Contacts of the helix formed by residues 338 - 351 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331O VAL* 5.2 0.2 - - - -
337O GLY* 1.3 71.8 - - - +
339O ARG* 1.3 72.2 + - - +
340O GLU* 3.0 29.1 + - - +
341O VAL* 3.0 38.0 + - + +
342O THR* 2.8 25.2 + - - -
471O THR* 3.9 33.8 - - + +
473O ASP 4.3 10.0 + - - +
474O LYS* 5.7 5.6 - - + -
475O LEU* 4.8 4.8 + - - +
1483O EDO 4.8 2.8 + - - -
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Residues in contact with ARG 339 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331O VAL* 4.0 26.5 - - + +
337O GLY 3.6 2.0 + - - -
338O GLU* 1.3 80.9 + - - +
340O GLU* 1.3 72.4 + - + +
342O THR* 3.5 1.4 - - - -
343O LEU* 2.9 58.8 + - + +
389O ALA* 6.2 0.4 - - - +
392O GLU* 2.8 43.2 + - - -
393O ILE* 3.5 27.9 - - + +
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Residues in contact with GLU 340 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338O GLU* 3.0 20.4 + - - +
339O ARG* 1.3 95.1 + - + +
341O VAL* 1.3 66.7 + - - +
343O LEU* 4.2 5.0 - - - +
344O GLY 3.1 18.0 + - - -
359O SER* 3.7 20.1 + - - +
360O ARG* 3.0 48.2 + - + +
475O LEU* 4.6 5.2 - - + -
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Residues in contact with VAL 341 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310O HIS* 3.4 36.3 - - + +
312O ARG* 4.4 2.1 + - - +
338O GLU* 3.0 29.0 + - + +
340O GLU* 1.3 76.6 - - - +
342O THR* 1.3 61.4 + - - +
344O GLY* 3.4 1.6 + - - -
345O PHE* 3.2 34.1 + - + -
360O ARG 4.1 10.6 - - - +
473O ASP* 4.0 23.3 - - - +
474O LYS 5.0 0.2 - - - -
475O LEU* 3.8 31.6 - - + +
1483O EDO 4.1 6.3 - - - +
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Residues in contact with THR 342 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328O SER 3.7 20.8 + - - +
329O GLY* 5.1 1.5 - - - +
331O VAL* 3.9 19.9 + - + +
337O GLY* 3.6 18.2 + - - -
338O GLU 2.8 21.2 + - - -
339O ARG 3.5 3.6 - - - -
341O VAL* 1.3 74.4 - - - +
343O LEU* 1.3 60.8 + - - +
345O PHE* 3.2 19.9 + - + -
346O VAL* 2.8 43.7 + - + +
393O ILE* 5.2 3.1 - - + -
394O PHE* 4.4 11.0 - - + -
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Residues in contact with LEU 343 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339O ARG* 2.9 51.8 + - + +
340O GLU* 3.9 6.5 - - - +
342O THR* 1.3 74.9 - - - +
344O GLY* 1.3 62.7 + - - +
346O VAL* 3.9 10.0 - - + +
347O ASP* 3.2 29.3 + - - +
360O ARG* 3.4 41.3 - - - +
393O ILE* 3.5 39.5 - - + +
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Residues in contact with GLY 344 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312O ARG* 6.2 0.2 - - - -
340O GLU 3.1 11.6 + - - -
341O VAL 3.7 4.0 - - - -
342O THR 3.2 0.2 - - - -
343O LEU* 1.3 78.3 - - - +
345O PHE* 1.3 60.8 + - - +
347O ASP* 3.3 6.4 + - - +
348O LEU* 3.2 24.3 + - - +
360O ARG* 3.7 22.6 - - - +
362O ILE* 3.8 19.9 - - - +
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Residues in contact with PHE 345 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295O ARG* 4.7 0.2 - - - -
310O HIS* 4.1 14.4 - + - -
311O PHE* 3.7 38.1 - + - -
312O ARG* 3.7 28.1 - - + +
315O ALA* 5.0 2.9 - - + +
328O SER* 3.2 34.3 - - - -
337O GLY* 6.1 0.4 - - - -
341O VAL* 3.2 29.9 + - + +
342O THR* 3.6 29.2 - - + -
344O GLY* 1.3 72.7 - - - +
346O VAL* 1.3 64.3 + - - +
348O LEU* 3.1 10.1 + - + +
349O MET* 2.8 39.4 + - - +
360O ARG 4.9 0.4 + - - -
1483O EDO 3.9 17.0 - - - -
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Residues in contact with VAL 346 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328O SER* 4.2 14.4 - - - -
342O THR* 2.8 29.3 + - + +
343O LEU* 3.9 12.6 - - + +
344O GLY 3.3 0.2 - - - -
345O PHE* 1.3 77.9 - - + +
347O ASP* 1.3 63.9 + - - +
349O MET* 3.1 8.7 + - - +
350O ARG* 3.0 62.6 + - - +
376O PRO* 4.4 7.4 - - + -
393O ILE 5.9 0.4 - - - +
394O PHE* 3.9 29.6 - - + -
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Residues in contact with ASP 347 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343O LEU 3.2 15.2 + - - +
344O GLY* 3.5 10.5 - - - +
346O VAL* 1.3 75.8 - - - +
348O LEU* 1.3 57.2 + - - +
350O ARG* 4.4 13.7 + - - -
351O ASP* 2.9 58.3 + - - +
354O VAL* 3.6 18.9 - - + +
360O ARG* 4.2 15.2 + - - -
362O ILE* 5.3 0.2 - - + -
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Residues in contact with LEU 348 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137O ASP* 5.0 0.7 - - - +
312O ARG* 4.0 31.2 - - + +
315O ALA* 6.1 1.6 - - + -
316O LYS* 3.8 38.8 - - + +
319O ARG* 2.8 23.6 + - - -
344O GLY 3.2 14.5 + - - +
345O PHE* 3.1 11.3 + - + +
347O ASP* 1.3 77.1 - - - +
349O MET* 1.3 53.0 + - + +
354O VAL* 3.8 30.1 - - + -
362O ILE* 4.2 20.9 - - + -
366O GLN* 3.9 16.4 - - + -
368O TRP* 3.0 16.3 + - - +
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Residues in contact with MET 349 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311O PHE* 4.7 2.5 - - - -
315O ALA* 3.9 23.3 - - + +
319O ARG* 3.0 23.2 + - + +
326O LEU* 3.6 48.5 - - + +
328O SER* 4.4 10.5 - - - -
345O PHE* 2.8 34.2 + - - +
346O VAL* 3.1 12.7 + - - +
348O LEU* 1.3 77.4 - - - +
350O ARG* 1.3 57.8 + - + +
374O VAL* 2.8 41.1 + - + +
376O PRO* 3.7 19.5 - - + -
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Residues in contact with ARG 350 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155O ILE* 3.8 16.0 - - + +
319O ARG* 3.9 1.6 + - - -
346O VAL* 3.0 37.4 + - - +
347O ASP* 4.4 9.5 + - - -
349O MET* 1.3 77.1 - - + +
351O ASP* 1.3 76.5 + - - +
373O GLY* 3.5 19.7 + - - -
374O VAL 3.6 15.9 - - - +
376O PRO* 3.6 17.1 - - + +
393O ILE 5.2 2.4 + - - -
394O PHE* 2.8 32.3 + - - +
397O ASP* 2.9 39.9 + - - +
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Residues in contact with ASP 351 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319O ARG* 2.8 25.8 + - - -
347O ASP* 2.9 43.8 + - - +
350O ARG* 1.3 90.9 + - - +
352O ASP* 1.3 61.3 + - - +
353O TYR 4.2 7.2 - - - +
354O VAL* 3.9 13.7 - - + +
368O TRP* 3.2 8.4 - - - -
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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