Contacts of the helix formed by residues 402 - 430 (chain A) in PDB entry 5SY1
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 PHE 402 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LYS* 4.7 11.0 - - + +
275A LEU* 3.9 25.4 - - + -
278A SER* 4.2 11.2 - - - -
367A HIS* 4.8 3.1 - + - -
398A CYS 3.8 11.9 - - - +
399A TRP 3.5 6.1 + - - +
401A GLY* 1.3 75.8 - - - +
403A THR* 1.3 67.6 + - - +
404A SER 3.2 2.2 - - - -
405A TYR* 3.2 15.2 + - + +
406A GLN* 3.2 15.6 + - - +
526A LEU* 3.6 31.2 - - + -
544A CYS* 3.9 18.6 - - + -
545A TYR* 3.8 36.1 - + - -
548A TYR* 4.0 34.1 - + + -
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Residues in contact with THR 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 5.0 4.6 - - + -
274A LYS* 3.2 47.8 - - + +
277A ILE* 4.1 14.6 - - + -
278A SER* 3.9 26.8 - - - +
281A VAL* 5.0 5.0 - - - +
401A GLY* 4.8 3.8 - - - -
402A PHE* 1.3 76.5 + - + +
404A SER* 1.3 62.5 + - - +
406A GLN* 3.4 2.9 + - - +
407A ALA* 3.4 21.1 + - - +
497B PHE* 3.7 24.0 - - - -
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A GLY* 3.5 14.2 + - - -
403A THR* 1.3 79.6 + - - +
405A TYR* 1.3 63.9 + - - +
407A ALA* 3.5 3.1 + - - +
408A ALA* 3.0 30.7 + - - +
497B PHE* 4.0 12.6 - - - -
500B ASN* 3.1 47.0 + - - +
501B VAL* 3.6 19.6 - - - +
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Residues in contact with TYR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A VAL* 5.5 4.8 + - - +
398A CYS* 4.9 6.5 - - - -
400A MET 5.6 0.8 + - - -
401A GLY 3.2 20.9 - - - -
402A PHE* 3.2 11.8 + - + +
404A SER* 1.3 88.0 + - - +
406A GLN* 1.3 60.1 + - - +
408A ALA* 4.4 2.7 - - - -
409A PHE* 3.1 39.1 + + + -
526A LEU* 4.1 12.3 - - + -
544A CYS* 3.6 38.1 - - + -
465B GLN* 5.7 0.9 + - - -
500B ASN* 3.9 13.3 + - + -
503B ILE* 3.8 14.1 - - + +
504B GLY* 3.6 32.3 - - - -
507B LEU* 3.7 24.6 - - + +
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Residues in contact with GLN 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER* 3.4 37.2 - - - +
282A ALA* 4.2 6.2 - - + +
360A LEU* 3.7 27.0 - - - +
363A SER* 5.4 4.0 + - - -
367A HIS* 5.5 6.1 - - - -
402A PHE* 3.2 18.6 + - + +
403A THR 3.8 7.9 - - - +
404A SER 3.2 0.4 - - - -
405A TYR* 1.3 79.6 - - - +
407A ALA* 1.3 60.2 + - - +
408A ALA 3.5 0.2 + - - -
409A PHE* 3.6 3.1 + - - +
410A LEU* 3.5 18.7 + - - +
524A GLY 3.9 15.2 + - - -
525A ARG* 5.2 1.0 - - - +
526A LEU* 3.3 33.8 + - + +
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Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 4.3 17.1 - - + -
278A SER 5.8 0.2 - - - +
281A VAL* 3.9 39.3 - - + +
282A ALA* 4.5 6.3 - - - +
285A ALA* 4.2 3.6 - - + +
403A THR 3.4 10.7 + - - +
404A SER* 3.5 3.6 + - - +
406A GLN* 1.3 77.8 - - + +
408A ALA* 1.3 62.3 + - - +
410A LEU* 4.1 3.3 - - - +
411A CYS* 3.4 26.2 + - - -
497B PHE* 6.4 0.2 - - + -
501B VAL* 5.5 2.6 - - + +
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Residues in contact with ALA 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A SER 3.0 19.3 + - - +
405A TYR 4.0 2.9 - - - +
407A ALA* 1.3 77.2 - - - +
409A PHE* 1.3 65.5 + - - +
410A LEU 3.1 1.0 + - - -
411A CYS* 3.4 13.2 + - - +
412A LEU* 3.5 16.3 + - - +
501B VAL* 3.9 16.4 - - + +
504B GLY* 3.3 35.7 - - - +
505B VAL* 4.2 6.4 - - + +
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR* 3.1 25.9 + + + +
406A GLN* 3.6 3.3 + - - +
408A ALA* 1.3 75.9 - - - +
410A LEU* 1.3 57.5 - - - +
412A LEU* 4.0 7.6 + - - +
413A GLY* 3.3 15.6 + - - -
523A LEU* 4.3 10.1 - - - +
524A GLY* 3.7 18.9 - - - -
525A ARG 4.9 1.1 - - - -
526A LEU* 3.5 35.4 - - + -
540A PRO 5.2 0.4 - - - -
541A GLY* 3.7 18.2 - - - -
504B GLY* 3.4 25.8 - - - -
507B LEU* 3.7 26.2 - - + -
508B GLY* 3.5 21.3 - - - -
511B ARG* 3.8 23.1 - - - -
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ALA* 3.3 42.2 - - + +
285A ALA* 4.9 2.7 - - + -
286A LEU* 4.3 16.8 - - + +
356A ASN* 3.8 36.3 - - + +
360A LEU* 3.9 17.5 - - + -
406A GLN* 3.5 17.4 + - - +
407A ALA* 4.4 5.2 - - - +
408A ALA 3.1 1.0 - - - -
409A PHE* 1.3 78.5 - - - +
411A CYS* 1.3 60.6 + - - +
412A LEU 3.3 0.2 - - - -
413A GLY* 3.0 13.6 + - - +
414A MET* 3.0 18.0 + - + +
524A GLY* 4.7 15.3 - - - +
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Residues in contact with CYS 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 4.4 10.1 - - - -
285A ALA* 3.9 21.3 - - - -
288A GLN* 6.4 0.4 - - - -
289A MET* 3.6 43.7 - - + +
407A ALA 3.4 17.0 + - - -
408A ALA* 3.4 8.6 + - - +
410A LEU* 1.3 78.2 - - - +
412A LEU* 1.3 62.6 + - + +
414A MET* 3.6 0.9 + - - -
415A ALA* 3.3 16.6 + - - +
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA 3.5 14.7 + - - +
409A PHE* 4.3 6.5 - - - +
410A LEU 3.3 0.2 - - - -
411A CYS* 1.3 76.6 - - + +
413A GLY* 1.3 64.2 + - - +
415A ALA* 3.5 10.0 + - + +
416A ILE* 3.3 36.2 + - + +
523A LEU* 4.8 4.6 - - + +
505B VAL* 4.3 23.1 - - + +
508B GLY* 3.6 38.1 - - - +
509B ILE* 4.1 11.7 - - + +
512B VAL* 6.0 2.9 - - + -
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Residues in contact with GLY 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A ASN* 4.4 3.1 - - - -
409A PHE 3.3 13.4 + - - -
410A LEU* 3.0 11.7 + - - -
412A LEU* 1.3 77.2 - - - +
414A MET* 1.3 57.2 + - - +
415A ALA 3.2 0.2 + - - -
416A ILE* 4.4 0.3 - - - +
417A GLN* 3.0 46.6 + - - +
523A LEU* 4.8 13.9 - - - -
524A GLY* 5.1 5.2 - - - -
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Residues in contact with MET 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A LEU* 3.7 23.1 - - + -
289A MET* 4.0 25.6 - - + -
290A ALA* 4.9 10.8 - - + +
293A LEU* 4.0 10.4 - - + +
349A VAL* 4.5 9.9 - - + +
352A SER* 3.3 32.1 - - - +
353A CYS* 3.7 19.5 - - + +
356A ASN* 2.7 31.4 - - - +
410A LEU* 3.0 14.9 + - + +
411A CYS 3.6 2.0 + - - +
413A GLY* 1.3 75.4 - - - +
415A ALA* 1.3 60.4 + - - +
417A GLN* 4.2 1.3 - - - -
418A THR* 2.8 30.3 + - - +
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Residues in contact with ALA 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A MET* 4.7 10.7 - - + +
293A LEU* 5.4 5.8 - - + -
411A CYS 3.3 13.6 + - - +
412A LEU* 3.7 16.4 - - + +
413A GLY 3.2 0.8 - - - -
414A MET* 1.3 80.0 - - - +
416A ILE* 1.3 66.5 + - + +
418A THR* 3.9 1.8 - - - -
419A LEU* 3.1 23.9 + - - +
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Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A LEU* 3.3 20.8 + - + +
413A GLY 4.4 0.4 - - - +
415A ALA* 1.3 77.9 - - + +
417A GLN* 1.3 61.6 + - - +
419A LEU* 3.1 12.3 + - + +
420A VAL* 2.9 34.4 + - + +
520A ILE* 4.0 26.0 - - + -
523A LEU* 4.1 13.7 - - + -
701A CLR 4.1 23.1 - - + -
512B VAL* 3.9 34.3 - - + -
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Residues in contact with GLN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A SER* 3.6 21.4 - - - +
355A VAL* 4.6 7.8 - - - +
356A ASN* 3.0 38.2 + - - +
413A GLY* 3.0 23.1 + - - +
414A MET 4.7 0.2 - - - +
416A ILE* 1.3 78.7 - - + +
418A THR* 1.3 58.4 + - - +
420A VAL* 4.6 3.4 - - - -
421A PHE* 3.1 47.1 + - + -
520A ILE* 2.6 42.9 + - + +
521A VAL* 3.4 13.3 + - - +
523A LEU* 4.9 3.9 - - + +
524A GLY 5.2 1.2 - - - +
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Residues in contact with THR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A LEU* 3.9 14.6 - - + +
345A TYR* 4.5 13.0 - - + -
348A ALA* 3.9 18.4 - - + -
349A VAL* 3.7 27.1 - - + -
352A SER* 2.8 21.4 + - - -
414A MET* 2.8 20.0 + - - +
415A ALA 3.4 3.4 + - - -
416A ILE 3.2 0.4 - - - -
417A GLN* 1.3 75.8 - - - +
419A LEU* 1.3 61.0 + - - +
421A PHE* 4.0 0.8 - - - -
422A PHE* 3.0 31.4 + - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ALA 3.1 18.1 + - - +
416A ILE* 3.7 13.0 - - + +
418A THR* 1.3 76.9 - - - +
420A VAL* 1.3 60.7 + - + +
422A PHE* 4.1 8.7 - - + +
423A ILE* 3.6 28.5 + - + +
701A CLR 3.6 32.5 - - + +
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Residues in contact with VAL 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ILE* 2.9 25.9 + - + +
417A GLN 4.1 2.0 - - - +
419A LEU* 1.3 76.7 - - + +
421A PHE* 1.3 70.4 + - + +
422A PHE 3.1 1.6 - - - -
423A ILE* 3.1 15.4 + - - +
424A CYS* 3.1 27.6 + - - -
517A LEU* 6.1 1.1 - - + -
520A ILE* 3.8 32.5 - - + -
701A CLR 3.7 53.6 - - + -
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Residues in contact with PHE 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ALA* 4.3 13.0 - - + +
351A LEU* 3.6 41.7 - - + -
352A SER* 4.4 12.8 - - - -
355A VAL* 4.8 11.0 - - + -
417A GLN* 3.1 32.3 + - + +
418A THR 4.3 1.6 - - - +
420A VAL* 1.3 78.6 - - + +
422A PHE* 1.3 64.7 + - - +
424A CYS* 3.3 18.2 + - + -
425A ILE* 3.3 24.9 + - + +
517A LEU* 4.8 11.7 - - + -
520A ILE* 3.7 28.0 - - + -
521A VAL* 5.1 12.1 - - + -
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Residues in contact with PHE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 4.2 20.0 - - + -
344A CYS* 3.5 28.8 - - + -
345A TYR* 3.6 47.8 - + + -
348A ALA* 4.0 8.0 - - + +
418A THR 3.0 19.6 + - - +
419A LEU* 4.2 11.2 - - + +
420A VAL 3.1 0.2 - - - -
421A PHE* 1.3 76.9 - - - +
423A ILE* 1.3 70.0 + - + +
424A CYS 3.2 1.0 + - - -
426A LEU* 3.4 42.7 + - + +
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Residues in contact with ILE 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 3.6 26.7 - - + +
420A VAL* 3.1 8.3 + - - +
422A PHE* 1.3 86.9 - - + +
424A CYS* 1.3 62.6 + - - +
425A ILE 3.4 0.7 - - - -
426A LEU* 4.4 8.8 - - + +
427A PHE* 3.7 18.4 + - - +
701A CLR 4.8 25.8 - - + -
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Residues in contact with CYS 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A VAL* 3.1 35.3 + - - +
421A PHE* 3.8 15.3 - - + +
422A PHE 3.2 0.8 - - - -
423A ILE* 1.3 80.8 - - - +
425A ILE* 1.3 64.3 + - + +
427A PHE* 4.3 10.1 - - - +
428A ALA* 4.0 12.8 + - - +
517A LEU* 6.2 4.5 - - - -
701A CLR 5.1 11.2 - - - -
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Residues in contact with ILE 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A CYS* 3.9 18.4 - - + -
347A SER* 3.9 24.5 - - - +
348A ALA* 4.7 11.0 - - - -
351A LEU* 4.8 16.4 - - + -
421A PHE* 3.3 20.5 + - - +
422A PHE 3.7 0.2 + - - -
424A CYS* 1.3 81.6 - - + +
426A LEU* 1.3 53.2 + - - +
427A PHE 3.2 1.6 - - - -
428A ALA* 2.8 8.3 + - + +
429A VAL* 2.5 51.3 + - + +
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A CYS 4.6 5.8 - - - +
341A VAL* 5.1 9.6 - - + -
344A CYS* 3.7 24.7 - - + -
422A PHE* 3.4 45.2 + - + +
423A ILE* 4.9 6.5 - - + +
425A ILE* 1.3 78.4 - - - +
427A PHE* 1.3 56.0 + - - +
429A VAL* 4.2 6.7 - - + +
430A PHE* 2.9 60.6 + - + +
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Residues in contact with PHE 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE 3.7 19.4 + - - +
424A CYS* 4.4 8.1 - - - +
425A ILE 3.2 0.4 - - - -
426A LEU* 1.3 78.4 - - - +
428A ALA* 1.3 58.9 + - + +
431A LEU* 3.3 47.9 - - + +
432A ILE* 5.3 0.9 - - - +
443A MET* 6.3 0.4 - - + -
444A LEU* 5.0 14.8 - - + +
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Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A CYS 4.0 11.8 + - - +
425A ILE* 2.8 13.1 + - + +
427A PHE* 1.3 81.4 - - + +
429A VAL* 1.3 61.2 + - + +
430A PHE 3.5 0.2 - - - -
432A ILE* 2.9 41.8 + - + +
433A ILE* 3.1 16.3 + - + +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A CYS* 4.5 20.2 - - + +
344A CYS* 5.7 3.6 - - + -
425A ILE* 2.5 40.5 + - + +
426A LEU* 4.3 8.3 - - + +
428A ALA* 1.3 74.6 - - + +
430A PHE* 1.3 68.4 + - + +
431A LEU 3.1 1.3 + - - -
433A ILE* 3.7 20.6 - - + -
434A ILE* 3.1 47.1 + - + +
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Residues in contact with PHE 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A TYR* 3.9 40.2 - + + -
340A CYS* 4.4 16.2 - - + -
341A VAL* 5.1 7.9 - - + -
426A LEU* 2.9 41.7 + - + +
429A VAL* 1.3 77.9 - - + +
431A LEU* 1.3 72.2 + - + +
434A ILE* 3.6 22.3 - - + +
435A PRO* 4.7 7.0 - - - +
441A ASN* 5.6 6.4 + - - +
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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).
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