Contacts of the helix formed by residues 399 - 421 (chain B) in PDB entry 1SIW
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 THR 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B VAL* 4.2 20.0 - - + -
388B GLN* 3.2 36.1 - - - +
391B ALA* 3.7 18.6 - - + -
397B GLY 3.4 1.5 + - - +
398B ASP* 1.3 74.0 + - - +
400B LYS* 1.3 67.7 + - - +
401B PRO 3.5 0.2 - - - -
402B VAL* 3.2 5.1 + - - +
403B LEU* 3.0 35.7 + - - +
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B ASP* 3.0 15.0 + - - +
399B THR* 1.3 80.4 + - - +
401B PRO* 1.3 71.6 - - + +
403B LEU* 3.3 8.6 + - - +
404B ARG* 3.1 24.7 + - + +
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Residues in contact with PRO 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR* 3.8 30.5 - - + -
338B LYS 4.8 1.0 - - - +
341B LEU* 4.0 16.0 - - + +
395B THR* 3.5 26.0 - - + -
398B ASP* 3.5 21.3 - - + +
400B LYS* 1.3 96.7 - - + +
402B VAL* 1.3 59.9 + - - +
404B ARG* 3.6 21.6 + - + +
405B ALA* 3.2 22.0 + - - +
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Residues in contact with VAL 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 4.0 19.7 - - + -
357B PRO* 4.5 6.5 - - + -
387B VAL* 3.5 23.8 - - + -
390B LEU* 3.8 22.7 - - + +
391B ALA* 3.8 18.6 - - + +
394B LEU* 4.9 2.2 - - + -
395B THR* 3.7 23.6 - - + +
398B ASP 4.3 0.9 - - - +
399B THR 3.2 7.5 + - - +
401B PRO* 1.3 74.3 - - - +
403B LEU* 1.3 66.5 + - - +
405B ALA* 3.3 4.0 + - - +
406B LEU* 3.0 34.6 + - + +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B VAL* 3.5 31.1 - - + +
381B GLU* 5.9 0.7 - - - +
387B VAL* 3.8 28.5 - - + -
399B THR* 3.0 33.4 + - - +
400B LYS* 3.7 6.7 - - - +
402B VAL* 1.3 78.7 - - - +
404B ARG* 1.3 52.2 + - - +
406B LEU* 3.3 4.7 + - + +
407B LYS* 2.8 51.1 + - - +
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Residues in contact with ARG 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR* 3.4 32.9 + - - -
294B GLN* 5.4 3.4 - - - +
338B LYS* 3.9 39.2 + - - +
341B LEU* 5.7 0.2 - - - +
400B LYS* 3.1 17.7 + - + +
401B PRO* 3.8 16.4 + - - +
403B LEU* 1.3 76.1 - - - +
405B ALA* 1.3 61.8 + - - +
407B LYS* 3.4 13.6 - - - +
408B ARG* 3.0 63.8 + - + +
433B VAL* 5.4 2.0 - - + +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LYS 3.7 15.2 + - - +
339B LEU* 3.7 30.4 - - + +
341B LEU* 4.8 2.2 - - + -
357B PRO* 3.8 15.0 - - + -
401B PRO 3.2 12.1 + - - +
402B VAL* 3.3 8.0 + - - +
404B ARG* 1.3 80.7 - - - +
406B LEU* 1.3 63.3 + - - +
408B ARG* 3.7 2.1 - - - +
409B MET* 3.1 31.0 + - + +
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B PRO* 4.0 12.6 - - + -
358B PRO 3.3 28.5 - - - +
359B LEU* 3.6 19.5 - - + +
380B VAL* 4.0 16.6 - - + -
383B LEU* 4.1 16.4 - - + -
385B ILE 6.1 0.4 - - - +
387B VAL* 4.6 9.9 - - + -
390B LEU* 4.4 10.1 - - + -
402B VAL* 3.0 35.2 + - + +
403B LEU* 3.8 2.9 - - + +
405B ALA* 1.3 77.9 - - - +
407B LYS* 1.3 62.1 + - - +
409B MET* 3.3 15.2 + - + +
410B LEU* 3.0 29.6 + - - +
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Residues in contact with LYS 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B VAL* 4.0 33.1 - - + +
381B GLU* 5.2 2.2 - - - +
403B LEU* 2.8 60.1 + - - +
404B ARG* 3.4 13.2 - - - +
406B LEU* 1.3 72.9 - - - +
408B ARG* 1.3 57.9 + - - +
410B LEU* 3.1 8.9 + - + +
411B ALA* 2.8 28.4 + - - +
432B GLU* 5.5 10.8 - - + +
433B VAL* 3.7 25.0 - - + +
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Residues in contact with ARG 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLU 4.0 6.1 + - - -
337B TRP* 3.0 36.5 + - - +
338B LYS* 4.6 4.0 - - - +
339B LEU* 4.0 11.2 - - + -
404B ARG* 3.0 52.7 + - + +
405B ALA 3.7 3.4 - - - +
407B LYS* 1.3 75.8 - - - +
409B MET* 1.3 61.3 + - - +
411B ALA* 3.3 8.4 + - - +
412B MET* 3.0 22.9 + - - +
433B VAL* 3.1 38.8 + - + -
434B GLY* 4.0 11.5 + - - -
435B LEU* 3.4 35.5 - - + +
439B GLN* 5.6 1.0 - - - +
443B MET* 4.0 5.5 - - + +
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Residues in contact with MET 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 4.8 12.1 - - + -
12B ASN* 5.4 1.1 - - - -
14B ASP* 4.8 11.2 - - + +
339B LEU* 4.2 17.3 - - + -
356B VAL* 3.5 25.4 - - + -
357B PRO* 3.2 26.5 - - + +
359B LEU* 4.2 18.4 - - + -
405B ALA 3.1 20.5 + - - +
406B LEU* 3.7 23.1 - - + +
407B LYS 3.2 0.2 - - - -
408B ARG* 1.3 77.2 - - - +
410B LEU* 1.3 62.7 + - - +
412B MET* 3.4 15.1 + - + +
413B ARG* 3.2 25.6 + - - +
443B MET* 4.6 3.8 - - + -
447B LEU* 5.2 7.9 - - + -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 3.8 26.9 - - + -
374B ASN* 4.1 14.8 + - - +
377B LEU* 5.1 2.7 - - + +
378B PRO* 3.8 24.5 - - + +
379B ASP* 3.8 2.2 - - - +
380B VAL* 3.5 38.4 - - + +
383B LEU* 4.4 14.6 - - + -
406B LEU 3.0 19.1 + - - +
407B LYS* 3.5 7.2 - - - +
409B MET* 1.3 73.4 - - - +
411B ALA* 1.3 66.1 + - - +
413B ARG* 3.1 25.3 + - - +
414B HIS* 2.9 21.9 + - - +
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ASN* 5.1 2.0 - - - +
407B LYS 2.8 16.1 + - - +
408B ARG 3.5 5.8 - - - +
409B MET 3.3 0.2 - - - -
410B LEU* 1.3 74.5 - - - +
412B MET* 1.3 66.5 + - - +
414B HIS* 3.0 3.9 + - - +
415B TYR* 2.9 24.4 + - - +
429B ALA* 3.7 40.4 - - + +
430B LEU* 4.1 8.2 - - + +
433B VAL* 3.8 16.6 - - + -
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Residues in contact with MET 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.4 49.8 - - + +
408B ARG 3.0 13.3 + - - +
409B MET* 3.5 15.5 - - + +
410B LEU 3.3 0.2 - - - -
411B ALA* 1.3 74.3 - - - +
413B ARG* 1.3 58.4 + - - +
415B TYR* 3.4 2.9 + - - +
416B LYS* 2.9 45.7 + - + +
430B LEU* 4.3 10.7 - - - +
435B LEU* 5.7 0.2 - - + -
440B ALA* 4.1 17.0 - - + +
443B MET* 3.8 24.2 - - + +
444B TYR* 3.7 31.6 - - + -
447B LEU* 4.2 11.0 - - + -
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Residues in contact with ARG 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ARG* 2.9 39.4 + - - +
272A TYR* 4.1 22.0 - - + -
274A GLY* 3.4 10.7 - - - -
275A THR 3.0 22.8 + - - -
292A ASP* 2.7 45.6 + - - -
359B LEU* 4.1 17.6 - - - +
377B LEU* 3.8 22.9 - - + +
378B PRO* 3.9 12.3 - - - +
409B MET 3.2 14.8 - - - +
410B LEU* 3.1 25.9 + - + +
412B MET* 1.3 77.1 - - + +
414B HIS* 1.3 57.3 + - - +
416B LYS 3.3 0.7 + - - -
417B ARG* 2.9 27.4 + - - +
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Residues in contact with HIS 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B SER 3.9 1.8 + - - -
374B ASN* 3.5 48.6 - - + +
375B GLY* 5.1 0.6 + - - -
377B LEU* 3.8 10.5 - - + +
410B LEU 2.9 12.5 + - - +
411B ALA 3.0 7.6 + - - +
413B ARG* 1.3 77.0 - - - +
415B TYR* 1.3 63.7 + - - +
417B ARG* 3.3 2.6 + - - +
418B ALA* 3.1 22.1 + - + +
426B ASP* 3.2 43.6 + - + -
428B ARG* 3.6 20.4 + - - -
429B ALA* 3.6 16.4 - - + +
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Residues in contact with TYR 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B ALA 2.9 15.0 + - - +
412B MET 3.7 2.0 - - - +
414B HIS* 1.3 77.0 + - - +
416B LYS* 1.3 77.1 + - + +
418B ALA* 3.4 5.1 + - - +
419B GLU* 3.2 41.9 + - + +
424B LYS 4.9 0.8 - - - +
425B VAL* 4.7 6.7 - - + -
426B ASP 3.7 26.7 - - - +
427B THR* 4.1 4.7 - - + -
430B LEU* 3.6 24.9 - - + -
437B GLU* 3.2 43.8 + - + +
440B ALA* 4.0 20.6 - - + -
441B GLN* 2.9 34.1 + - - -
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Residues in contact with LYS 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR 3.2 15.7 - - - +
273A LYS* 3.4 21.1 - - - +
412B MET* 2.9 27.9 + - + +
413B ARG 3.8 0.7 - - - +
415B TYR* 1.3 93.0 - - + +
417B ARG* 1.3 58.2 + - - +
419B GLU* 3.1 28.2 + - - +
420B THR* 2.9 41.9 + - - +
440B ALA 5.1 1.6 - - - +
441B GLN* 3.5 17.1 - - - +
444B TYR* 3.8 45.6 - - + -
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER 2.9 22.4 + - - -
248A TYR* 4.3 3.8 - - - -
273A LYS 3.6 2.4 + - - -
274A GLY* 2.7 43.4 + - - +
275A THR* 3.8 0.4 - - - +
276A LYS 3.8 4.4 - - - +
528A ASN* 3.1 29.3 + - - +
531A LYS* 6.0 1.2 - - - +
376B ILE* 3.4 34.6 - - - +
377B LEU* 4.2 15.9 - - + -
413B ARG 2.9 16.9 + - - +
414B HIS* 3.7 4.5 - - - +
416B LYS* 1.3 74.0 - - - +
418B ALA* 1.3 67.6 + - - +
420B THR* 4.0 2.5 - - - -
421B VAL* 2.8 48.8 + - + +
422B ASP* 3.6 4.5 + - - +
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B HIS* 3.1 12.8 + - + +
415B TYR* 3.6 9.0 - - - +
417B ARG* 1.3 75.8 - - - +
419B GLU* 1.3 59.0 + - - +
422B ASP* 3.1 20.4 + - - +
423B GLY 2.8 25.1 + - - -
424B LYS* 3.0 21.5 + - + +
426B ASP* 3.7 29.2 - - + +
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Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B TYR* 3.2 26.6 + - + +
416B LYS* 3.1 31.7 + - - +
417B ARG 3.1 0.4 - - - -
418B ALA* 1.3 81.2 - - - +
420B THR* 1.3 66.9 + - + +
423B GLY* 3.2 21.5 + - - -
424B LYS 3.3 13.2 + - - +
425B VAL* 6.0 0.4 - - - -
441B GLN* 3.6 19.8 + - - -
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Residues in contact with THR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER* 5.8 0.3 - - - -
273A LYS* 3.2 45.9 + - + +
535A ARG* 3.0 22.9 + - - -
416B LYS* 2.9 25.0 + - - +
417B ARG* 3.9 2.8 + - - -
419B GLU* 1.3 91.3 - - + +
421B VAL* 1.3 67.6 + - - +
423B GLY* 4.6 0.7 - - - -
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Residues in contact with VAL 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER* 3.4 30.7 - - - -
274A GLY 5.8 1.1 - - - -
528A ASN* 4.2 6.5 - - - +
531A LYS* 4.1 30.3 - - + +
532A THR* 4.1 20.1 - - + +
535A ARG* 4.4 4.4 + - - +
417B ARG* 2.8 47.4 + - + +
420B THR* 1.3 83.7 - - - +
422B ASP* 1.3 67.3 + - - +
423B GLY 3.4 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