Contacts of the helix formed by residues 409 - 432 (chain B) in PDB entry 1ISS
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 LYS 409 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 4.0 13.7 - - - +
185B TYR* 5.0 5.2 - - + +
186B SER* 4.3 23.7 + - - +
318B ASP* 5.3 1.6 + - - -
342B LEU* 4.1 32.1 - - + +
344B SER* 4.4 4.7 - - - -
407B ASP* 2.9 17.4 + - - +
408B SER* 1.3 92.1 + - - +
410B MET* 1.3 66.7 + - - +
411B GLY 3.4 1.8 - - - -
412B PHE* 3.2 36.8 + - + +
413B VAL* 3.4 11.5 + - + +
2001B MCG 4.3 26.4 + - - +
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Residues in contact with MET 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLN* 4.4 14.8 - - + +
78B ARG* 5.0 4.9 - - - +
81B ALA* 4.1 11.2 - - + -
345B PRO 5.7 0.4 - - - +
347B VAL* 4.2 12.3 - - + -
350B PHE* 3.5 47.1 - - + -
406B GLN* 4.1 14.4 - - + +
407B ASP* 3.1 42.1 + - + +
408B SER 3.4 1.2 - - - -
409B LYS* 1.3 74.1 - - - +
411B GLY* 1.3 56.2 + - - +
413B VAL* 2.6 33.0 + - + +
414B ILE* 3.1 32.2 + - + -
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Residues in contact with GLY 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B SER* 4.0 11.4 + - - -
345B PRO* 4.7 5.6 + - - -
347B VAL* 4.3 18.3 - - - +
409B LYS 3.4 1.0 + - - -
410B MET* 1.3 78.6 - - - +
412B PHE* 1.3 63.1 + - - +
414B ILE* 3.4 5.0 + - - +
415B ASN* 3.0 32.3 + - - -
462B VAL* 4.4 6.9 - - - +
463B SER* 5.3 3.8 - - - -
465B GLU* 5.5 1.6 - - - -
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Residues in contact with PHE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B TYR* 3.4 26.0 - - + +
204B VAL* 3.7 18.2 - - + +
205B VAL* 3.3 33.2 - - + -
206B PRO* 5.3 2.9 - - + -
342B LEU* 3.4 30.3 - - + -
343B GLN 3.9 22.9 - - - -
344B SER* 4.1 13.6 + - - -
345B PRO* 6.1 0.7 - - + -
409B LYS* 3.2 28.6 + - + +
410B MET 2.9 2.4 + - - -
411B GLY* 1.3 75.5 - - - +
413B VAL* 1.3 54.1 + - - +
415B ASN* 3.1 8.2 + - - +
416B ALA* 2.7 35.3 + - - +
465B GLU* 5.6 4.7 - - - -
478B ARG* 5.6 10.1 - - + -
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PHE* 4.3 20.2 - - + -
78B ARG* 3.7 30.5 - - - +
81B ALA* 4.8 14.4 - - + -
160B ILE* 5.6 0.4 - - + -
185B TYR* 3.9 30.3 - - + -
409B LYS 3.4 12.1 + - - +
410B MET* 2.6 17.9 + - + +
412B PHE* 1.3 70.7 - - - +
414B ILE* 1.3 67.5 + - + +
416B ALA* 2.8 15.1 + - - +
417B ILE* 3.1 28.1 + - + +
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA* 5.4 2.7 - - + -
84B HIS* 5.7 5.2 - - + -
85B THR* 3.3 22.7 - - - +
88B LYS* 5.4 2.0 - - - +
347B VAL* 3.9 27.1 - - + -
350B PHE* 4.9 5.4 - - + -
410B MET* 3.1 39.7 + - + +
411B GLY 3.8 4.0 - - - +
413B VAL* 1.3 75.6 - - + +
415B ASN* 1.3 57.3 + - - +
417B ILE* 3.2 14.8 - - - +
418B TYR* 2.8 48.7 + - + +
462B VAL* 4.0 16.8 - - + -
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Residues in contact with ASN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B VAL* 4.4 11.0 - - + -
411B GLY 3.0 17.5 + - - +
412B PHE* 3.3 14.6 - - - +
414B ILE* 1.3 75.4 - - - +
416B ALA* 1.3 55.9 + - - +
417B ILE 3.0 1.6 - - - -
418B TYR* 2.9 7.1 + - - +
419B ALA* 2.6 37.4 + - - +
459B PHE* 3.7 14.6 - - + -
461B GLY* 3.4 8.6 - - - -
462B VAL* 3.0 27.8 + - - +
465B GLU* 3.3 33.7 + - - +
467B VAL* 4.6 5.3 - - + +
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Residues in contact with ALA 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ILE* 4.0 19.7 - - + +
183B ILE* 3.8 20.0 - - + +
184B ALA 4.0 7.9 - - - +
185B TYR* 4.3 6.7 - - + -
204B VAL* 3.5 22.1 - - + +
412B PHE 2.7 16.3 + - - +
413B VAL 2.8 10.7 + - - +
415B ASN* 1.3 71.0 - - - +
417B ILE* 1.3 64.5 + - - +
419B ALA* 3.4 4.6 + - - +
420B MET* 3.2 17.2 + - - +
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 5.0 10.5 - - + +
51B PHE* 5.7 0.2 - - + -
81B ALA 5.1 0.4 - - - -
82B MET* 3.6 47.8 - - + +
85B THR* 3.6 29.4 - - + +
86B LEU* 5.0 2.5 - - + -
89B ILE* 4.1 10.1 - - + -
160B ILE* 4.4 13.0 - - + -
413B VAL* 3.1 29.5 + - + +
414B ILE* 3.2 15.7 - - - +
415B ASN 3.0 0.4 - - - -
416B ALA* 1.3 73.1 - - - +
418B TYR* 1.3 58.4 + - - +
420B MET* 2.5 37.2 + - - +
421B ALA* 3.0 4.9 + - - +
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Residues in contact with TYR 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR* 4.5 4.7 - - + -
88B LYS* 3.1 34.2 + - - +
89B ILE* 3.3 34.2 + - + +
95B LEU* 4.2 20.6 - - + -
414B ILE* 2.8 39.6 + - + +
415B ASN* 2.9 11.9 + - - +
417B ILE* 1.3 77.4 - - - +
419B ALA* 1.3 61.2 + - - +
421B ALA* 3.1 13.7 + - - +
422B HIS* 3.1 24.1 + + + -
459B PHE* 4.1 14.8 - + + -
462B VAL* 4.2 22.4 - - + -
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ILE* 4.2 5.6 - - + -
204B VAL* 4.6 3.6 - - + -
415B ASN 2.6 18.7 + - - +
416B ALA* 3.6 10.1 - - - +
418B TYR* 1.3 71.9 - - - +
420B MET* 1.3 59.2 + - - +
422B HIS* 4.2 2.4 - - - +
423B GLY* 3.3 8.1 + - - -
454B LEU* 3.2 20.1 - - - +
457B SER* 5.1 3.7 - - - -
459B PHE* 3.2 27.5 - - + -
467B VAL* 5.0 0.2 - - + -
469B PHE* 4.0 26.4 - - + -
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Residues in contact with MET 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.5 33.7 - - + -
157B ALA 4.6 2.2 - - - +
158B GLY* 3.1 46.2 - - - +
159B VAL 3.6 4.7 - - - +
160B ILE* 4.1 9.2 - - + -
181B PRO* 4.2 8.3 - - + +
183B ILE* 3.7 21.1 - - + -
416B ALA 3.2 11.1 + - - +
417B ILE* 2.5 21.9 + - - +
419B ALA* 1.3 71.7 - - - +
421B ALA* 1.3 59.7 + - - +
423B GLY* 3.7 1.0 + - - -
424B LEU* 3.0 28.2 + - + +
450B LEU* 4.9 6.5 - - - -
454B LEU* 4.2 13.7 - - - -
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 5.0 0.8 - - - +
89B ILE* 4.4 9.6 - - + -
95B LEU* 3.9 22.7 - - + -
96B LEU* 4.2 7.5 - - + +
101B LEU* 4.2 19.7 - - + -
417B ILE 3.0 7.9 + - - +
418B TYR 3.5 9.0 - - - +
420B MET* 1.3 74.3 - - - +
422B HIS* 1.3 53.7 + - - +
423B GLY 3.0 1.3 - - - -
424B LEU* 2.7 35.7 + - - +
425B GLN* 2.8 18.1 + - - +
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Residues in contact with HIS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.2 28.8 - - + +
418B TYR* 3.1 25.9 + + + +
419B ALA 4.3 3.1 - - - +
421B ALA* 1.3 75.9 - - - +
423B GLY* 1.3 66.4 + - - +
425B GLN* 3.8 12.8 - - + +
426B ASN* 2.9 27.7 + - - +
457B SER* 3.8 12.0 + - - -
458B SER 4.5 5.4 + - - +
459B PHE* 3.4 47.9 - + + +
460B VAL 5.6 0.6 + - - -
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Residues in contact with GLY 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ALA 3.3 7.9 + - - -
420B MET 3.7 0.4 + - - -
421B ALA 3.0 1.6 + - - -
422B HIS* 1.3 79.4 - - - +
424B LEU* 1.3 57.5 + - - +
426B ASN* 3.6 0.5 + - - +
427B MET* 3.0 22.0 + - - +
450B LEU* 3.9 6.7 - - - -
453B PHE* 3.4 13.3 - - - +
454B LEU* 3.4 31.0 - - - -
457B SER* 3.6 12.3 + - - -
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Residues in contact with LEU 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.8 35.4 - - + -
47B ILE* 4.6 7.0 - - + -
96B LEU* 4.4 13.2 - - + -
101B LEU* 4.1 14.6 - - + -
157B ALA* 4.7 2.2 - - + -
420B MET* 3.0 23.8 - - + +
421B ALA* 2.7 18.5 + - - +
423B GLY* 1.3 69.0 - - - +
425B GLN* 1.3 67.4 + - - +
427B MET* 2.7 18.0 + - - +
428B HIS* 2.7 16.3 + - - +
442B MET* 4.6 11.3 - - + +
445B ILE* 4.1 17.0 - - + -
450B LEU* 4.3 22.2 - - + -
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Residues in contact with GLN 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.2 15.9 - - - +
95B LEU* 3.5 27.1 - - + -
96B LEU* 3.0 39.9 + - + +
97B PRO* 3.9 7.0 - - - +
421B ALA 2.8 12.3 + - - +
422B HIS* 3.8 11.2 - - + +
424B LEU* 1.3 75.9 - - - +
426B ASN* 1.3 62.7 + - - +
428B HIS* 3.2 7.4 + - - +
429B HIS* 2.8 59.2 + - + -
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Residues in contact with ASN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B HIS 2.9 19.3 + - - +
423B GLY 3.9 2.9 - - - +
425B GLN* 1.3 79.3 - - + +
427B MET* 1.3 61.3 + - - +
429B HIS* 3.8 11.0 + - - +
430B ALA* 3.5 12.6 + - - +
453B PHE* 3.3 23.0 - - + +
456B LYS 6.0 0.7 - - - +
457B SER* 4.3 11.0 - - - +
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Residues in contact with MET 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B GLY 3.0 12.1 + - - +
424B LEU* 2.7 18.0 + - - +
426B ASN* 1.3 70.3 - - - +
428B HIS* 1.3 65.1 + - - +
430B ALA* 3.3 2.4 + - - +
431B LEU* 3.0 45.5 + - + +
441B ALA 4.9 2.9 - - - +
442B MET* 3.8 34.1 - - + -
445B ILE* 4.0 8.7 - - + -
446B ASP* 3.9 31.9 - - + +
449B LYS* 4.3 7.2 - - + -
450B LEU* 4.0 25.1 - - + -
453B PHE* 3.4 27.8 - - + -
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Residues in contact with HIS 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 5.2 1.3 - - + -
97B PRO* 6.0 4.9 - - + +
99B ILE* 3.8 21.2 - - + +
424B LEU 2.7 15.0 + - - +
425B GLN* 3.4 15.5 + - - +
427B MET* 1.3 73.1 - - - +
429B HIS* 1.3 80.7 + + - +
430B ALA 2.9 0.5 + - - -
432B CYS* 2.8 52.6 + - + +
435B HIS 3.4 22.5 + - - -
436B VAL 3.8 9.0 + - - -
437B GLY 2.7 29.4 + - - -
438B LEU* 4.8 0.7 - - - -
442B MET* 3.8 17.7 - - + -
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Residues in contact with HIS 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO* 5.6 2.0 - - - +
425B GLN* 2.8 54.7 + - + +
426B ASN* 4.0 9.2 - - - +
428B HIS* 1.3 88.9 - + - +
430B ALA* 1.3 62.7 + - - +
432B CYS 5.3 1.6 - - - -
433B PRO* 4.0 17.6 - - - +
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ASN 3.5 2.9 + - - +
427B MET 3.3 1.2 + - - -
428B HIS 2.9 1.6 + - - -
429B HIS* 1.3 82.8 - - - +
431B LEU* 1.3 64.5 + - + +
432B CYS 3.7 0.7 + - - -
433B PRO* 3.7 9.2 - - - +
453B PHE* 3.6 34.3 - - + -
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Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B MET* 3.0 47.6 + - + +
430B ALA* 1.3 79.7 - - + +
432B CYS* 1.3 62.0 + - - +
433B PRO* 3.5 6.5 - - - +
439B CYS* 2.8 18.7 - - - -
441B ALA* 3.5 24.3 - - + +
442B MET* 4.9 2.5 - - + -
449B LYS* 4.3 29.2 - - + +
453B PHE* 4.5 12.6 - - + -
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Residues in contact with CYS 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B HIS* 2.8 45.3 + - + +
429B HIS* 4.4 0.7 - - - -
431B LEU* 1.3 77.1 - - - +
433B PRO* 1.3 71.1 - - - +
434B GLY 3.3 0.5 + - - -
435B HIS* 3.1 21.5 + - + +
439B CYS* 2.0 59.7 - - + -
442B MET* 4.1 19.5 - - - -
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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