Contacts of the helix formed by residues 404 - 426 (chain H) in PDB entry 4UJ4
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 SER 404 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLU* 4.9 2.8 + - - -
379H CYS* 3.7 22.6 - - - -
382H THR* 4.3 6.0 - - - +
384H GLN* 5.9 0.9 - - - -
386H LYS* 4.7 13.9 - - - -
388H CYS* 3.8 7.3 - - - -
390H HIS* 6.3 0.2 - - - -
403H ILE* 1.3 76.6 - - - +
405H PRO* 1.3 64.4 - - - +
406H PHE* 3.5 10.4 + - - +
407H CYS* 2.8 29.6 + - - -
408H ARG* 2.7 33.0 + - - +
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Residues in contact with PRO 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386H LYS* 5.1 7.4 - - + -
387H SER 3.6 23.1 - - - +
388H CYS* 4.7 0.9 - - - -
389H LYS* 5.2 8.1 - - + +
390H HIS* 5.6 4.5 - - + +
403H ILE 3.8 1.5 - - - +
404H SER* 1.3 88.2 - - - +
406H PHE* 1.3 62.1 + - + +
408H ARG* 3.7 13.3 - - + +
409H TYR* 3.2 22.2 + - - +
456H PHE* 3.8 12.7 - - + -
457H LYS 4.6 2.1 - - - +
458H GLU* 4.0 36.8 - - + +
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Residues in contact with PHE 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLU* 3.4 45.8 - - + +
297B ALA 5.0 0.4 - - - -
298B ASP* 4.6 11.9 - - - -
335H PHE* 5.5 0.7 - + - -
382H THR* 5.3 5.4 - - + -
404H SER* 3.1 9.1 + - - +
405H PRO* 1.3 79.0 - - - +
407H CYS* 1.3 73.8 + - - +
409H TYR* 3.4 4.7 + - - +
410H ARG* 3.4 62.5 + - + +
451H ALA 4.0 4.0 - - - -
454H GLY* 3.4 33.7 - - - -
456H PHE* 3.3 37.0 - + + -
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Residues in contact with CYS 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H PHE* 3.7 27.1 - - + -
379H CYS* 3.6 21.3 - - - -
381H LEU* 4.0 8.5 - - + -
382H THR* 4.0 11.9 - - - -
403H ILE* 3.3 25.8 - - + -
404H SER* 2.8 24.2 + - - +
406H PHE* 1.3 77.4 - - - +
408H ARG* 1.3 63.2 + - - +
410H ARG* 3.0 8.6 + - - +
411H ILE* 2.9 25.8 + - - +
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Residues in contact with ARG 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G HIS 5.1 5.7 + - - -
131G LEU* 5.7 7.5 + - - +
355H ILE* 4.3 14.0 - - + +
390H HIS* 2.9 57.2 + - + +
403H ILE* 3.5 10.5 - - + +
404H SER 2.7 18.6 + - - +
405H PRO* 3.7 11.0 - - + +
406H PHE 3.3 0.4 - - - -
407H CYS* 1.3 72.1 - - - +
409H TYR* 1.3 64.5 + - - +
411H ILE* 4.9 3.6 - - - -
412H THR* 3.0 54.3 + - + +
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Residues in contact with TYR 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405H PRO 3.2 9.3 + - - +
406H PHE 3.6 8.5 - - - +
407H CYS 3.2 0.2 - - - -
408H ARG* 1.3 82.4 - - - +
410H ARG* 1.3 55.6 + - + +
412H THR* 3.4 6.6 + - - -
413H SER* 2.6 41.8 + - - -
447H GLU* 2.5 43.4 + - - -
450H LEU* 4.7 6.1 - - - +
451H ALA* 3.4 30.1 - - + -
455H TYR 3.5 14.6 + - - -
456H PHE* 3.2 27.6 - - + -
457H LYS* 3.5 37.0 - - + +
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Residues in contact with ARG 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ASP* 2.8 32.0 + - - -
331H PRO 2.9 25.9 + - - -
332H CYS* 3.2 30.9 + - - +
333H LEU* 5.1 0.2 - - - -
334H THR* 3.7 12.9 + - - -
335H PHE* 3.9 19.7 - - + -
406H PHE* 3.4 47.6 - - + +
407H CYS* 3.0 7.0 + - - +
409H TYR* 1.3 77.8 - - + +
411H ILE* 1.3 62.6 + - - +
413H SER* 3.5 2.3 + - - -
414H VAL* 3.2 28.2 + - - +
451H ALA* 3.4 34.5 + - + +
452H LYS 3.7 14.3 + - - -
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Residues in contact with ILE 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H LEU* 4.3 17.9 - - + -
335H PHE* 4.4 6.7 - - + -
344H VAL* 4.1 13.5 - - + -
348H VAL* 4.4 5.8 - - + -
353H LEU* 4.1 13.9 - - + -
355H ILE* 3.8 19.7 - - + -
381H LEU* 3.6 28.9 - - + -
392H ILE* 4.4 17.5 - - + -
403H ILE* 4.8 3.8 - - + -
407H CYS 2.9 17.4 + - - +
408H ARG* 4.1 2.7 - - - +
410H ARG* 1.3 74.8 - - - +
412H THR* 1.3 53.8 + - - +
414H VAL* 2.8 6.6 + - - +
415H CYS* 2.7 47.0 + - - +
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Residues in contact with THR 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G HIS* 4.3 18.2 - - + +
131G LEU* 4.9 5.4 - - + -
355H ILE* 3.5 22.9 - - + -
408H ARG* 3.0 45.2 + - + +
409H TYR* 3.4 10.9 + - - -
411H ILE* 1.3 74.9 - - - +
413H SER* 1.3 56.7 + - - +
415H CYS* 4.2 8.3 - - - -
416H ASN* 2.7 47.1 + - - +
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Residues in contact with SER 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409H TYR* 2.6 45.8 + - - -
410H ARG* 3.5 8.3 - - - -
412H THR* 1.3 78.6 + - - +
414H VAL* 1.3 61.4 + - - +
416H ASN* 3.5 7.6 + - - +
417H PHE* 3.2 17.2 + - - +
444H LEU* 4.5 4.0 - - - +
447H GLU* 4.1 11.3 + - - +
448H MET* 3.8 34.0 - - - +
451H ALA* 4.6 0.9 - - - -
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Residues in contact with VAL 414 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H ILE* 3.9 20.0 - - + +
332H CYS* 3.7 25.8 - - + -
333H LEU* 4.1 16.8 - - + -
348H VAL* 3.8 11.2 - - + -
410H ARG 3.2 15.7 - - - +
411H ILE 2.8 7.9 + - - +
413H SER* 1.3 74.6 - - - +
415H CYS* 1.3 65.9 + - - +
417H PHE* 3.1 11.4 + - - +
418H PHE* 3.1 39.3 + - + -
448H MET* 3.9 15.3 - - + -
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Residues in contact with CYS 415 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G HIS* 3.3 43.7 + - + +
348H VAL* 3.6 40.2 - - - -
353H LEU* 4.1 8.3 - - - -
411H ILE* 2.7 29.9 + - - +
412H THR* 3.9 0.4 - - - +
414H VAL* 1.3 72.5 - - - +
416H ASN* 1.3 57.4 + - - +
418H PHE* 3.5 2.9 + - - +
419H THR* 3.0 30.0 + - - +
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Residues in contact with ASN 416 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G HIS* 3.1 19.9 + - - -
131G LEU* 4.3 13.4 - - - +
412H THR* 2.7 37.2 + - - +
413H SER* 3.8 6.2 - - - +
415H CYS* 1.3 71.3 - - - +
417H PHE* 1.3 63.1 + - - +
419H THR* 2.9 23.4 - - - +
420H TYR* 3.2 8.8 + - - +
444H LEU* 3.4 22.0 - - + +
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Residues in contact with PHE 417 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H LEU* 4.1 15.3 - - + -
324H ILE* 3.4 47.1 - - + -
329H ILE* 4.0 22.4 - - + -
413H SER 3.2 10.4 + - - +
414H VAL 3.1 7.8 + - - +
416H ASN* 1.3 78.6 - - - +
418H PHE* 1.3 76.7 + + - +
420H TYR* 3.3 2.3 + - - +
421H ILE* 3.0 53.4 + - + +
441H VAL* 4.1 11.7 - - + -
444H LEU* 3.3 30.9 - - + +
445H ARG* 5.0 2.0 - - + -
448H MET* 4.1 20.9 - - + -
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Residues in contact with PHE 418 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H MET* 4.1 24.9 - - + -
321H LEU* 5.6 3.6 - - + -
325H TYR* 3.2 33.2 - + - -
329H ILE* 3.3 34.8 - - + -
345H LEU* 5.6 0.2 - - + -
348H VAL* 3.6 26.9 - - + +
349H GLU* 4.0 22.7 - - + -
414H VAL* 3.1 34.4 + - + +
415H CYS* 3.9 4.0 - - - +
417H PHE* 1.3 90.0 - + - +
419H THR* 1.3 56.9 + - - +
421H ILE* 3.2 4.7 + - - +
422H ARG* 2.9 39.3 + - + +
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Residues in contact with THR 419 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G LEU* 4.8 6.6 - - + +
130G HIS* 4.3 13.5 - - + -
415H CYS 3.0 17.6 + - - +
416H ASN* 2.9 33.2 - - - +
418H PHE* 1.3 76.7 - - - +
420H TYR* 1.3 62.2 + - + +
422H ARG* 3.7 22.8 + - - +
423H TYR* 3.2 50.7 + - + -
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Residues in contact with TYR 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416H ASN 3.2 9.6 + - - +
417H PHE 3.9 0.2 - - - +
419H THR* 1.3 78.2 - - + +
421H ILE* 1.3 67.8 + - + +
423H TYR* 3.2 25.5 + + + +
424H ILE* 3.2 37.2 + - + +
429H VAL* 4.6 13.2 - - + +
432H GLN* 2.7 26.4 + - - -
437H MET* 3.5 27.9 - - - +
440H GLU* 3.4 33.4 - - + +
441H VAL* 4.1 9.2 - - + -
444H LEU* 3.5 33.2 - - + -
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Residues in contact with ILE 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H TRP* 3.5 25.1 - - + -
314H MET* 3.3 29.4 - - + -
320H PHE* 3.8 26.9 - - + -
321H LEU* 4.9 7.0 - - + -
417H PHE* 3.0 50.0 + - + +
418H PHE* 3.2 6.9 + - + +
420H TYR* 1.3 78.8 - - + +
422H ARG* 1.3 60.3 + - - +
424H ILE* 2.9 25.3 + - + +
425H GLN* 3.0 11.6 + - - +
441H VAL* 4.6 8.5 - - + -
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Residues in contact with ARG 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G ASP* 4.7 11.5 + - - +
156G LEU* 5.1 5.7 - - - +
314H MET* 4.0 26.5 - - + -
348H VAL 6.0 0.2 + - - -
349H GLU 5.7 4.0 - - - -
351H ASN* 3.0 36.5 + - - +
418H PHE* 2.9 22.8 + - + +
419H THR* 3.7 26.3 + - - +
421H ILE* 1.3 76.0 - - - +
423H TYR* 1.3 80.6 + - - +
425H GLN* 3.3 4.4 + - - +
426H GLN* 2.9 48.4 + - - +
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Residues in contact with TYR 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G LEU* 3.4 37.2 - - + +
127G ASP* 4.1 1.6 + - - -
128G LEU* 3.8 19.6 - - - +
156G LEU* 3.8 31.4 - - + +
419H THR* 3.2 33.0 + - + -
420H TYR* 3.2 23.8 + + + +
422H ARG* 1.3 96.1 - - + +
424H ILE* 1.3 57.6 + - - +
426H GLN* 4.9 2.2 - - - -
427H GLY* 2.9 24.9 + - - -
428H LEU* 3.1 19.6 - - + +
429H VAL* 3.8 10.8 - - + +
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Residues in contact with ILE 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305H PHE* 4.3 17.3 - - + -
308H TRP* 3.8 22.0 - - + -
309H LYS* 4.7 11.9 - - + +
312H PRO* 4.2 8.8 - - + +
420H TYR* 3.4 37.7 - - + +
421H ILE* 2.9 13.2 + - + +
423H TYR* 1.3 76.1 - - - +
425H GLN* 1.3 61.3 - - - +
427H GLY* 2.9 17.6 + - - -
429H VAL* 4.3 9.4 - - + -
437H MET* 3.1 37.5 - - + -
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Residues in contact with GLN 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H TRP* 4.6 2.7 - - + -
312H PRO* 3.4 45.7 + - + +
313H THR* 4.3 1.3 - - - +
314H MET* 4.2 32.9 - - + +
421H ILE 3.0 14.0 + - - +
422H ARG* 3.8 4.5 - - - +
424H ILE* 1.3 77.0 - - - +
426H GLN* 1.3 73.6 + - - +
427H GLY 3.6 0.7 + - - -
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Residues in contact with GLN 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G LEU* 5.2 8.1 - - - +
422H ARG* 2.9 43.8 + - - +
423H TYR* 4.8 2.6 - - - +
425H GLN* 1.3 86.4 - - - +
427H GLY* 1.3 64.5 + - - +
428H LEU* 3.2 32.2 + - + +
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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