Contacts of the helix formed by residues 394 - 421 (chain A) in PDB entry 2XOA
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 GLN 394 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ARG 4.7 5.2 - - - +
393A CYS* 1.3 79.7 - - - +
395A GLN* 1.3 67.7 + - - +
396A GLU* 3.4 3.1 - - + +
397A GLU* 3.2 11.6 + - + +
398A SER* 3.1 21.9 + - - -
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Residues in contact with GLN 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A HIS 5.1 0.7 - - - +
115A ARG* 3.7 32.8 - - - +
393A CYS 4.2 0.2 + - - -
394A GLN* 1.3 74.2 - - - +
396A GLU* 1.3 74.9 + - - +
397A GLU 3.1 0.2 + - - -
398A SER* 4.0 6.3 - - - -
399A GLN* 2.7 53.2 + - - +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLN* 3.4 3.2 - - + +
395A GLN* 1.3 92.3 - - - +
397A GLU* 1.3 59.4 + - + +
399A GLN* 4.0 4.7 - - - +
400A ALA* 3.1 25.6 + - - +
451A TYR* 4.4 2.4 + - - +
470A SER* 3.3 35.4 + - - -
473A ASN* 3.4 23.6 + - - +
474A ARG* 3.7 28.4 + - + +
477A LEU* 6.0 0.2 - - + -
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ARG* 2.5 45.1 + - - -
254A THR* 3.4 15.9 - - - +
255A HIS 4.3 0.9 - - - +
259A LEU* 3.8 7.6 - - + -
393A CYS* 3.7 14.2 - - - -
394A GLN* 3.2 13.5 + - + +
395A GLN 3.1 0.6 - - - -
396A GLU* 1.3 79.4 - - + +
398A SER* 1.3 62.4 + - - +
400A ALA* 3.3 2.8 + - - +
401A ALA* 2.9 28.6 + - - +
473A ASN* 5.4 6.1 - - - +
477A LEU* 4.1 25.1 - - + +
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Residues in contact with SER 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A VAL* 3.4 32.7 - - - +
259A LEU* 4.6 5.4 - - - -
285A VAL* 4.8 2.3 - - - +
393A CYS* 3.6 13.2 - - - -
394A GLN 3.1 18.6 + - - -
395A GLN* 3.4 9.0 - - - -
397A GLU* 1.3 72.9 - - - +
399A GLN* 1.3 65.8 + - - -
401A ALA* 3.1 4.3 + - - +
402A ARG* 3.1 21.7 + - - +
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Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 3.8 14.7 - - - -
113A HIS* 2.9 43.1 + - + +
114A SER* 4.1 6.7 + - - +
115A ARG* 4.5 5.9 - - - +
395A GLN* 2.7 39.5 + - - +
396A GLU* 4.0 4.4 - - - +
398A SER* 1.3 72.7 - - - +
400A ALA* 1.3 63.3 + - - +
402A ARG* 3.1 3.6 + - - -
403A MET* 2.9 60.1 + - + +
451A TYR* 4.2 7.1 + - - -
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLU 3.1 16.6 + - - +
397A GLU 3.4 8.7 - - - +
398A SER 3.3 0.2 - - - -
399A GLN* 1.3 76.7 - - - +
401A ALA* 1.3 64.2 + - - +
403A MET* 3.1 7.9 + - - +
404A ILE* 2.9 28.5 + - - +
451A TYR* 3.6 20.6 - - - +
474A ARG* 5.1 2.7 - - + -
477A LEU* 3.7 24.2 - - + -
478A PHE* 4.1 10.2 - - + -
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Residues in contact with ALA 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ALA* 4.0 4.9 - - + +
259A LEU* 3.8 20.4 - - + -
285A VAL* 3.8 15.3 - - + -
286A THR* 3.8 27.3 - - + +
397A GLU 2.9 19.7 + - - +
398A SER* 3.1 5.1 + - - +
400A ALA* 1.3 73.6 - - - +
402A ARG* 1.3 63.5 + - - +
404A ILE* 3.1 9.4 + - - +
405A HIS* 3.1 19.4 + - - +
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Residues in contact with ARG 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 2.8 33.7 + - - +
61A ASP* 2.7 43.2 + - - -
63A ALA* 4.4 13.3 - - + +
64A ILE* 3.4 20.9 - - + +
113A HIS* 3.2 39.3 - - + +
283A ARG* 3.8 15.0 - - - +
285A VAL* 3.7 15.0 - - + +
398A SER 3.1 12.1 + - - +
399A GLN 3.8 1.1 - - - +
401A ALA* 1.3 76.4 - - - +
403A MET* 1.3 61.4 + - - +
405A HIS* 3.0 33.4 + - - +
406A SER* 3.0 15.8 + - - -
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Residues in contact with MET 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 5.4 0.2 - - - -
42A PHE* 3.7 32.3 - - + -
113A HIS* 3.9 13.9 - - + -
399A GLN* 2.9 63.7 + - + +
400A ALA 3.6 4.9 - - - +
402A ARG* 1.3 72.3 - - - +
404A ILE* 1.3 55.8 + - - +
406A SER* 4.0 4.8 - - - +
407A THR* 2.6 40.5 + - - +
448A LEU* 5.0 7.9 - - + -
451A TYR* 3.3 44.6 - - + +
478A PHE* 4.0 10.5 - - + -
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Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ALA* 4.2 14.1 - - + -
286A THR* 4.3 6.5 - - + +
400A ALA 2.9 22.1 + - - +
401A ALA* 3.6 6.5 - - - +
402A ARG 3.1 0.2 - - - -
403A MET* 1.3 76.3 - - - +
405A HIS* 1.3 59.4 + - - +
407A THR* 3.8 4.4 - - - -
408A ALA* 2.8 31.2 + - + +
477A LEU* 3.7 33.2 - - + +
478A PHE* 3.8 29.8 - - + -
481A GLU* 3.7 35.0 - - + +
483A MET* 3.8 15.1 - - + +
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Residues in contact with HIS 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 5.2 1.4 + - - -
283A ARG* 3.9 11.9 + - - -
285A VAL 3.7 13.9 - - - +
286A THR 3.2 25.9 + - - +
287A THR* 3.7 24.6 - - - -
288A GLY* 3.8 7.4 - - - -
401A ALA 3.1 8.5 + - - +
402A ARG* 3.0 41.9 + - - +
404A ILE* 1.3 78.0 - - - +
406A SER* 1.3 65.2 + - - +
408A ALA* 3.6 2.4 + - - +
409A GLY* 3.2 17.9 + - - -
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Residues in contact with SER 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 2.6 45.3 + - - -
42A PHE 5.7 1.1 - - - -
402A ARG* 3.0 17.3 + - - -
403A MET* 4.0 5.2 - - - -
405A HIS* 1.3 75.9 - - - +
407A THR* 1.3 62.5 + - - +
409A GLY* 3.1 2.5 + - - -
410A LEU* 2.9 31.2 + - - +
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Residues in contact with THR 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A MET* 2.6 24.1 + - - +
404A ILE* 3.8 4.3 - - - -
406A SER* 1.3 74.2 - - - +
408A ALA* 1.3 68.3 + - - +
409A GLY 3.1 0.2 + - - -
410A LEU* 3.1 5.0 + - - -
411A TYR* 3.0 55.8 + - + -
444A SER* 4.6 4.7 + - - +
448A LEU* 3.7 29.5 - - + +
478A PHE* 4.6 1.9 - - + -
483A MET* 4.1 15.0 - - - -
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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
----------------------------------------------------------
286A THR 5.6 2.5 - - - +
404A ILE* 2.8 23.5 + - + +
405A HIS* 4.1 4.0 - - - +
407A THR* 1.3 73.6 - - - +
409A GLY* 1.3 63.8 + - - +
411A TYR* 4.5 0.3 - - - +
412A ASN* 2.9 39.1 + - - +
483A MET* 3.8 22.1 - - + -
486A LEU* 4.4 7.4 - - + -
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Residues in contact with GLY 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A HIS 3.2 11.6 + - - -
406A SER* 3.1 6.3 + - - -
407A THR 3.1 0.8 - - - -
408A ALA* 1.3 77.4 - - - +
410A LEU* 1.3 61.9 + - - +
412A ASN* 3.8 3.9 - - - +
413A GLN* 3.0 24.4 + - - +
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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
----------------------------------------------------------
43A GLY* 5.1 4.7 - - - -
406A SER 2.9 16.8 + - - +
407A THR* 3.8 4.3 - - - +
409A GLY* 1.3 75.8 - - - +
411A TYR* 1.3 65.9 + - + +
413A GLN* 3.3 24.3 + - - +
414A PHE* 3.0 23.9 + - - +
437A PRO* 4.0 11.0 - - + -
440A ALA* 3.8 34.1 - - + -
441A VAL* 3.9 7.9 - - + +
444A SER* 3.5 33.0 - - - +
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Residues in contact with TYR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A THR* 3.0 30.6 + - + +
410A LEU* 1.3 88.8 - - + +
412A ASN* 1.3 58.4 + - - +
414A PHE* 3.7 6.4 - + - +
415A ILE* 2.9 34.7 + - - +
441A VAL* 4.4 15.7 - - + -
444A SER* 2.7 34.4 + - - -
445A LEU* 2.8 36.1 + - + +
448A LEU* 3.7 9.4 - - - +
483A MET* 5.9 0.2 - - - -
486A LEU* 3.2 33.2 - - + -
487A VAL* 4.5 10.3 - - + -
490A CYS* 4.1 18.3 - - - -
522A LEU* 5.2 2.0 - - + -
525A LEU* 4.5 11.2 - - + -
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Residues in contact with ASN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ALA* 2.9 33.0 + - - +
409A GLY* 3.9 4.9 - - - +
411A TYR* 1.3 75.1 - - - +
413A GLN* 1.3 60.2 + - - +
415A ILE* 3.2 14.1 + - - +
416A LYS* 3.0 28.7 + - - +
486A LEU* 3.8 23.2 - - - +
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Residues in contact with GLN 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A GLY 3.0 16.8 + - - +
410A LEU* 3.3 15.5 + - - +
412A ASN* 1.3 76.5 - - - +
414A PHE* 1.3 61.8 + - - +
416A LYS* 3.1 8.8 + - - +
417A GLY* 3.1 19.9 + - - -
437A PRO* 3.3 34.0 - - + +
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Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU 3.0 16.3 + - - +
411A TYR* 3.7 5.2 - + - +
412A ASN 3.2 0.4 - - - -
413A GLN* 1.3 77.8 - - - +
415A ILE* 1.3 61.5 + - - +
417A GLY* 3.8 1.1 + - - +
418A LEU* 3.4 41.0 + - + +
436A LEU* 3.9 25.0 - - + +
437A PRO* 4.1 21.3 - - + -
438A ILE* 4.6 7.6 - - + -
441A VAL* 3.7 30.1 - - + -
490A CYS* 4.1 26.0 - - + -
494A LEU* 3.9 30.3 - - + -
518A ILE* 4.4 22.2 - - + -
522A LEU* 5.2 0.2 - - + -
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A TYR 2.9 19.7 + - - +
412A ASN* 3.6 13.7 - - - +
413A GLN 3.2 0.2 - - - -
414A PHE* 1.3 80.6 - - + +
416A LYS* 1.3 58.6 + - - +
418A LEU* 3.3 8.2 + - + +
419A ASP* 3.0 30.4 + - - +
486A LEU* 3.8 22.9 - - + -
489A ASN* 3.7 27.1 - - + -
490A CYS* 3.8 22.4 - - - +
493A ARG* 3.7 35.9 - - - +
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Residues in contact with LYS 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ASN 3.0 15.7 + - - +
413A GLN* 3.1 11.0 + - - +
415A ILE* 1.3 79.7 - - + +
417A GLY* 1.3 59.5 + - - +
419A ASP* 3.4 8.7 + - + +
420A SER* 3.1 31.5 + - - +
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Residues in contact with GLY 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A GLN 3.1 12.2 + - - -
416A LYS* 1.3 74.9 - - - +
418A LEU* 1.3 64.5 + - - +
420A SER* 3.3 20.3 - - - -
421A PHE* 3.4 15.6 - - - -
436A LEU* 3.6 23.6 - - - -
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Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 3.4 44.4 + - + +
415A ILE* 3.3 13.1 + - + +
417A GLY* 1.3 78.8 - - - +
419A ASP* 1.3 66.5 + - - +
420A SER 3.3 0.3 + - - -
421A PHE* 3.5 26.6 + - + -
422A SER* 3.5 12.4 + - - -
436A LEU* 3.8 27.6 - - + -
490A CYS* 4.8 1.8 - - - +
493A ARG* 4.0 30.5 - - + +
494A LEU* 4.2 19.7 - - + -
497A TYR* 5.3 3.9 + - + -
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Residues in contact with ASP 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ILE* 3.0 18.7 + - - +
416A LYS* 3.8 9.3 - - + +
417A GLY 3.3 0.4 - - - -
418A LEU* 1.3 75.9 - - - +
420A SER* 1.3 62.6 + - - +
422A SER* 3.1 23.7 + - - -
423A GLY 4.7 0.5 + - - -
493A ARG* 2.8 45.8 + - - +
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Residues in contact with SER 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LYS* 3.1 18.9 + - - +
417A GLY* 3.3 16.8 - - - -
418A LEU 3.2 0.4 - - - -
419A ASP* 1.3 75.4 - - - +
421A PHE* 1.3 59.4 + - - +
422A SER 3.8 0.2 + - - -
424A LYS* 3.4 27.5 - - - +
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Residues in contact with PHE 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A GLY 3.4 19.1 - - - -
418A LEU* 3.5 32.0 + - + -
419A ASP 3.3 0.4 - - - -
420A SER* 1.3 78.6 - - - +
422A SER* 1.3 63.8 + - - +
423A GLY 3.5 2.0 - - - -
424A LYS* 3.5 16.7 + - + +
436A LEU* 4.1 19.1 - - + -
497A TYR* 3.9 22.9 - + - -
506A TYR* 3.5 38.5 - - + +
507A ALA* 3.5 34.1 - - + -
508A GLY 5.5 0.2 - - - -
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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