Contacts of the helix formed by residues 338 - 351 (chain V) in PDB entry 1UW9
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 GLU 338 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331V VAL* 5.2 0.4 - - - -
336V GLU* 4.9 0.2 - - - +
337V GLY* 1.3 72.0 - - - +
339V ARG* 1.3 79.2 + - - +
340V GLU* 3.0 28.6 + - - +
341V VAL* 3.0 37.5 + - + +
342V THR* 2.9 23.3 + - - -
471V THR* 3.9 34.0 - - + +
473V ASP 4.3 10.2 + - - +
474V LYS* 5.7 6.1 - - + -
475V LEU* 4.8 4.7 + - - +
1482V EDO 4.8 3.4 + - - -
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Residues in contact with ARG 339 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331V VAL* 4.1 26.1 - - + +
337V GLY 3.6 1.8 + - - -
338V GLU* 1.3 79.1 - - - +
340V GLU* 1.3 70.6 + - - +
342V THR* 3.3 2.8 + - - -
343V LEU* 2.9 57.7 + - + +
389V ALA* 6.2 0.4 - - - +
392V GLU* 2.8 43.6 + - - -
393V ILE* 3.4 27.9 - - + +
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Residues in contact with GLU 340 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338V GLU* 3.0 20.8 + - - +
339V ARG* 1.3 94.3 + - + +
341V VAL* 1.3 67.2 + - - +
343V LEU* 3.5 5.2 + - - +
344V GLY 3.1 18.2 + - - -
359V SER* 3.7 19.6 + - - +
360V ARG* 3.0 48.1 + - - +
475V LEU* 4.6 4.9 - - + -
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Residues in contact with VAL 341 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310V HIS* 3.4 36.5 - - + +
312V ARG* 4.4 1.9 + - - +
338V GLU* 3.0 28.7 + - + +
340V GLU* 1.3 77.5 - - - +
342V THR* 1.3 60.3 + - - +
344V GLY* 3.4 1.7 + - - -
345V PHE* 3.2 34.0 + - + -
360V ARG 4.1 10.5 - - - +
473V ASP* 4.0 17.9 - - - +
474V LYS 5.0 0.2 - - - -
475V LEU* 3.7 31.8 - - + +
1482V EDO 4.0 11.4 - - - -
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Residues in contact with THR 342 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328V SER 3.7 21.8 + - - +
329V GLY* 5.1 1.3 - - - +
331V VAL* 3.9 19.8 + - + +
337V GLY* 3.6 18.9 + - - -
338V GLU 2.9 20.8 + - - -
339V ARG 3.5 4.0 - - - -
341V VAL* 1.3 74.0 - - - +
343V LEU* 1.3 59.5 + - - +
345V PHE* 3.3 18.4 + - + -
346V VAL* 2.8 45.3 + - + +
393V ILE* 5.2 2.7 - - + -
394V PHE* 4.4 10.8 - - + -
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Residues in contact with LEU 343 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339V ARG* 2.9 52.2 + - + +
340V GLU* 3.9 7.4 - - - +
342V THR* 1.3 75.2 - - + +
344V GLY* 1.3 61.5 + - - +
346V VAL* 3.6 9.9 + - + +
347V ASP* 3.2 29.6 + - - +
360V ARG* 3.4 41.1 - - - +
393V ILE* 3.4 41.1 - - + +
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Residues in contact with GLY 344 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312V ARG* 6.2 0.4 - - - -
340V GLU 3.1 11.3 + - - -
341V VAL 3.7 4.0 - - - -
342V THR 3.2 0.2 - - - -
343V LEU* 1.3 76.1 - - - +
345V PHE* 1.3 61.5 + - - +
347V ASP* 3.3 8.3 + - - +
348V LEU* 3.1 24.6 + - - +
360V ARG* 3.8 22.3 - - - +
362V ILE* 3.8 19.6 - - - +
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Residues in contact with PHE 345 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295V ARG* 4.6 0.2 - - - -
310V HIS* 4.1 9.6 - + - -
311V PHE* 3.6 36.1 - + - -
312V ARG* 3.7 27.5 - - + +
315V ALA* 5.0 2.9 - - + -
328V SER* 3.3 35.0 - - - -
337V GLY* 6.1 0.2 - - - -
341V VAL* 3.2 25.4 + - + -
342V THR* 3.6 28.3 - - + -
344V GLY* 1.3 71.9 - - - +
346V VAL* 1.3 64.1 + - + +
348V LEU* 3.2 10.2 + - + +
349V MET* 2.9 38.7 + - - +
360V ARG 4.9 0.2 + - - -
1482V EDO 3.8 30.3 - - - -
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Residues in contact with VAL 346 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328V SER* 4.1 15.0 - - - -
342V THR* 2.8 29.3 + - + +
343V LEU* 3.8 12.8 - - + +
344V GLY 3.3 0.2 - - - -
345V PHE* 1.3 78.5 - - + +
347V ASP* 1.3 57.9 + - - +
349V MET* 3.2 7.0 + - - +
350V ARG* 3.0 67.7 + - - +
376V PRO* 4.3 7.6 - - + -
393V ILE 5.9 0.7 - - - +
394V PHE* 3.9 29.6 - - + -
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Residues in contact with ASP 347 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343V LEU 3.2 16.2 + - - +
344V GLY* 3.5 10.3 - - - +
345V PHE 3.3 0.2 - - - -
346V VAL* 1.3 76.5 - - - +
348V LEU* 1.3 59.3 + - - +
350V ARG* 4.5 12.9 + - - -
351V ASP* 2.8 58.2 + - - +
354V VAL* 3.5 18.6 - - + +
360V ARG* 4.2 15.0 + - - -
362V ILE* 5.3 1.8 - - + +
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Residues in contact with LEU 348 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137V ASP* 5.0 1.1 - - - +
312V ARG* 4.1 30.1 - - + +
315V ALA* 6.1 2.0 - - + -
316V LYS* 3.9 31.3 - - + +
319V ARG* 2.8 18.4 + - - -
344V GLY 3.1 15.1 + - - +
345V PHE* 3.2 9.8 + - + +
347V ASP* 1.3 77.4 - - - +
349V MET* 1.3 56.7 + - + +
354V VAL* 3.7 31.4 - - + -
362V ILE* 4.1 20.4 - - + -
366V GLN* 3.8 23.8 - - + -
368V TRP* 2.9 17.4 + - - +
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Residues in contact with MET 349 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311V PHE* 4.8 1.8 - - - -
315V ALA* 3.9 22.9 - - + +
319V ARG* 3.1 23.6 + - - +
326V LEU* 3.6 48.0 - - + +
328V SER* 4.4 9.6 - - - -
345V PHE* 2.9 33.7 + - - +
346V VAL* 3.2 11.6 + - - +
348V LEU* 1.3 77.9 - - - +
350V ARG* 1.3 56.8 + - + +
374V VAL* 2.8 40.6 + - + +
376V PRO* 3.6 19.7 - - + -
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Residues in contact with ARG 350 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155V ILE* 3.8 15.5 - - + +
319V ARG* 3.9 1.2 + - - -
346V VAL* 3.0 35.6 + - - +
347V ASP* 4.5 9.5 + - - -
349V MET* 1.3 79.6 - - + +
351V ASP* 1.3 73.2 + - - +
373V GLY* 3.6 19.7 + - - -
374V VAL 3.6 16.2 - - - +
376V PRO* 3.5 16.9 - - + +
393V ILE 5.3 1.6 + - - -
394V PHE* 2.8 33.1 + - - +
397V ASP* 2.8 47.7 + - - +
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Residues in contact with ASP 351 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319V ARG* 2.8 25.0 + - - -
347V ASP* 2.8 47.9 + - - +
350V ARG* 1.3 89.1 + - - +
352V ASP* 1.3 59.9 + - - +
353V TYR 3.5 8.4 - - - +
354V VAL* 3.9 12.6 - - + +
368V TRP* 3.2 8.1 - - - -
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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