Contacts of the helix formed by residues 377 - 387 (chain A) in PDB entry 1UPX
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 LEU 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ILE* 4.2 8.1 - - + -
369A PHE* 3.9 32.1 - - + -
373A GLN* 3.5 30.1 - - - +
374A VAL* 2.9 11.5 + - + +
376A ALA* 1.3 78.8 - - + +
378A ALA* 1.3 64.0 + - - +
379A ASP* 3.3 2.5 - - - -
380A LYS* 3.1 28.0 + - + +
381A VAL* 3.1 21.4 + - + +
443A ILE* 6.3 5.4 - - + -
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A VAL* 3.0 10.8 + - + +
375A LEU* 3.2 25.3 + - + +
376A ALA 3.4 1.2 + - - -
377A LEU* 1.3 77.4 - - - +
379A ASP* 1.3 60.0 + - - +
381A VAL* 3.2 6.7 + - - +
382A ILE* 2.8 46.8 + - + +
464A LYS* 5.0 17.9 - - + -
465A LEU* 5.8 3.8 - - + -
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Residues in contact with ASP 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376A ALA 5.3 0.6 + - - -
377A LEU 3.3 0.8 - - - -
378A ALA* 1.3 77.6 - - - +
380A LYS* 1.3 71.6 + - + +
382A ILE* 3.5 13.3 + - - +
383A ASP* 2.9 39.4 + - - +
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Residues in contact with LYS 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A LEU* 3.1 21.9 + - + +
379A ASP* 1.3 87.7 - - + +
381A VAL* 1.3 65.3 + - + +
383A ASP* 3.5 16.2 + - + +
384A ALA* 3.0 24.1 + - - +
443A ILE* 4.4 11.3 - - + +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A VAL* 4.8 16.2 - - + -
377A LEU* 3.1 25.3 + - + +
378A ALA* 3.6 9.4 - - - +
380A LYS* 1.3 74.8 - - + +
382A ILE* 1.3 64.3 + - + +
384A ALA* 3.2 3.9 + - - +
385A VAL* 3.0 24.4 + - + +
390A ILE* 4.8 2.7 - - + -
393A PHE* 3.7 32.8 - - + -
443A ILE* 4.4 24.7 - - + -
447A LEU* 5.9 4.3 - - + -
461A ILE* 6.4 0.4 - - + -
465A LEU* 4.5 17.5 - - + -
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Residues in contact with ILE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A ALA* 2.8 34.3 + - + +
379A ASP* 3.7 13.0 - - - +
381A VAL* 1.3 75.9 - - - +
383A ASP* 1.3 60.3 + - - +
385A VAL* 3.2 4.7 + - - +
386A LYS* 2.9 55.0 + - + +
464A LYS* 6.1 0.2 - - + -
465A LEU* 4.0 21.5 - - + -
468A VAL* 3.4 41.3 - - + -
469A PHE* 3.9 18.2 - - + -
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Residues in contact with ASP 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ASP* 2.9 29.6 + - - +
380A LYS* 3.8 21.1 + - + +
381A VAL 3.3 0.2 - - - -
382A ILE* 1.3 80.5 - - - +
384A ALA* 1.3 57.3 + - - +
386A LYS* 3.4 12.8 + - - +
387A SER* 2.9 31.5 + - - -
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Residues in contact with ALA 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A LYS 3.0 17.7 + - - +
381A VAL 3.2 5.6 + - - +
383A ASP* 1.3 72.7 - - - +
385A VAL* 1.3 63.4 + - - +
387A SER* 3.3 6.5 + - - -
388A GLY 3.2 2.3 + - - -
389A ALA* 3.0 37.0 + - + -
390A ILE* 3.1 30.7 + - + -
440A ILE* 5.3 1.8 - - + +
443A ILE* 4.4 7.4 - - + -
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A VAL* 3.0 20.4 + - + +
382A ILE* 3.2 7.8 + - - +
384A ALA* 1.3 76.3 - - - +
386A LYS* 1.3 64.0 + - - +
388A GLY* 3.2 12.8 + - - -
390A ILE* 3.6 18.6 - - + +
393A PHE* 3.7 32.8 - - + -
465A LEU* 5.9 0.9 - - + -
469A PHE* 3.8 26.0 - - + -
478A PRO* 4.2 21.3 - - + -
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Residues in contact with LYS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ILE* 2.9 40.1 + - + +
383A ASP* 3.4 13.7 + - - +
385A VAL* 1.3 76.2 - - - +
387A SER* 1.3 60.8 + - - +
388A GLY 3.5 0.7 + - - -
468A VAL* 6.1 1.6 - - - +
469A PHE* 4.0 22.2 - - + -
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Residues in contact with SER 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A ASP 2.9 14.7 + - - -
384A ALA* 3.3 7.3 + - - -
386A LYS* 1.3 76.1 - - - +
388A GLY* 1.3 58.2 + - - +
389A ALA* 3.2 22.7 + - - +
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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