Contacts of the helix formed by residues 408 - 426 (chain B) in PDB entry 1JQO
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 408 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406B PHE* 4.8 1.4 - - - +
407B THR* 1.3 88.0 + - - +
409B ILE* 1.3 66.4 + - - +
410B GLU* 3.4 18.5 + - - +
411B GLU* 3.2 36.4 + - - +
412B PHE* 3.5 9.5 + - - +
448B LEU* 3.9 4.7 - - - +
527B ASP* 4.7 3.1 - - - -
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Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER* 1.3 73.2 - - - +
410B GLU* 1.3 61.0 + - - +
412B PHE* 3.0 7.3 + - + +
413B LEU* 2.7 60.5 + - + +
443B VAL* 3.7 21.3 - - + +
444B PHE* 5.9 2.2 - - + -
447B GLY* 3.8 21.3 - - - -
448B LEU* 3.1 25.3 - - + +
527B ASP* 4.8 13.6 + - + +
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Residues in contact with GLU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B SER* 3.1 21.7 - - - +
409B ILE* 1.3 87.1 + - - +
411B GLU* 1.3 62.9 + - + +
413B LEU* 4.3 11.2 - - + +
414B GLU* 2.9 28.8 + - - +
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Residues in contact with GLU 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B LYS* 4.1 9.4 + - - +
403B GLU* 6.0 1.6 - - - -
405B SER 3.4 7.3 - - - +
406B PHE* 3.4 24.6 - - + -
407B THR* 3.0 44.3 + - - +
408B SER* 3.2 17.0 + - - +
410B GLU* 1.3 78.3 - - + +
412B PHE* 1.3 57.1 + - - +
414B GLU* 4.1 2.9 - - - +
415B PRO* 3.0 26.7 - - - +
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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
----------------------------------------------------------
319B TYR* 3.5 52.3 - + + -
323B ILE* 4.7 6.7 - - + -
378B VAL* 3.7 22.4 - - + +
382B LEU* 4.0 16.8 - - + -
406B PHE* 3.5 28.5 - + + -
408B SER 3.5 7.8 + - - +
409B ILE* 3.0 10.5 + - + +
411B GLU* 1.3 79.2 - - - +
413B LEU* 1.3 64.1 + - - +
415B PRO* 3.3 9.7 - - - +
416B LEU* 3.5 24.0 - - + +
439B LEU* 5.4 0.7 - - + -
443B VAL* 3.8 20.9 - - + -
447B GLY 5.8 0.4 - - - -
448B LEU* 3.9 20.0 - - + -
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ILE* 2.7 43.0 + - + +
410B GLU* 3.9 10.3 - - + +
412B PHE* 1.3 70.3 - - - +
414B GLU* 1.3 69.4 + - - +
415B PRO 2.7 4.1 - - - -
416B LEU* 2.8 16.7 + - + -
417B GLU* 2.9 25.2 + - + +
440B LEU* 3.8 18.8 - - + -
443B VAL* 3.4 22.9 - - + -
444B PHE* 3.5 44.4 - - + -
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLU* 5.0 3.3 - - - +
342B ARG* 3.0 39.0 + - - -
410B GLU 2.9 20.6 + - - +
411B GLU* 4.1 3.4 - - - +
413B LEU* 1.3 71.0 - - - +
415B PRO* 1.3 70.7 - - + +
417B GLU* 3.6 11.8 + - - +
418B LEU* 3.0 26.2 + - - +
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Residues in contact with PRO 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B ARG* 5.1 2.2 - - - +
374B ILE* 4.2 12.0 - - + +
377B HIS* 6.1 2.2 - - + +
378B VAL* 3.8 29.2 - - + -
406B PHE* 5.4 3.4 - - + -
411B GLU 3.0 25.8 - - - +
412B PHE* 3.3 6.1 - - - +
413B LEU 3.2 4.5 - - - -
414B GLU* 1.3 97.7 - - + +
416B LEU* 1.3 66.4 + - - +
418B LEU* 2.9 22.9 + - + +
419B CYS* 3.1 14.1 + - - -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ILE* 3.8 26.0 - - + -
375B LEU* 4.0 14.6 - - + -
378B VAL* 4.9 4.7 - - + -
412B PHE* 3.5 37.2 - - + +
413B LEU* 2.8 12.0 + - - +
415B PRO* 1.3 72.3 - - + +
417B GLU* 1.3 61.5 + - - +
419B CYS* 3.1 17.9 + - - +
420B TYR* 3.2 12.6 + - - +
436B LEU* 4.1 13.3 - - + +
439B LEU* 4.1 17.3 - - + -
440B LEU* 3.8 22.7 - - + -
443B VAL* 4.0 22.2 - - + -
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.1 34.2 + - - +
413B LEU* 2.9 34.9 + - + +
414B GLU* 3.8 10.9 + - - +
416B LEU* 1.3 73.1 - - - +
418B LEU* 1.3 67.5 + - - +
420B TYR* 3.3 8.3 + - - +
421B LYS* 3.1 26.5 + - - +
440B LEU* 4.2 13.9 - - + -
444B PHE* 3.9 8.6 - - - -
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASN* 4.5 5.6 - - - +
338B GLU* 3.5 35.4 - - + +
339B LEU* 3.7 21.5 - - + +
342B ARG* 3.2 43.1 - - + +
374B ILE* 3.9 20.0 - - + -
414B GLU* 3.0 18.3 + - - +
415B PRO* 2.9 15.3 + - + +
417B GLU* 1.3 76.6 - - - +
419B CYS* 1.3 61.2 + - - +
421B LYS* 4.1 4.0 - - + +
422B SER* 3.1 20.3 + - - -
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Residues in contact with CYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 4.7 3.8 - - + -
339B LEU* 3.9 16.2 - - - -
371B TYR* 4.1 22.9 - - + -
374B ILE* 4.3 19.1 - - - -
375B LEU* 4.6 18.4 - - - -
415B PRO 3.1 16.6 + - - -
416B LEU* 3.1 10.4 + - - +
417B GLU 3.1 0.4 - - - -
418B LEU* 1.3 76.7 - - - +
420B TYR* 1.3 68.0 + - - +
422B SER* 2.9 3.9 + - - -
423B LEU* 2.8 26.6 + - - +
436B LEU* 3.9 15.5 - - + -
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Residues in contact with TYR 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B TYR* 3.9 25.2 - + - +
416B LEU 3.2 7.9 + - - +
417B GLU* 3.8 8.1 - - - +
419B CYS* 1.3 78.3 - - - +
421B LYS* 1.3 60.4 + - + +
423B LEU* 3.5 2.9 + - - +
424B CYS* 3.1 48.1 + - - -
429B LYS* 3.6 12.7 + - - -
432B ALA* 3.4 31.8 - - + +
433B ASP* 2.6 31.0 + - - -
436B LEU* 3.3 16.9 - - + +
437B LEU* 4.1 17.5 - - + +
440B LEU* 4.0 18.8 - - + -
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Residues in contact with LYS 421 (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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336B ASN* 3.6 10.7 + - - +
338B GLU* 4.4 12.1 + - - +
417B GLU 3.1 16.0 + - - +
418B LEU* 4.1 5.8 - - + +
420B TYR* 1.3 78.4 - - + +
422B SER* 1.3 60.2 + - - +
424B CYS* 3.2 8.1 + - + +
425B ASP* 2.8 71.1 + - - +
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Residues in contact with SER 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B CYS* 3.6 2.8 - - - +
336B ASN* 3.2 39.8 + - - +
339B LEU* 3.6 13.9 - - - +
371B TYR* 2.8 24.7 + - - -
418B LEU 3.1 20.1 + - - -
419B CYS 2.9 4.9 + - - -
421B LYS* 1.3 74.6 - - - +
423B LEU* 1.3 64.1 + - - +
425B ASP* 3.8 1.4 - - - +
426B CYS* 3.0 27.0 + - - +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 3.7 21.8 - - + -
332B MET* 4.1 13.0 - - + -
371B TYR* 3.6 31.6 - - + +
419B CYS 2.8 9.4 + - - +
422B SER* 1.3 76.0 - - - +
424B CYS* 1.3 61.0 + - - +
426B CYS* 3.6 2.2 + - - -
427B GLY 3.4 2.9 + - - -
428B ASP* 2.8 54.6 + - + +
431B ILE* 3.8 19.5 - - + -
432B ALA* 3.6 31.6 - - + +
436B LEU* 3.8 17.0 - - + -
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Residues in contact with CYS 424 (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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420B TYR* 3.1 47.2 + - - +
421B LYS* 3.4 11.9 - - + +
422B SER 3.2 0.2 - - - -
423B LEU* 1.3 73.8 - - - +
425B ASP* 1.3 69.6 + - - +
427B GLY* 2.9 15.8 + - - -
429B LYS* 3.5 39.5 + - + +
432B ALA* 4.6 1.1 - - - -
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Residues in contact with ASP 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASN* 2.9 30.0 + - - +
421B LYS* 2.8 54.8 + - - +
424B CYS* 1.3 76.1 - - - +
426B CYS* 1.3 60.6 + - - +
427B GLY 3.2 4.7 + - - -
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Residues in contact with CYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ARG* 3.9 14.2 + - - -
334B ARG* 4.1 36.7 + - + +
335B CYS* 3.4 42.4 - - - +
336B ASN* 4.9 3.1 - - - -
371B TYR* 5.0 0.7 - - - +
422B SER 3.0 16.3 + - - +
423B LEU* 4.4 3.1 - - - +
424B CYS 3.2 0.2 - - - -
425B ASP* 1.3 77.1 - - - +
427B GLY* 1.3 59.1 + - - +
428B ASP* 3.4 8.9 + - - +
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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) + - + + + + + -
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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