Contacts of the helix formed by residues 419 - 446 (chain B) in PDB entry 6I53
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 ASP 419 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ILE* 4.4 4.5 - - - +
416B ASP* 4.4 6.4 - - - +
417B LEU 3.2 8.3 - - - +
418B THR* 1.3 80.5 - - - +
420B VAL* 1.3 73.8 + - - +
421B ASN* 3.7 7.9 + - - +
422B ALA* 3.4 29.5 + - + +
423B ILE* 3.3 27.4 + - - +
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B TYR* 3.6 44.2 - - + -
302B VAL* 3.7 22.0 - - + +
305B ILE* 4.7 8.5 - - + -
306B PHE* 3.6 42.6 - - + +
419B ASP* 1.3 77.8 + - - +
421B ASN* 1.3 66.4 + - - +
422B ALA 3.2 1.1 + - - -
423B ILE* 3.6 14.1 + - - +
424B ASP* 3.7 13.7 + - - +
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Residues in contact with ASN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B TYR* 5.7 5.6 - - + -
419B ASP* 3.7 6.6 + - - +
420B VAL* 1.3 78.4 - - - +
422B ALA* 1.3 59.7 + - - +
423B ILE 3.3 0.2 - - - -
424B ASP* 3.5 12.1 + - - +
425B ARG* 3.1 66.9 + - - +
428B ARG* 5.0 5.9 + - - -
323C ASN* 5.5 6.5 - - - +
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ASP* 3.8 29.2 - - + +
419B ASP* 3.4 34.4 + - + +
420B VAL 3.2 1.0 - - - -
421B ASN* 1.3 77.6 - - - +
423B ILE* 1.3 60.3 + - - +
425B ARG* 3.6 7.4 + - - +
426B TRP* 3.0 28.2 + - - +
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Residues in contact with ILE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 3.3 22.2 - - + +
301B PHE* 3.7 36.3 - - + -
302B VAL* 4.2 13.5 - - + -
305B ILE* 3.7 16.2 - - + -
416B ASP 3.6 20.0 - - - +
417B LEU* 4.5 3.8 - - + -
419B ASP 3.3 20.4 - - - +
420B VAL* 3.6 7.5 + - - +
421B ASN 3.3 0.4 - - - -
422B ALA* 1.3 72.7 - - - +
424B ASP* 1.3 61.7 + - - +
426B TRP* 3.3 14.7 + - + +
427B SER* 2.9 37.1 + - - +
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Residues in contact with ASP 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PHE* 4.0 23.1 - - - +
242B ILE 4.8 3.1 - - - +
244B TYR* 4.7 8.8 + - - +
250B ARG* 3.0 40.7 + - - -
298B GLU* 3.2 12.9 - - - +
302B VAL* 4.0 4.2 - - - +
420B VAL* 3.7 12.8 + - - +
421B ASN* 3.5 16.8 + - - +
422B ALA 3.3 0.4 - - - -
423B ILE* 1.3 78.0 - - - +
425B ARG* 1.3 58.2 + - - +
427B SER* 3.2 3.1 + - - +
428B ARG* 3.1 40.0 + - - +
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Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ASN* 3.1 49.8 + - - +
422B ALA* 3.8 6.5 - - - +
424B ASP* 1.3 76.6 - - - +
426B TRP* 1.3 61.2 + - - +
428B ARG* 4.1 24.6 + - - +
429B ILE* 3.9 21.8 - - - +
319C TYR* 5.6 3.8 + - - -
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Residues in contact with TRP 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 6.1 1.1 - - + -
415B PRO* 3.9 45.6 - - + +
416B ASP 5.2 4.5 - - - +
422B ALA 3.0 18.4 + - - +
423B ILE* 3.5 15.3 - - + +
424B ASP 3.1 0.4 - - - -
425B ARG* 1.3 78.6 - - - +
427B SER* 1.3 84.8 + - - +
429B ILE* 3.3 7.1 + - - +
430B VAL* 3.2 60.5 + - + +
431B PHE* 5.7 7.6 - + - -
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PHE* 3.6 35.2 - - - -
298B GLU* 3.7 16.4 + - - +
423B ILE* 2.9 18.5 + - - +
424B ASP 3.2 0.9 + - - -
426B TRP* 1.3 90.6 - - - +
428B ARG* 1.3 64.2 + - - +
429B ILE 3.2 2.6 + - - -
430B VAL* 4.0 6.3 - - - +
431B PHE* 3.5 31.9 + - - +
432B PRO* 3.9 1.2 - - - +
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Residues in contact with ARG 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B PHE* 2.8 41.8 + - + -
241B TRP* 3.5 50.0 - - + +
242B ILE 5.5 0.8 + - - -
421B ASN* 5.0 5.9 + - - -
424B ASP* 3.1 30.4 + - - +
425B ARG* 4.3 25.5 - - - +
426B TRP 3.3 0.6 - - - -
427B SER* 1.3 77.1 - - - +
429B ILE* 1.3 62.6 + - + +
432B PRO* 3.3 20.7 - - - +
319C TYR* 3.3 45.9 + - - -
323C ASN* 5.4 1.0 + - - -
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Residues in contact with ILE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ARG 3.9 17.3 - - - +
426B TRP* 3.3 6.1 + - - +
427B SER 3.2 0.2 - - - -
428B ARG* 1.3 85.1 - - + +
430B VAL* 1.3 66.6 + - + +
431B PHE 3.5 0.4 - - - -
432B PRO* 3.7 4.2 - - - +
433B PHE* 3.3 23.9 + - + +
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Residues in contact with VAL 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B TRP* 3.2 61.3 + - + +
427B SER* 3.8 4.5 + - - -
429B ILE* 1.3 81.1 - - + +
431B PHE* 1.3 63.9 + - + +
433B PHE* 2.9 9.1 + - + +
434B THR* 2.5 53.3 + - - +
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B TRP* 3.2 37.0 - + + +
240B PHE* 3.4 38.1 - + + -
291B PHE* 5.0 14.1 - + + -
294B LEU* 4.1 39.5 - - + -
295B ALA* 4.1 7.0 - - + -
298B GLU* 4.8 4.0 - - + -
426B TRP* 5.7 7.6 - + - -
427B SER* 3.5 18.1 + - - +
430B VAL* 1.3 91.9 - - + +
432B PRO* 1.3 66.4 - - + +
434B THR* 4.3 9.9 - - + +
435B PHE* 3.3 15.6 + - - +
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Residues in contact with PRO 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B TRP* 3.9 30.5 - - + -
241B TRP* 5.2 8.7 - - + -
427B SER 3.9 1.3 - - - +
428B ARG* 3.3 29.4 - - - +
429B ILE* 3.7 7.0 - - - +
431B PHE* 1.3 91.8 - - + +
433B PHE* 1.3 54.4 + - - -
436B SER* 3.3 21.9 - - - -
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Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ILE* 3.3 20.9 + - + +
430B VAL* 2.9 9.0 + - + +
432B PRO* 1.3 78.9 - - - +
434B THR* 1.3 64.3 + - - +
435B PHE 3.4 0.2 - - - -
436B SER* 3.8 4.7 - - - -
437B LEU* 3.2 59.9 + - + +
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B PHE* 3.6 20.6 - - + -
430B VAL* 2.5 39.6 + - - +
431B PHE* 4.5 7.6 - - + -
433B PHE* 1.3 75.3 - - - +
435B PHE* 1.3 60.9 + - - +
437B LEU* 3.3 9.3 + - + +
438B PHE* 3.0 23.7 + - - +
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Residues in contact with PHE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 4.6 20.2 - - + -
233B THR* 4.1 20.0 - - + -
234B ILE* 5.3 2.9 - - + -
237B TRP* 3.6 26.0 - + + -
284B TYR* 4.1 7.9 - - - -
288B CYS* 3.6 31.9 - - - -
291B PHE* 3.6 38.7 - + + -
431B PHE 3.3 18.4 + - - +
434B THR* 1.3 76.3 - - - +
436B SER* 1.3 62.4 + - - +
438B PHE* 3.1 21.4 + + - +
439B ASN* 3.2 35.9 + - - -
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Residues in contact with SER 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B PRO 3.3 21.6 + - - -
433B PHE* 3.6 8.9 + - - -
434B THR 3.3 0.6 - - - -
435B PHE* 1.3 80.5 - - - +
437B LEU* 1.3 61.4 + - - +
439B ASN* 3.8 7.8 + - - +
440B LEU* 3.4 20.1 + - - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B PHE* 3.2 55.7 + - + +
434B THR* 3.7 9.0 - - + +
435B PHE 3.3 0.2 - - - -
436B SER* 1.3 75.7 - - - +
438B PHE* 1.3 60.5 + - - +
440B LEU* 3.7 21.6 - - + +
441B VAL* 3.1 37.1 + - + +
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Residues in contact with PHE 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET* 3.6 25.6 - - + -
284B TYR* 3.8 25.1 - + - -
287B GLY* 3.7 26.5 - - - -
288B CYS* 4.4 2.7 - - - -
291B PHE* 3.7 27.4 - + + -
434B THR 3.0 13.5 + - - +
435B PHE* 3.1 21.4 + + - +
437B LEU* 1.3 78.4 - - - +
439B ASN* 1.3 62.6 + - - +
441B VAL* 3.7 5.4 + - + +
442B TYR* 3.1 33.1 + + + +
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Residues in contact with ASN 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 5.1 7.7 - - - +
284B TYR* 3.2 35.6 + - - -
435B PHE* 3.2 41.6 + - - +
436B SER* 3.8 7.5 + - - +
437B LEU 3.4 0.2 - - - -
438B PHE* 1.3 75.6 - - - +
440B LEU* 1.3 60.2 + - - +
442B TYR* 4.3 1.6 - - - -
443B TRP* 2.8 52.8 + - + +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B SER 3.4 16.4 + - - +
437B LEU* 3.9 22.9 - - + +
438B PHE 3.3 0.6 - - - -
439B ASN* 1.3 76.4 - - - +
441B VAL* 1.3 64.0 + - + +
443B TRP* 5.3 0.4 - - - -
444B LEU* 3.3 48.0 + - + +
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B LEU* 3.1 21.6 + - + +
438B PHE* 4.2 6.1 - - + +
440B LEU* 1.3 76.6 - - + +
442B TYR* 1.3 63.8 + - - +
444B LEU* 4.4 1.2 - - - +
445B TYR* 3.2 27.2 + - + +
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Residues in contact with TYR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.5 6.7 - - + +
226B TYR* 2.8 39.9 + + - -
280B ALA* 2.3 36.7 + - - +
283B MET* 4.4 10.3 - - + -
284B TYR* 3.8 26.4 - + + +
438B PHE* 3.1 27.2 + + + +
439B ASN* 3.3 4.7 + - - +
441B VAL* 1.3 78.9 - - - +
443B TRP* 1.3 86.2 + + - +
444B LEU 3.1 5.0 + - - -
445B TYR* 3.3 1.6 + - - -
446B TYR* 3.2 59.1 + + - +
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Residues in contact with TRP 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.9 20.6 - - + -
218B ILE* 4.2 17.9 - - + -
222B ILE* 3.9 23.1 - - + -
226B TYR* 3.5 44.2 - + + -
230B ILE* 5.9 2.6 - - - +
284B TYR* 4.5 4.2 + + - -
439B ASN* 2.8 53.0 + - + +
440B LEU* 4.4 1.1 - - - -
442B TYR* 1.3 84.9 - + - +
444B LEU* 1.3 66.0 + - + +
447B VAL* 3.4 39.8 - - + +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B LEU* 3.3 44.0 + - + +
441B VAL* 4.4 1.3 - - - +
442B TYR 3.1 0.8 - - - -
443B TRP* 1.3 84.4 - - - +
445B TYR* 1.3 61.4 + - - +
446B TYR 3.4 1.6 - - - -
447B VAL* 4.1 11.8 + - + +
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Residues in contact with TYR 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ARG* 3.5 22.9 + - - -
441B VAL* 3.2 24.4 + - + +
442B TYR 3.3 2.0 + - - +
444B LEU* 1.3 79.4 - - - +
446B TYR* 1.3 98.6 + + + +
447B VAL 3.5 1.0 - - - -
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Residues in contact with TYR 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG 4.4 4.6 + - - -
142B ARG* 3.4 42.5 + - + +
145B LEU* 3.5 42.4 - - + +
280B ALA* 3.6 26.1 - - + +
283B MET* 3.7 27.6 - - + +
442B TYR* 3.2 49.8 + + + +
445B TYR* 1.3 108.4 - + + +
447B VAL* 1.3 60.8 + - - +
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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