Contacts of the helix formed by residues 369 - 380 (chain A) in PDB entry 1UWV
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 ALA 369 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A PHE* 4.2 11.9 - - + -
362A LEU* 3.7 19.1 - - + -
364A PRO* 4.3 2.9 - - + -
368A GLY* 1.3 73.3 - - - +
370A ALA* 1.3 66.4 + - - +
371A GLY 3.4 2.0 - - - -
372A VAL* 2.8 28.0 + - + -
373A MSE 3.1 32.8 + - + +
386A TYR* 4.4 0.2 - - - +
397A ASP* 3.1 9.2 + - - +
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Residues in contact with ALA 370 (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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368A GLY 3.7 3.2 + - - -
369A ALA* 1.3 76.1 - - - +
371A GLY* 1.3 64.1 + - - +
373A MSE 3.1 17.2 + - - +
374A GLN* 4.4 3.1 + - - +
397A ASP* 3.5 17.4 + - - +
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Residues in contact with GLY 371 (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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343A LEU 5.7 0.2 - - - -
369A ALA 3.4 0.4 - - - -
370A ALA* 1.3 77.7 - - - +
372A VAL* 1.3 59.7 + - - +
374A GLN* 4.0 9.3 + - - +
375A GLN* 3.1 24.0 + - - +
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Residues in contact with VAL 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A LEU* 3.8 18.8 - - + -
294A PHE* 4.2 20.2 - - + -
343A LEU* 3.4 32.8 - - + +
362A LEU* 4.8 0.4 - - + -
369A ALA* 2.8 21.1 + - + +
371A GLY* 1.3 74.2 - - - +
373A MSE 1.3 66.9 + - + -
374A GLN 3.3 2.9 - - - -
375A GLN* 3.0 19.2 + - + +
376A ILE* 3.0 41.8 + - + +
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Residues in contact with MSE 373 (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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362A LEU* 3.9 13.9 - - + -
369A ALA* 3.1 46.7 + - + +
370A ALA 3.1 10.8 + - - +
372A VAL* 1.3 78.9 - - + +
374A GLN* 1.3 63.3 + - + +
376A ILE* 3.3 14.7 + - + +
377A ILE* 3.0 29.9 + - + +
386A TYR* 4.1 10.5 - - + -
397A ASP* 3.6 47.8 - - + +
400A ALA* 4.0 17.9 - - + -
401A LEU* 4.1 22.3 - - + +
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Residues in contact with GLN 374 (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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370A ALA 4.4 2.6 + - - +
371A GLY* 4.0 7.8 + - - +
372A VAL 3.3 0.6 - - - -
373A MSE 1.3 79.7 - - + +
375A GLN* 1.3 59.7 + - + +
377A ILE* 3.3 32.2 + - - +
378A LYS* 3.0 31.6 + - - +
400A ALA* 3.9 19.4 + - - +
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Residues in contact with GLN 375 (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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343A LEU* 4.4 2.7 + - - +
344A GLU 5.4 1.4 - - - -
345A GLU 3.4 20.7 + - - +
346A ASP* 4.1 15.2 - - - +
347A VAL* 3.0 39.9 + - + +
348A THR* 3.6 16.0 + - + +
371A GLY 3.1 29.1 + - - +
372A VAL* 3.0 23.8 + - + +
374A GLN* 1.3 79.0 - - + +
376A ILE* 1.3 61.9 + - + +
378A LYS* 3.2 20.0 - - - +
379A LEU* 3.3 15.1 + - + +
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Residues in contact with ILE 376 (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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293A LEU* 3.9 14.8 - - + -
360A VAL* 4.1 12.3 - - + -
362A LEU* 3.8 28.5 - - + -
372A VAL* 3.0 31.6 + - + +
373A MSE 3.6 21.5 - - + +
375A GLN* 1.3 75.0 - - + +
377A ILE* 1.3 63.4 + - - +
379A LEU* 3.1 20.3 + - + +
381A PRO* 3.2 23.6 - - + +
384A ILE* 3.5 34.5 - - + -
401A LEU* 4.7 3.1 - - + -
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Residues in contact with ILE 377 (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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373A MSE 3.0 19.3 + - - +
374A GLN* 3.4 40.4 - - - +
376A ILE* 1.3 76.6 - - - +
378A LYS* 1.3 64.5 + - - +
380A GLU* 3.0 19.8 + - - +
400A ALA* 3.9 20.6 - - + +
401A LEU* 3.8 19.7 - - + -
404A ALA* 3.9 24.7 - - + -
406A TYR* 4.8 11.5 + - + -
431A ARG* 5.8 0.2 + - - -
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Residues in contact with LYS 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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348A THR* 3.6 32.5 - - + +
374A GLN 3.0 13.9 + - - +
375A GLN* 3.2 12.1 - - - +
377A ILE* 1.3 78.1 - - - +
379A LEU* 1.3 61.3 + - - +
380A GLU* 3.4 14.3 - - - +
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Residues in contact with LEU 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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291A LEU* 3.8 28.7 - - + -
347A VAL* 6.6 0.2 - - + -
348A THR* 4.4 13.5 - - + -
352A TRP* 5.9 1.3 - - + -
353A ALA* 4.3 26.0 - - + +
356A GLY* 5.1 3.1 - - - -
357A PHE* 3.7 40.8 + - + +
360A VAL* 4.9 3.4 - - + -
375A GLN* 3.5 17.0 - - + +
376A ILE* 3.1 18.4 + - + +
378A LYS* 1.3 77.0 - - - +
380A GLU* 1.3 71.2 + - - +
381A PRO* 3.4 5.5 - - + -
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Residues in contact with GLU 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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357A PHE 4.1 3.2 - - - +
358A ASP* 5.4 0.2 - - - -
377A ILE 3.0 14.0 + - - +
378A LYS 3.4 13.5 - - - +
379A LEU* 1.3 80.1 - - - +
381A PRO* 1.3 73.1 - - - +
382A ILE* 3.6 4.0 + - - +
406A TYR* 3.9 6.1 - - - -
431A ARG* 3.3 32.6 + - - +
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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