Contacts of the helix formed by residues 488 - 512 (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 ARG 488 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLN* 3.2 12.5 + - - +
140B GLU* 2.7 49.0 + - - +
141B VAL* 5.1 2.2 - - - +
174B PHE* 5.5 1.0 - - - -
177B LEU* 3.7 24.1 - - - +
178B ASP* 3.3 33.0 + - - +
179B ALA 3.8 2.6 + - - -
180B VAL* 3.8 18.7 - - - +
193B GLN 5.4 0.4 + - - -
195B PHE* 4.1 1.8 - - - +
196B ARG 3.0 34.4 + - - +
197B ALA* 4.2 1.6 - - - +
478B PHE* 3.7 23.6 - - + -
481B GLN* 3.4 19.0 - - - +
487B TYR* 1.3 72.0 - - - +
489B PHE* 1.4 61.5 + - - +
491B GLY 3.1 1.2 + - - -
492B ILE* 2.9 29.5 + - + +
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Residues in contact with PHE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 3.5 23.1 - - + -
127B PRO* 3.7 27.8 - - + -
134B LEU* 4.0 8.1 - - + -
137B GLN* 3.0 51.0 + - + -
178B ASP* 3.5 24.5 - - - +
347B PHE* 3.9 11.7 - + - -
414B TYR* 3.6 17.6 - + + -
487B TYR* 3.3 37.0 - + + -
488B ARG* 1.4 74.6 - - - +
490B ASP* 1.3 87.3 + - - +
493B GLN* 3.0 30.0 + - + +
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Residues in contact with ASP 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B SER* 2.7 42.0 + - - +
414B TYR* 3.3 18.1 - - - +
415B PRO* 3.8 0.5 - - - +
416B SER* 3.1 24.8 + - - +
486B HIS* 2.7 24.2 + - + +
487B TYR* 2.9 27.2 + - - +
489B PHE* 1.3 91.4 - - - +
491B GLY* 1.4 57.3 + - - +
494B GLY* 3.2 19.2 + - - -
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Residues in contact with GLY 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B SER* 4.5 2.5 - - - -
419B ALA* 3.1 19.9 - - - +
477B ALA* 4.1 5.4 - - - -
478B PHE* 4.9 0.7 - - - -
481B GLN* 3.5 19.1 - - - -
487B TYR 3.2 3.6 + - - -
488B ARG 3.1 3.4 + - - -
490B ASP* 1.4 79.2 - - - +
492B ILE* 1.3 60.9 + - - +
495B LEU* 3.0 32.5 + - - +
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Residues in contact with ILE 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 3.6 38.4 - - + +
179B ALA* 4.3 8.3 - - + +
197B ALA* 3.9 19.3 - - + -
199B PHE* 3.6 28.7 - - + -
474B VAL* 5.3 0.7 - - + -
478B PHE* 3.8 26.0 - - + -
488B ARG* 2.9 24.2 + - + +
491B GLY* 1.3 69.3 - - - -
493B GLN* 1.3 69.6 + - - +
495B LEU* 3.4 9.3 + - + +
496B LEU* 3.1 33.7 + - + +
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Residues in contact with GLN 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 4.2 9.5 - - + +
124B PRO* 3.3 29.8 - - + +
178B ASP* 2.8 30.1 + - - +
414B TYR* 3.4 31.4 - - + +
415B PRO* 4.6 2.2 - - - -
489B PHE* 3.0 23.1 + - + +
492B ILE* 1.3 79.1 - - - +
494B GLY* 1.3 58.3 + - - +
496B LEU* 3.3 18.6 + - - +
497B LEU* 2.9 30.9 + - - +
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Residues in contact with GLY 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B PRO* 3.7 10.0 - - - +
419B ALA* 3.7 0.7 - - - -
420B THR* 3.3 34.1 - - - -
490B ASP 3.2 21.2 + - - -
491B GLY 3.9 0.4 - - - -
493B GLN* 1.3 76.4 - - - +
495B LEU* 1.4 61.0 + - - +
497B LEU* 3.1 4.8 + - - +
498B GLY 3.0 20.4 + - - -
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Residues in contact with LEU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 3.9 19.3 - - + -
419B ALA* 3.2 25.3 + - + +
422B ASN 4.1 0.4 - - - -
423B GLY* 3.5 20.6 - - - +
473B ALA* 3.8 25.8 - - + +
474B VAL* 3.8 28.3 - - + -
477B ALA* 4.1 11.7 - - + -
478B PHE* 5.5 0.2 - - + -
491B GLY 3.0 25.4 + - - +
492B ILE* 3.6 10.5 - - + +
494B GLY* 1.4 74.0 - - - +
496B LEU* 1.3 60.3 + - - +
498B GLY 3.5 0.7 + - - -
499B GLU 3.1 17.7 + - - -
524B PHE* 3.6 18.1 - - + -
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B PHE* 4.0 22.4 - - + -
492B ILE* 3.1 34.2 + - + +
493B GLN* 3.7 24.5 - - - +
495B LEU* 1.3 72.2 - - - +
497B LEU* 1.3 67.5 + - - +
499B GLU* 3.3 21.8 + - - +
500B THR* 3.0 28.6 + - - +
524B PHE* 4.7 5.8 - - + -
525B THR* 4.6 12.8 - - + +
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Residues in contact with LEU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 3.6 32.1 - - + +
122B THR 4.4 4.9 - - - +
123B ILE* 3.9 26.9 - - + +
336B SER* 4.4 3.4 - - - -
337B SER* 4.1 28.3 - - - +
340B GLN* 4.5 6.7 - - + -
415B PRO* 4.4 6.1 - - + -
420B THR* 4.1 14.1 - - + +
493B GLN 2.9 14.2 + - - +
494B GLY* 3.4 8.1 - - - +
496B LEU* 1.3 76.8 - - - +
498B GLY* 1.3 62.2 + - - +
500B THR* 3.3 5.7 + - - -
501B ILE* 3.2 37.2 + - + +
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Residues in contact with GLY 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ALA* 4.5 4.7 - - - -
420B THR* 3.3 32.9 - - - +
424B ALA* 3.7 11.2 - - - -
494B GLY 3.0 11.1 + - - -
495B LEU 3.8 2.0 - - - -
497B LEU* 1.3 75.3 - - - +
499B GLU* 1.3 59.2 + - - +
501B ILE* 3.9 1.4 - - - +
502B THR* 2.8 30.3 + - - -
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Residues in contact with GLU 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLY 4.1 1.0 - - - -
427B THR* 3.5 24.6 + - + +
430B LYS* 4.5 2.6 + - - -
495B LEU 3.1 14.3 + - - +
496B LEU* 3.6 23.8 - - - +
497B LEU 3.3 0.2 - - - -
498B GLY* 1.3 75.3 - - - +
500B THR* 1.4 69.3 + - - +
502B THR* 3.8 1.0 - - - -
503B VAL* 2.9 30.8 + - + +
521B PHE* 5.4 0.5 - - - -
523B LEU* 3.5 34.8 - - + +
524B PHE* 2.9 43.0 + - + +
525B THR* 5.5 1.4 + - - -
549B TYR* 4.4 8.1 + - - +
552B VAL* 5.6 1.4 - - - +
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Residues in contact with THR 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR* 4.5 18.8 - - + -
496B LEU* 3.0 18.7 + - - +
497B LEU* 3.3 6.2 + - - -
499B GLU* 1.4 79.7 + - - +
501B ILE* 1.3 56.7 + - - +
503B VAL* 3.3 4.0 + - - +
504B ARG* 3.0 30.0 + - + +
549B TYR* 3.9 36.7 + - + +
550B THR* 4.3 16.8 - - - +
551B GLY* 4.4 6.4 - - - -
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Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PRO* 3.7 25.6 - - + +
121B THR* 4.0 19.5 - - + +
332B LEU 5.4 0.4 - - - -
333B ALA* 3.9 33.7 - - + +
336B SER* 3.4 36.3 - - - +
497B LEU* 3.2 32.3 + - + +
498B GLY 3.9 3.1 - - - +
500B THR* 1.3 75.5 - - - +
502B THR* 1.3 64.0 + - - +
504B ARG* 3.2 6.7 + - - +
505B THR* 3.1 23.4 + - - +
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Residues in contact with THR 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ALA* 4.3 8.5 + - + +
424B ALA* 3.1 30.1 - - - +
427B THR* 3.8 23.3 - - + -
428B VAL* 3.9 16.8 - - + -
498B GLY 2.8 20.5 + - - -
499B GLU 3.8 3.1 - - - -
501B ILE* 1.3 76.6 - - - +
503B VAL* 1.3 58.8 + - - +
505B THR* 3.2 6.4 + - - -
506B LEU* 2.8 38.3 + - + +
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Residues in contact with VAL 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B THR* 4.4 3.5 - - + +
499B GLU* 2.9 20.8 + - + +
500B THR 3.5 7.4 - - - +
502B THR* 1.3 75.2 - - - +
504B ARG* 1.3 64.2 + - - +
506B LEU* 3.8 8.2 - - - +
507B HIS* 3.0 24.3 + - + +
521B PHE* 4.1 25.1 - - + -
523B LEU* 4.4 11.4 - - + -
529B ILE* 3.9 14.1 - - + -
531B LEU* 4.0 13.6 - - + +
549B TYR* 3.4 42.2 - - + -
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Residues in contact with ARG 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 2.9 42.9 + - - +
36B GLY 5.4 0.2 + - - -
37B THR* 3.3 19.6 + - - +
115B GLY* 5.3 1.3 - - - -
116B PRO* 3.8 29.9 - - + +
120B ALA* 4.0 14.3 + - - +
121B THR* 5.0 7.2 - - + +
500B THR* 3.0 18.3 + - + +
501B ILE* 3.2 10.1 + - - +
503B VAL* 1.3 77.9 - - - +
505B THR* 1.3 61.3 + - - +
507B HIS* 3.8 4.3 - - - +
508B GLN* 3.1 22.9 + - - +
548B VAL* 3.6 30.8 - - - +
549B TYR* 2.9 35.9 + - + +
550B THR* 3.8 11.1 - - - +
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Residues in contact with THR 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER* 5.3 7.4 - - - +
115B GLY* 3.4 27.9 - - - +
116B PRO* 3.6 2.9 - - - +
326B LEU* 5.2 9.6 - - + -
329B ALA* 6.6 0.2 - - + -
330B ALA* 6.3 3.1 - - - -
332B LEU* 5.9 2.9 - - + +
501B ILE* 3.1 15.2 + - - +
502B THR* 3.2 10.7 + - - -
504B ARG* 1.3 71.1 - - - +
506B LEU* 1.3 65.8 + - + +
508B GLN* 3.2 9.3 + - - +
509B GLU* 2.9 39.8 + - + +
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.7 30.7 - - + -
427B THR* 4.1 13.9 - - + +
428B VAL* 5.2 4.7 - - + +
431B ALA* 3.8 26.2 - - + -
432B LEU* 5.8 1.1 - - + -
502B THR* 2.8 42.6 + - + +
503B VAL* 3.8 6.7 - - - +
505B THR* 1.3 74.1 - - - +
507B HIS* 1.3 57.1 + - - +
509B GLU* 3.5 5.3 + - - +
510B LEU* 2.9 29.5 + - - +
519B PHE* 3.5 35.0 - - + -
521B PHE* 4.5 6.3 - - + -
531B LEU* 4.3 4.7 - - + -
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Residues in contact with HIS 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 3.7 13.5 + - - +
503B VAL* 3.0 18.2 + - + +
504B ARG* 3.8 6.1 - - - +
506B LEU* 1.3 76.0 - - - +
508B GLN* 1.3 65.6 + - - +
510B LEU* 3.3 6.4 + - + +
511B MET* 3.2 27.7 + - + +
531B LEU* 4.0 27.9 - - + +
532B PHE 2.8 30.4 + - - -
535B GLY* 3.4 18.6 - - - -
536B THR 3.3 19.7 + - - -
537B PHE* 4.0 18.2 - + + -
549B TYR* 5.3 7.2 + - + +
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Residues in contact with GLN 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 5.7 0.6 - - - +
113A ILE* 3.9 33.0 - - + +
29B ALA* 4.3 19.8 + - + +
30B ALA* 5.6 0.2 - - - +
32B ARG* 6.1 0.4 - - - +
33B GLU* 4.0 26.1 - - - +
113B ILE 4.8 0.8 + - - -
114B SER* 3.8 7.4 - - - -
115B GLY* 3.0 31.4 + - - +
504B ARG 3.1 12.5 + - - +
505B THR* 3.6 8.8 - - - +
507B HIS* 1.3 81.0 - - - +
509B GLU* 1.3 66.2 + - + +
511B MET* 3.5 16.9 + - - +
512B THR* 3.6 15.4 - - + +
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Residues in contact with GLU 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASP* 5.1 10.8 - - - +
332A LEU* 5.3 0.7 - - - +
322B HIS* 4.1 8.5 + - - +
325B ARG* 2.8 45.2 + - - -
326B LEU* 3.8 16.8 - - - +
329B ALA* 6.0 0.2 - - - +
505B THR* 2.9 28.1 + - + +
506B LEU* 3.9 5.4 - - - +
508B GLN* 1.3 77.3 - - + +
510B LEU* 1.3 68.5 + - - +
512B THR* 2.7 29.8 + - - +
513B PHE* 3.4 17.6 - - + -
519B PHE* 6.0 0.7 - - + -
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Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B PHE* 4.2 8.1 - - + -
506B LEU 2.9 19.0 + - - +
507B HIS* 3.3 6.5 + - + +
509B GLU* 1.3 77.6 - - - +
511B MET* 1.3 59.4 + - - +
512B THR 3.2 0.5 + - - -
513B PHE* 3.3 20.7 + - + +
517B SER* 3.6 34.3 - - - +
518B THR* 4.0 5.6 - - - +
519B PHE* 3.9 18.2 - - + +
531B LEU* 3.3 43.1 - - + +
532B PHE 4.0 13.2 - - - +
533B GLN* 3.0 32.9 + - + +
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Residues in contact with MET 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 3.4 43.7 - - - +
507B HIS* 3.2 27.8 + - + +
508B GLN* 3.7 10.3 - - - +
509B GLU 3.2 0.4 - - - -
510B LEU* 1.3 75.7 - - - +
512B THR* 1.3 61.0 + - + +
513B PHE 3.5 2.8 + - - +
532B PHE 4.2 0.4 - - - +
533B GLN* 3.4 36.7 + - - +
534B ASP 4.0 3.4 - - - +
535B GLY* 3.7 18.2 - - - +
----------------------------------------------------------
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Residues in contact with THR 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PHE 3.6 1.9 - - - +
110A ALA* 3.4 20.5 - - - +
111A ILE* 3.4 33.2 + - - +
112A ASP* 4.7 8.2 + - - -
113A ILE* 5.5 2.5 - - + +
25B SER* 5.1 6.3 - - - +
508B GLN* 3.6 18.4 - - + +
509B GLU* 2.7 20.2 + - - +
511B MET* 1.3 79.1 - - + +
513B PHE* 1.3 73.6 + - - +
514B ALA* 3.5 1.0 + - - -
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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