Contacts of the helix formed by residues 501 - 526 (chain A) in PDB entry 6S1M
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 ASN 501 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLY* 1.3 82.9 - - - +
502A ASP* 1.3 64.6 + - - +
503A GLN* 4.4 6.3 - - + +
504A THR* 2.5 33.5 + - + +
505A ARG* 3.3 24.5 - - - +
51D GLN* 3.8 21.5 + - - +
54D LEU* 3.9 23.6 + - - +
55D ALA* 4.2 14.5 - - - +
56D TRP* 5.5 8.6 - - + -
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Residues in contact with ASP 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A PRO* 3.5 23.0 - - + +
360A CYS* 4.1 15.0 - - - +
361A ALA* 3.9 10.0 + - - +
501A ASN* 1.3 75.0 - - - +
503A GLN* 1.3 82.2 + - - +
504A THR 3.4 0.9 - - - -
505A ARG* 3.8 13.3 - - - +
506A ARG* 3.0 24.9 + - - +
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Residues in contact with GLN 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A ALA* 4.1 18.7 - - + +
501A ASN* 3.5 4.2 - - + +
502A ASP* 1.3 99.3 + - - +
504A THR* 1.3 60.0 + - + +
506A ARG* 3.3 14.9 + - - +
507A ARG* 3.0 26.5 + - - +
83B CYS* 5.8 4.6 - - - -
139B LEU* 4.1 38.6 - - + +
56D TRP* 4.2 29.0 - - + -
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Residues in contact with THR 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 3.3 42.7 + - + +
500A GLY 4.1 0.2 - - - -
501A ASN* 2.5 42.1 + - + +
503A GLN* 1.3 76.9 - - + +
505A ARG* 1.3 54.1 + - - -
507A ARG* 3.2 8.3 + - - +
508A LEU* 3.0 27.0 + - - +
54D LEU* 4.3 35.0 - - + +
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Residues in contact with ARG 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLN* 3.6 14.2 + - - +
356A THR* 6.2 2.5 - - - -
358A ARG* 3.4 54.5 - - - +
359A PRO* 3.1 33.2 + - - +
360A CYS* 4.0 12.1 - - + -
497A LEU 3.8 12.3 - - - +
498A GLN* 3.1 37.2 + - + +
499A ASN 4.9 0.4 - - - -
500A GLY 4.3 9.1 + - - +
501A ASN* 3.3 31.5 + - - +
502A ASP* 3.8 10.9 - - - +
503A GLN 3.3 0.2 - - - -
504A THR* 1.3 72.4 + - - +
506A ARG* 1.3 60.3 + - - +
508A LEU* 3.3 10.5 + - + +
509A ALA* 2.9 25.8 + - - +
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Residues in contact with ARG 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A CYS* 3.8 8.2 - - - -
361A ALA* 3.5 34.5 - - + +
362A PRO 3.2 18.8 + - - -
363A ILE* 3.9 17.4 - - + +
364A LEU 5.6 0.8 - - - +
502A ASP 3.0 18.7 + - - +
503A GLN* 3.5 16.4 + - - +
504A THR 3.3 0.4 - - - -
505A ARG* 1.3 76.0 - - - +
507A ARG* 1.3 64.0 + - - +
509A ALA* 3.3 4.1 + - - +
510A VAL* 3.0 45.3 + - - +
139B LEU* 4.3 15.8 + - - +
140B GLN* 4.1 30.9 + - - +
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Residues in contact with ARG 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 4.9 19.4 - - + +
503A GLN 3.0 13.3 + - - +
504A THR* 3.4 10.8 - - - +
506A ARG* 1.3 81.0 - - - +
508A LEU* 1.3 63.1 + - - +
510A VAL* 3.3 7.0 + - - +
511A TYR* 3.1 23.7 + - + +
1062A GLN* 3.2 32.9 - - - +
1064A SER* 6.2 0.6 - - - -
1067A GLU* 4.2 27.7 + - - +
1068A ASP* 3.3 14.5 + - - +
1070A ILE* 4.3 25.4 - - - +
102D TRP* 5.9 0.8 - - - -
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 4.7 13.7 - - + +
335A ILE* 4.4 8.5 - - + -
336A GLN* 3.9 22.7 - - - +
494A ILE* 3.8 34.3 - - + +
497A LEU* 4.5 22.3 - - + +
498A GLN* 4.2 29.6 - - + -
504A THR 3.0 12.2 + - - +
505A ARG* 3.5 9.6 - - - +
507A ARG* 1.3 76.4 - - - +
509A ALA* 1.3 56.6 + - - +
511A TYR* 3.4 14.2 + - + +
512A CYS* 3.0 27.7 + - - +
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Residues in contact with ALA 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A GLN* 3.5 20.6 + - - +
338A CYS* 4.3 2.0 - - - -
354A ALA* 5.1 10.1 - - + -
356A THR* 4.9 9.2 - - + -
360A CYS* 4.9 3.1 - - - -
363A ILE* 4.0 17.5 - - + -
368A VAL* 6.1 1.1 - - + -
505A ARG 2.9 16.7 + - - +
506A ARG* 3.7 6.7 - - - +
507A ARG 3.3 0.2 - - - -
508A LEU* 1.3 73.1 - - - +
510A VAL* 1.3 61.5 + - - +
512A CYS* 3.4 2.5 + - - +
513A LEU* 3.0 33.3 + - - +
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Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 3.8 28.9 - - + -
506A ARG* 3.0 33.1 + - - +
507A ARG* 3.3 7.1 + - - +
509A ALA* 1.3 76.3 - - - +
511A TYR* 1.3 61.8 + - - +
513A LEU* 3.4 7.7 + - + +
514A LYS* 3.1 23.8 + - + +
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Residues in contact with TYR 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A GLU* 5.0 9.4 - - - -
494A ILE* 5.2 12.8 - - + -
507A ARG* 3.1 15.2 + - + +
508A LEU* 3.5 19.3 - - + +
510A VAL* 1.3 77.9 - - - +
512A CYS* 1.3 62.6 + - - +
514A LYS* 3.3 10.3 + - + +
515A ASP* 3.0 47.4 + - - +
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Residues in contact with CYS 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP* 4.0 21.9 - - - +
317A ILE 4.6 0.4 - - - -
318A GLU* 3.9 33.9 - - + +
336A GLN* 4.1 9.0 - - - +
338A CYS* 3.6 28.9 - - - -
508A LEU 3.0 16.5 + - - +
509A ALA 3.4 4.2 + - - +
511A TYR* 1.3 77.1 - - - +
513A LEU* 1.3 57.2 + - - +
515A ASP* 3.3 7.8 + - - +
516A ALA* 2.9 26.9 + - - +
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Residues in contact with LEU 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A CYS* 4.3 14.1 - - + -
340A LEU* 3.3 32.0 - - + +
352A ARG* 4.1 17.3 - - + +
353A LEU 4.4 12.1 - - - +
354A ALA* 4.3 16.2 - - + -
363A ILE* 4.6 16.6 - - + -
366A ALA* 4.5 17.7 - - + -
509A ALA 3.0 19.7 + - - +
510A VAL* 3.8 6.7 - - + +
512A CYS* 1.3 74.4 - - - +
514A LYS* 1.3 59.5 + - - +
516A ALA* 3.4 4.4 + - - +
517A TYR* 3.0 29.2 + - - +
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Residues in contact with LYS 514 (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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510A VAL* 3.1 15.1 + - + +
511A TYR* 3.3 13.4 + - + +
513A LEU* 1.3 73.4 - - - +
515A ASP* 1.3 67.9 + - - +
517A TYR* 3.2 14.6 + - + +
518A LEU* 3.2 40.3 + - - +
521A ARG* 3.4 32.3 - - - +
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Residues in contact with ASP 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A ASP* 4.0 22.7 - - - +
318A GLU* 4.6 5.0 - - - +
474A LEU* 4.7 18.8 - - + +
511A TYR* 3.0 43.8 + - - +
512A CYS* 3.4 9.4 - - - +
514A LYS* 1.3 79.9 - - - +
516A ALA* 1.3 61.5 + - - +
517A TYR 3.3 0.9 + - - -
518A LEU* 3.5 7.2 + - - +
519A PRO* 3.3 18.9 - - - +
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Residues in contact with ALA 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 3.7 24.4 - - - +
315A PHE* 4.1 7.2 - - - -
316A ASP* 3.9 17.4 - - + +
338A CYS 3.7 26.9 - - - +
340A LEU* 4.4 13.1 - - + +
512A CYS 2.9 16.3 + - - +
513A LEU* 3.4 6.7 + - - +
514A LYS 3.4 0.2 - - - -
515A ASP* 1.3 75.4 - - - +
517A TYR* 1.3 59.0 + - - +
519A PRO* 4.0 5.6 - - - +
520A LEU* 4.9 0.9 - - - +
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Residues in contact with TYR 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 4.3 16.2 - - + -
342A LEU* 6.0 0.4 - - + -
349A PRO* 4.5 26.0 - - + +
352A ARG* 5.2 14.6 - - - +
513A LEU 3.0 16.8 + - - +
514A LYS* 3.2 17.9 + - + +
515A ASP 3.2 0.6 - - - -
516A ALA* 1.3 78.9 - - - +
518A LEU* 1.3 65.6 + - - +
519A PRO 3.5 0.4 - - - -
520A LEU* 3.3 34.3 + - + +
521A ARG* 3.6 37.9 + - + +
524A GLU* 4.8 6.3 + - - -
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU* 3.7 36.1 - - + -
478A SER* 3.8 20.2 - - - +
482A LEU* 3.7 31.0 - - + -
484A GLU* 5.5 4.5 - - - +
514A LYS* 3.2 33.8 + - - +
515A ASP* 4.0 5.6 - - - +
517A TYR* 1.3 76.4 - - - +
519A PRO* 1.4 67.7 - - + +
521A ARG* 3.3 11.2 + - - +
522A LEU* 3.1 24.2 + - + +
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Residues in contact with PRO 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A SER* 5.3 4.3 - - - +
394A THR* 5.3 3.8 + - - +
395A GLY* 3.9 37.2 - - - +
396A TYR* 4.1 17.3 - - + +
459A MET* 4.3 13.3 - - + +
474A LEU* 5.3 4.7 - - + -
515A ASP 3.3 16.6 - - - +
516A ALA* 4.0 7.4 - - - +
517A TYR 3.7 3.4 - - - -
518A LEU* 1.4 85.9 - - + +
520A LEU* 1.3 59.6 + - - +
522A LEU* 3.4 10.6 + - + +
523A LEU* 2.9 29.6 + - - +
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Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 4.1 23.6 - - + +
314A SER* 3.2 26.3 + - - +
340A LEU* 3.9 34.1 - - + +
341A GLY* 5.1 0.4 - - - +
342A LEU* 3.8 33.9 - - + -
349A PRO* 5.5 1.3 - - + -
394A THR* 4.7 0.4 - - - +
516A ALA 4.9 0.9 - - - +
517A TYR* 3.3 27.6 + - + +
519A PRO* 1.3 74.9 - - - +
521A ARG* 1.3 61.9 + - - +
523A LEU* 3.2 13.4 + - + +
524A GLU* 3.0 35.5 + - - +
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Residues in contact with ARG 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A LEU* 3.7 30.7 - - + +
514A LYS* 3.4 23.9 - - - +
517A TYR* 3.6 47.7 + - + +
518A LEU* 3.3 13.9 + - + +
520A LEU* 1.3 78.4 - - - +
522A LEU* 1.3 59.3 + - - +
524A GLU* 3.5 14.4 + - - +
525A ARG* 2.9 64.6 + - - +
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Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A TYR* 5.1 5.4 - - + -
459A MET* 4.5 14.4 - - + -
463A LEU* 5.0 9.6 - - + -
474A LEU* 4.9 12.1 - - + -
477A VAL* 4.5 25.4 - - + +
478A SER* 5.5 1.6 - - - +
481A PHE* 4.2 23.8 - - + -
482A LEU* 4.7 13.2 - - + -
518A LEU* 3.1 23.4 + - + +
519A PRO* 3.7 11.4 - - + +
520A LEU 3.2 0.2 - - - -
521A ARG* 1.3 77.9 - - - +
523A LEU* 1.3 60.8 + - - +
525A ARG* 4.6 3.4 - - + -
526A LEU* 3.1 55.2 + - + +
528A VAL* 4.4 0.7 - - - +
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A VAL* 4.3 24.7 - - + -
344A TRP* 6.4 1.1 - - + -
392A VAL* 6.3 0.2 - - + -
394A THR* 4.3 17.5 - - + +
457A MET* 5.2 7.4 - - + -
459A MET* 4.3 14.3 - - + +
519A PRO 2.9 16.3 + - - +
520A LEU* 3.2 15.7 + - + +
522A LEU* 1.3 79.5 - - - +
524A GLU* 1.3 62.9 + - + +
527A MET* 3.9 1.0 + - - -
528A VAL* 3.5 47.1 + - + -
529A LEU* 4.0 31.8 + - + +
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Residues in contact with GLU 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU* 5.8 6.2 - - - +
344A TRP* 5.9 6.3 - - + +
346A GLU 5.8 0.3 - - - +
347A PRO* 5.2 11.2 - - - +
517A TYR* 4.8 6.1 + - - -
520A LEU* 3.0 18.1 + - - +
521A ARG* 3.5 21.7 + - - +
523A LEU* 1.3 77.5 - - + +
525A ARG* 1.3 67.5 + - - +
526A LEU 3.7 0.2 + - - -
527A MET* 3.9 10.6 + - - +
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Residues in contact with ARG 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A PHE* 5.0 5.2 + - - -
482A LEU* 3.4 29.9 - - - +
521A ARG* 2.9 52.5 + - - +
522A LEU* 4.3 4.0 - - + +
524A GLU* 1.3 81.5 - - + +
526A LEU* 1.3 61.5 + - + +
527A MET* 3.2 4.6 + - - +
681A LEU* 4.5 13.2 - - + +
682A ARG* 2.3 54.7 + - - +
685A VAL* 4.8 0.7 - - - +
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Residues in contact with LEU 526 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A MET* 4.7 7.6 - - + -
463A LEU* 4.5 21.3 - - + -
467A TYR* 3.7 26.9 + - + +
481A PHE* 4.1 27.1 - - + -
522A LEU* 3.1 42.5 + - + +
524A GLU 3.5 0.2 - - - -
525A ARG* 1.3 78.6 - - + +
527A MET* 1.3 69.8 - - - +
528A VAL* 3.5 13.1 + - + +
531A ASN* 4.7 2.8 + - - -
681A LEU* 5.3 4.0 - - + -
684A GLN* 4.9 2.0 - - - +
685A VAL* 4.2 24.7 - - + +
----------------------------------------------------------
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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