Contacts of the helix formed by residues 402 - 416 (chain B) in PDB entry 5UO5
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 402 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385B ARG* 3.4 27.9 - - - +
388B GLU* 3.5 25.1 + - - -
400B GLN 5.4 0.7 - - - +
401B LEU* 1.3 76.2 - - - +
403B ASP* 1.3 62.3 + - - +
404B THR* 3.3 13.0 - - + +
405B GLU* 2.8 33.0 + - - +
406B LEU* 2.9 24.9 + - - +
435B ARG* 4.5 0.2 - - - -
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Residues in contact with ASP 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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401B LEU 4.5 0.5 - - - +
402B LYS* 1.3 72.7 - - - +
404B THR* 1.3 63.7 + - + +
406B LEU* 3.2 9.6 + - - +
407B ILE* 3.1 35.0 + - + +
433B ASP* 3.7 12.1 - - - +
435B ARG* 3.0 22.2 + - - +
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Residues in contact with THR 404 (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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370B TYR* 3.1 29.6 + - - +
402B LYS* 4.0 11.7 - - + +
403B ASP* 1.3 75.6 - - + +
405B GLU* 1.3 65.0 + - - +
407B ILE* 3.4 11.0 + - + +
408B TYR* 2.9 29.3 + - - +
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Residues in contact with GLU 405 (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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366B PHE* 3.6 22.8 - - + -
367B ILE* 3.6 13.7 - - + +
370B TYR* 4.4 19.4 - - + -
371B TYR* 5.0 4.9 + - - -
385B ARG* 2.6 52.3 + - - +
401B LEU* 3.4 12.9 - - + +
402B LYS* 2.8 27.7 + - + +
404B THR* 1.3 83.3 + - - +
406B LEU* 1.3 55.3 + - - +
408B TYR* 3.6 6.6 - - - +
409B GLY* 2.7 32.7 + - - -
579B ILE* 4.9 0.3 - - - +
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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
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401B LEU* 3.9 24.1 - - + +
402B LYS 2.9 13.1 + - - +
403B ASP* 3.2 12.1 + - - +
405B GLU* 1.3 75.7 - - - +
407B ILE* 1.3 58.1 + - + +
409B GLY* 3.4 0.9 + - - -
410B ALA* 2.9 28.2 + - - +
431B VAL* 4.6 6.5 - - + -
433B ASP* 3.8 27.4 - - + +
435B ARG* 3.6 30.3 - - - +
466B ILE* 3.7 33.0 - - + -
579B ILE* 4.1 5.7 - - + +
584B PHE* 4.2 16.4 - - + -
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Residues in contact with ILE 407 (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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403B ASP* 3.1 26.3 + - + +
404B THR* 3.7 8.3 - - + +
406B LEU* 1.3 75.3 - - + +
408B TYR* 1.3 66.4 + - - +
410B ALA* 3.3 1.4 + - - +
411B LYS* 3.1 51.7 + - + +
431B VAL* 4.1 33.2 - - + +
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Residues in contact with TYR 408 (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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366B PHE* 3.7 21.8 - + - -
369B GLN* 3.0 48.1 + - + +
370B TYR* 3.6 28.3 - + + -
373B SER* 3.3 31.1 - - - -
374B ILE* 6.1 0.4 - - + -
404B THR 2.9 17.7 + - - +
405B GLU 3.6 2.9 - - - +
407B ILE* 1.3 77.6 - - - +
409B GLY* 1.3 64.3 + - - +
411B LYS* 3.5 3.5 + - - +
412B HIS* 3.0 72.4 + + + +
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Residues in contact with GLY 409 (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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366B PHE* 4.1 6.3 - - - -
405B GLU 2.7 21.4 + - - -
406B LEU 3.7 1.6 - - - -
408B TYR* 1.3 75.3 - - - +
410B ALA* 1.3 61.0 + - - +
412B HIS 3.3 0.3 + - - -
413B ALA* 3.1 20.1 + - - +
579B ILE* 3.7 19.0 - - - +
707B PRO* 3.4 24.6 - - - +
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Residues in contact with ALA 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B LEU 2.9 17.3 + - - +
407B ILE 3.3 3.3 + - - +
409B GLY* 1.3 73.6 - - - +
411B LYS* 1.3 67.2 + - - +
413B ALA* 3.4 7.2 + - - +
414B TRP* 3.3 20.1 + - - +
429B LEU* 4.0 5.7 - - + +
431B VAL* 4.1 17.3 - - + -
464B ILE* 4.1 15.0 - - + -
466B ILE* 4.1 21.3 - - + -
577B LEU* 4.6 3.8 - - + -
579B ILE* 4.0 3.5 - - - +
709B PHE* 4.3 4.0 - - - -
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Residues in contact with LYS 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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407B ILE* 3.1 37.0 + - + +
408B TYR* 3.9 5.2 - - - +
410B ALA* 1.3 76.0 - - - +
412B HIS* 1.3 60.0 + - + +
414B TRP* 3.3 5.4 + - - +
415B ARG* 2.9 25.8 + - - +
426B TRP* 3.6 35.7 - - + +
427B SER* 2.8 34.2 + - - +
429B LEU* 3.7 33.2 + - + -
431B VAL* 4.9 1.1 - - + -
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Residues in contact with HIS 412 (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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369B GLN* 4.3 2.8 + - - -
373B SER* 5.5 1.8 - - - -
408B TYR* 3.0 73.1 + + + +
409B GLY* 4.0 3.1 - - - +
410B ALA 3.2 0.2 - - - -
411B LYS* 1.3 77.9 - - + +
413B ALA* 1.3 59.7 + - - +
415B ARG* 3.2 35.4 + - - -
416B ASN* 2.8 40.5 + - - +
426B TRP* 3.7 21.8 - + - -
674B ARG* 4.0 15.4 + - - -
707B PRO* 4.1 17.3 - - + -
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Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLY 3.1 11.7 + - - +
410B ALA 3.7 2.0 - - - +
412B HIS* 1.3 77.4 - - - +
414B TRP* 1.3 62.1 + - - +
416B ASN* 3.5 1.9 + - - +
417B ALA* 3.2 17.3 + - - +
577B LEU* 3.5 27.6 - - + -
707B PRO* 3.3 12.6 + - - +
708B SER* 3.8 13.6 - - - +
709B PHE* 3.4 33.5 + - + -
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Residues in contact with TRP 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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410B ALA 3.3 7.4 + - - +
411B LYS 3.5 7.9 - - - +
412B HIS 3.2 0.2 - - - -
413B ALA* 1.3 76.9 - - - +
415B ARG* 1.3 65.3 + - - +
417B ALA* 3.0 13.1 + - - +
420B CYS* 3.5 11.0 - - + -
422B GLY 3.7 17.0 - - - -
423B ARG* 3.1 19.6 - - + +
425B GLN* 3.5 34.8 - - + -
426B TRP* 3.4 23.1 - - + -
428B LYS 3.7 13.9 - - - -
429B LEU* 4.0 12.1 - - + -
462B SER* 3.6 11.4 - - - -
709B PHE* 3.4 7.7 - - - -
801B HEM 3.2 88.2 + + + -
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Residues in contact with ARG 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 LYS 2.9 17.1 + - - +
412B HIS* 3.2 34.9 - - - +
414B TRP* 1.3 76.6 - - - +
416B ASN* 1.3 58.7 + - - +
423B ARG* 3.0 27.9 + - - +
426B TRP* 3.4 54.2 - - + +
666B HIS* 5.1 2.1 + - + -
670B GLU* 2.8 39.5 + - - +
673B CYS* 3.8 13.9 - - - -
674B ARG* 3.5 45.4 + - - +
677B CYS* 5.4 0.3 - - - -
678B PRO* 5.0 1.2 - - - +
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Residues in contact with ASN 416 (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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369B GLN* 5.5 0.6 - - - +
412B HIS* 2.8 20.6 + - - +
413B ALA 3.8 2.0 - - - +
415B ARG* 1.3 76.8 - - - +
417B ALA* 1.3 60.0 + - - +
418B SER* 2.9 10.9 + - - -
423B ARG* 4.1 2.9 - - - +
674B ARG* 2.8 38.8 + - - +
678B PRO* 4.0 12.3 - - - +
703B TYR 5.1 1.0 - - - +
705B LEU* 3.4 36.9 + - + +
706B THR 3.7 12.3 + - - -
707B PRO* 3.1 28.7 + - - +
708B SER* 5.3 2.3 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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