
325B ARG* 3.7 17.4 + - - +
326B LEU* 3.1 56.5 + - + +
432B LEU* 3.8 13.8 - - + +
506B LEU* 5.2 0.2 - - - +
509B GLU* 4.1 2.6 + - - +
513B PHE* 3.7 34.9 - + - -
519B PHE* 3.9 21.4 - + - -
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Residues in contact with TYR 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA* 2.9 44.7 + - + -
291B LEU* 3.7 15.1 - - - +
292B LEU* 3.9 6.8 + - + -
297B PHE* 3.5 49.2 - + + +
319B GLY 3.2 9.3 + - - +
320B ILE* 3.6 7.0 - - + +
321B SER 3.3 0.2 - - - -
322B HIS* 1.3 80.7 - - - +
324B PHE* 1.4 90.9 + + - +
326B LEU* 3.4 1.7 + - - +
327B ILE* 3.1 27.6 + - + +
428B VAL* 4.4 1.4 - - + +
429B LEU* 3.8 22.4 - - + +
432B LEU* 3.4 27.8 - - + -
433B ILE* 4.8 5.8 - - + -
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Residues in contact with PHE 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ASN* 3.5 31.6 - - + -
280A ILE* 3.7 28.0 - - + -
281A ASN* 4.1 10.8 + - - +
328A GLY* 3.9 8.8 - - - -
285B TYR* 3.7 34.2 - + - -
288B ALA* 4.4 15.7 - - + -
289B LEU* 3.9 21.8 - - + -
292B LEU* 4.1 10.8 - - + -
320B ILE* 2.8 36.2 + - + +
323B TYR* 1.4 94.5 - + - +
325B ARG* 1.3 68.4 + - - +
327B ILE* 3.4 16.8 + - + +
328B GLY 3.4 7.1 + - - -
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLY 3.3 28.5 - - - +
329A ALA* 4.0 9.4 + - - +
331A GLU* 3.8 10.6 - - + +
332A LEU* 3.5 48.4 - - - +
335A ARG* 4.5 12.3 - - - +
316B VAL* 5.0 7.7 + - - +
321B SER* 2.8 25.7 + - - +
322B HIS* 3.7 26.5 + - - +
324B PHE* 1.3 76.3 - - - +
326B LEU* 1.3 71.4 + - - +
328B GLY 3.2 0.5 + - - -
329B ALA* 2.9 29.4 + - - +
509B GLU* 2.8 43.0 + - - -
513B PHE* 5.1 1.6 - - - -
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Residues in contact with LEU 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B HIS* 3.1 44.9 + - + +
325B ARG* 1.3 97.3 - - - +
327B ILE* 1.4 64.8 + - - +
328B GLY 3.1 1.3 - - - -
329B ALA* 4.1 11.2 - - + +
330B ALA* 2.9 33.9 + - + +
428B VAL* 3.7 26.2 - - + -
432B LEU* 4.6 3.6 - - + -
505B THR* 5.2 10.3 - - + -
506B LEU* 3.7 27.6 - - + -
509B GLU* 3.8 14.4 - - - +
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Residues in contact with ILE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ASN* 3.0 31.9 + - + +
284B ALA* 4.9 6.5 - - + +
285B TYR* 4.2 27.1 - - + +
288B ALA* 3.5 28.7 - - + -
323B TYR* 3.1 32.9 + - + +
324B PHE* 3.7 12.8 - - + +
325B ARG 3.3 0.6 - - - -
326B LEU* 1.4 75.0 - - - +
328B GLY* 1.4 57.9 + - - +
425B PHE* 3.3 27.1 - - + +
428B VAL* 4.3 11.0 - - + -
429B LEU* 3.7 21.3 - - + -
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Residues in contact with GLY 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PHE 3.9 7.9 - - - -
325A ARG* 3.3 20.3 - - - -
328A GLY* 4.0 7.2 - - - -
281B ASN* 3.7 13.0 - - - +
324B PHE 3.4 4.2 + - - -
325B ARG 3.2 5.9 + - - -
326B LEU 3.1 0.2 - - - -
327B ILE* 1.4 79.1 - - - +
329B ALA* 1.3 64.3 + - - +
330B ALA 3.2 2.2 - - - -
331B GLU* 3.1 23.4 + - - +
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Residues in contact with ALA 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ARG* 3.6 6.6 + - - +
329A ALA* 3.8 25.8 - - + -
325B ARG* 2.9 23.1 + - - +
326B LEU* 4.1 17.7 - - + -
328B GLY* 1.3 76.7 - - - +
330B ALA* 1.3 57.3 + - - +
331B GLU 3.1 0.7 - - - -
332B LEU* 3.2 27.8 + - - +
505B THR* 6.6 0.2 - - + -
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Residues in contact with ALA 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 2.9 22.0 + - + +
328B GLY 3.2 0.2 - - - -
329B ALA* 1.3 72.7 - - - +
331B GLU* 1.3 55.2 + - - +
332B LEU* 3.0 10.3 + - - +
333B ALA* 3.4 11.6 + - - +
421B GLN* 5.5 0.2 - - - -
424B ALA* 3.6 27.8 - - + +
425B PHE* 4.2 9.6 - - + -
428B VAL* 3.7 21.8 - - + -
502B THR* 4.3 8.5 + - + +
505B THR* 6.3 2.5 - - - -
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Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A SER* 2.6 47.4 + - - +
325A ARG* 3.8 10.4 - - + -
280B ILE* 3.5 16.6 - - + +
328B GLY 3.1 16.8 + - - +
329B ALA 3.1 0.8 - - - -
330B ALA* 1.3 71.4 - - - +
332B LEU* 1.3 57.4 + - - +
333B ALA* 3.1 3.1 - - - -
334B GLN* 2.8 49.9 + - - +
421B GLN* 2.8 37.8 + - - +
425B PHE* 3.7 11.8 - - + -
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Residues in contact with LEU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 6.2 0.9 - - + -
325A ARG* 3.6 33.6 - - - +
509A GLU* 5.4 0.7 - - - +
112B ASP* 3.6 43.7 - - + +
114B SER* 3.8 28.5 - - - +
115B GLY* 5.5 2.0 - - - -
329B ALA 3.2 17.2 + - - +
330B ALA* 3.0 1.5 - - - -
331B GLU* 1.3 78.1 - - - +
333B ALA* 1.3 61.0 + - - +
334B GLN 3.0 1.4 + - - -
335B ARG* 3.1 24.5 + - + +
336B SER* 4.4 1.0 + - - -
501B ILE* 5.4 1.1 - - + -
505B THR* 5.9 3.4 - - + +
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Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA 3.4 14.7 + - - +
331B GLU* 3.1 0.6 - - - +
332B LEU* 1.3 78.1 - - - +
334B GLN* 1.3 59.5 + - - +
335B ARG 3.2 0.2 - - - -
336B SER* 3.1 16.8 + - - +
337B SER* 3.1 12.0 + - - -
420B THR* 4.0 21.7 - - + +
421B GLN* 5.6 1.6 - - - -
424B ALA* 4.5 12.3 - - + -
498B GLY* 4.5 1.8 - - - -
501B ILE* 3.9 35.6 - - + +
502B THR* 5.0 0.4 - - - +
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Residues in contact with GLN 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 3.7 23.5 - - + -
316A VAL* 3.8 15.2 - - + +
321A SER* 3.9 4.7 - - - +
331B GLU* 2.8 43.6 + - - +
333B ALA* 1.3 73.2 - - - +
335B ARG* 1.3 63.5 + - - +
337B SER* 2.9 30.5 + - - -
338B TRP* 3.0 33.7 + - + +
417B GLY* 3.2 25.2 + - - +
420B THR* 4.6 2.1 - - - +
421B GLN* 3.1 22.8 - - - +
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Residues in contact with ARG 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 3.5 25.7 + - + +
317A ASN* 2.7 31.1 + - - +
325A ARG* 4.6 8.7 - - - +
509A GLU* 6.0 0.2 - - - -
513A PHE* 3.8 12.7 - - - -
107B ALA 3.1 27.5 + - - -
108B ALA* 3.5 21.4 - - - +
110B ALA* 3.5 20.3 + - - +
112B ASP* 2.9 41.4 + - - +
118B PHE* 3.8 11.2 - - + +
332B LEU* 3.1 23.4 + - + +
334B GLN* 1.3 77.5 - - - +
336B SER* 1.3 62.8 + - - +
338B TRP* 3.3 7.4 + - - +
339B TYR* 3.1 19.2 + - - +
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Residues in contact with SER 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 4.6 4.5 + - - +
117B ALA 4.3 4.7 + - - -
118B PHE* 3.7 31.1 + - - +
121B THR* 4.3 8.3 + - - -
332B LEU 4.4 0.7 + - - -
333B ALA* 3.1 4.4 + - - -
335B ARG* 1.3 76.4 - - - +
337B SER* 1.3 66.1 + - - +
339B TYR* 3.0 4.3 + - - +
340B GLN* 2.9 26.9 + - - +
497B LEU* 4.4 5.2 - - - -
501B ILE* 3.4 34.0 - - - +
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA 3.1 10.3 + - - -
334B GLN* 2.9 29.4 + - - -
336B SER* 1.3 78.3 - - - +
338B TRP* 1.3 57.0 + - - +
340B GLN* 3.3 2.6 + - - +
341B LYS* 2.9 49.5 + - - +
415B PRO* 3.8 7.9 - - - +
417B GLY* 3.8 5.5 - - - -
420B THR* 3.7 21.3 + - - -
497B LEU* 4.1 10.4 - - - +
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Residues in contact with TRP 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A PHE* 3.3 33.7 - + - -
316A VAL* 3.7 10.8 - - + -
103B VAL* 3.0 27.6 + - + -
104B ASN* 3.2 22.6 + - - +
107B ALA* 3.6 16.6 - - + -
108B ALA* 4.3 4.0 - - - +
334B GLN* 3.0 45.1 + - + +
335B ARG 3.5 5.6 - - - +
336B SER 3.2 0.2 - - - -
337B SER* 1.3 74.5 + - - +
339B TYR* 1.3 64.6 + - - +
341B LYS* 3.4 19.0 + - + -
342B TRP* 3.1 44.3 + + - +
343B GLN* 3.5 6.9 - - - +
411B HIS* 3.6 44.6 - + - -
417B GLY* 4.6 2.7 - - - -
600B VO4 5.7 0.7 - - - -
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Residues in contact with TYR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 3.8 8.5 - - + +
11A ASP* 2.7 35.1 + - + +
18A ARG* 3.5 19.6 + - - -
42B GLN* 3.9 12.6 - - - -
108B ALA* 3.5 13.4 - - + +
109B PHE* 4.3 2.2 - + - -
118B PHE* 3.5 39.7 - + + +
119B SER* 3.5 23.2 - - - -
335B ARG 3.1 8.5 + - - +
336B SER 3.0 9.2 + - - +
338B TRP* 1.3 74.5 - - - +
340B GLN* 1.3 66.1 + - - +
343B GLN* 2.9 60.8 + - + +
344B VAL* 3.1 20.2 + - + -
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Residues in contact with GLN 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLN* 3.0 25.2 + - - +
118B PHE 5.1 1.0 + - - -
121B THR* 3.2 21.0 + - - -
122B THR* 3.8 4.2 - - - +
123B ILE* 3.7 21.8 + - + +
336B SER* 2.9 16.6 + - - +
337B SER 3.7 2.2 - - - +
339B TYR* 1.3 85.0 - - - +
341B LYS* 1.3 56.2 + - - +
344B VAL* 3.5 12.3 - - - +
345B HIS* 2.9 58.7 + - - -
414B TYR 3.6 3.6 - - - +
415B PRO* 3.6 19.3 - - + -
497B LEU* 4.5 13.2 - - + -
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Residues in contact with LYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B SER* 2.9 23.4 + - - +
338B TRP* 3.5 40.4 - - + +
339B TYR 3.3 0.2 - - - -
340B GLN* 1.3 76.7 - - - +
342B TRP* 1.3 63.0 + - + +
346B ARG* 2.9 30.1 + - - -
349B ARG* 4.0 1.4 - - - +
411B HIS* 3.1 25.5 + - + +
412B PRO* 3.0 37.7 + - + +
413B SER 4.0 1.0 + - - -
414B TYR 3.2 13.7 + - - +
415B PRO* 2.7 32.0 + - + +
417B GLY 4.0 1.6 - - - +
600B VO4 2.9 22.6 + - - -
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Residues in contact with TRP 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B PHE* 3.8 28.0 - + - -
74B LEU* 4.1 17.3 - - + -
78B ILE* 3.3 30.9 - - + +
102B LEU* 4.3 9.2 - - + -
103B VAL 3.4 23.4 + - - -
105B PRO* 3.9 23.7 - - + +
338B TRP* 3.1 54.0 + + - +
341B LYS* 1.3 82.8 - - + +
343B GLN* 1.3 74.3 + - - +
344B VAL 3.4 0.2 - - - -
346B ARG* 2.7 36.4 + - - +
410B THR 3.7 13.9 - - - -
411B HIS* 3.5 18.0 - - + +
412B PRO* 3.5 16.2 - - + -
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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