Contacts of the helix formed by residues 338 - 351 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331R VAL* 5.1 0.4 - - - -
336R GLU* 4.9 0.4 - - - +
337R GLY* 1.3 71.1 - - - +
339R ARG* 1.3 77.2 + - - +
340R GLU* 3.0 29.3 + - - +
341R VAL* 3.0 37.2 + - + +
342R THR* 2.8 29.6 + - - -
471R THR* 3.9 33.2 - - + +
473R ASP* 4.2 10.6 + - - +
474R LYS* 5.7 5.6 - - + -
475R LEU* 4.7 5.7 + - - +
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Residues in contact with ARG 339 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331R VAL* 4.1 26.7 - - + +
337R GLY 3.6 1.4 + - - -
338R GLU* 1.3 79.6 - - - +
340R GLU* 1.3 71.3 + - + +
342R THR* 3.2 3.1 + - - -
343R LEU* 2.9 57.8 + - + +
389R ALA* 6.2 0.2 - - - +
392R GLU* 2.8 43.0 + - - -
393R ILE* 3.4 29.4 - - + +
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Residues in contact with GLU 340 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338R GLU* 3.0 22.7 + - - +
339R ARG* 1.3 92.9 + - + +
341R VAL* 1.3 65.5 + - - +
343R LEU* 3.5 5.5 + - - +
344R GLY 3.1 17.7 + - - -
359R SER* 3.7 21.2 + - - +
360R ARG* 3.1 46.8 + - + +
475R LEU* 4.6 4.0 - - + -
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Residues in contact with VAL 341 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310R HIS* 3.4 37.1 - - + +
312R ARG* 4.5 2.4 + - - +
337R GLY* 6.0 0.9 - - - -
338R GLU* 3.0 31.6 + - + +
340R GLU* 1.3 76.4 - - - +
342R THR* 1.3 64.5 + - - +
344R GLY* 3.3 1.9 + - - -
345R PHE* 3.2 33.9 + - + -
360R ARG* 4.0 9.9 - - - +
473R ASP* 4.0 23.1 - - - +
474R LYS 5.0 0.2 - - - -
475R LEU* 3.7 31.2 - - + +
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Residues in contact with THR 342 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328R SER 3.7 21.6 + - - +
329R GLY* 5.1 1.3 - - - +
331R VAL* 3.9 20.0 - - + +
337R GLY* 3.6 19.4 + - - -
338R GLU 2.8 20.0 + - - -
339R ARG 3.5 4.0 - - - -
341R VAL* 1.3 74.0 - - - +
343R LEU* 1.3 60.9 + - - +
345R PHE* 3.3 18.9 + - + -
346R VAL* 2.8 44.7 + - + +
393R ILE* 5.2 2.9 - - + -
394R PHE* 4.4 11.0 - - + -
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Residues in contact with LEU 343 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339R ARG* 2.9 50.9 + - + +
340R GLU* 3.9 9.2 - - - +
342R THR* 1.3 74.9 - - - +
344R GLY* 1.3 61.7 + - - +
346R VAL* 3.8 10.2 - - + +
347R ASP* 3.2 29.3 + - - +
360R ARG* 3.3 39.9 - - - +
393R ILE* 3.5 41.7 - - + +
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Residues in contact with GLY 344 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312R ARG* 6.2 0.2 - - - -
340R GLU 3.1 11.2 + - - -
341R VAL 3.7 4.0 - - - -
342R THR 3.2 0.2 - - - -
343R LEU* 1.3 76.0 - - - +
345R PHE* 1.3 61.5 + - - +
347R ASP* 3.3 8.5 + - - +
348R LEU* 3.2 23.8 + - - +
360R ARG* 3.8 23.2 - - - +
362R ILE* 3.8 20.1 - - - +
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Residues in contact with PHE 345 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295R ARG* 4.7 2.5 - - - -
310R HIS* 4.1 13.0 - + - -
311R PHE* 3.7 39.5 - + + -
312R ARG* 3.7 27.9 - - + +
315R ALA* 4.9 3.4 - - + -
328R SER* 3.2 34.3 - - - -
337R GLY* 6.0 2.2 - - - -
341R VAL* 3.2 35.3 + - + -
342R THR* 3.6 30.1 - - + -
344R GLY* 1.3 73.8 - - - +
346R VAL* 1.3 62.7 + - + +
348R LEU* 3.1 10.0 + - + +
349R MET* 2.9 38.7 + - - +
360R ARG 4.9 0.4 + - - -
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Residues in contact with VAL 346 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328R SER* 4.1 14.6 - - - -
342R THR* 2.8 28.1 + - + +
343R LEU* 3.8 12.3 - - + +
345R PHE* 1.3 78.8 - - + +
347R ASP* 1.3 62.6 + - - +
349R MET* 3.1 9.4 + - - +
350R ARG* 3.0 62.9 + - - +
376R PRO* 4.3 7.6 - - + -
393R ILE 5.9 0.4 - - - +
394R PHE* 3.9 29.8 - - + -
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Residues in contact with ASP 347 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343R LEU 3.2 14.9 + - - +
344R GLY* 3.5 10.3 - - - +
346R VAL* 1.3 76.2 - - - +
348R LEU* 1.3 58.5 + - - +
350R ARG* 4.5 13.1 + - - -
351R ASP* 2.9 58.3 + - - +
354R VAL* 3.5 19.0 - - + +
360R ARG* 4.2 15.1 + - - -
362R ILE* 5.3 1.8 - - + +
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Residues in contact with LEU 348 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137R ASP* 5.0 1.1 - - - +
312R ARG* 4.1 30.7 - - + +
315R ALA* 6.1 1.6 - - + -
316R LYS* 3.8 38.4 - - + +
319R ARG* 2.8 25.5 + - - -
344R GLY 3.2 17.7 + - - +
345R PHE* 3.1 11.6 + - + +
347R ASP* 1.3 75.9 - - - +
349R MET* 1.3 52.4 + - + +
354R VAL* 3.7 30.1 - - + -
362R ILE* 4.1 21.8 - - + -
366R GLN* 3.9 16.6 - - + -
368R TRP* 2.9 16.7 + - - -
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Residues in contact with MET 349 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311R PHE* 4.8 1.8 - - - -
315R ALA* 3.9 23.6 - - + +
319R ARG* 3.1 21.3 + - - +
326R LEU* 3.6 48.2 - - + +
328R SER* 4.4 10.3 - - - -
345R PHE* 2.9 34.1 + - - +
346R VAL* 3.1 11.4 + - - +
348R LEU* 1.3 78.2 - - - +
350R ARG* 1.3 57.8 + - + +
374R VAL* 2.8 40.2 + - + +
376R PRO* 3.6 21.1 - - + -
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Residues in contact with ARG 350 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155R ILE* 3.8 14.9 - - + +
319R ARG* 3.9 1.6 + - - -
346R VAL* 3.0 35.4 + - - +
347R ASP* 4.5 9.3 + - - -
349R MET* 1.3 79.1 - - + +
351R ASP* 1.3 74.0 + - - +
373R GLY* 3.5 19.6 + - - -
374R VAL 3.6 16.2 - - - +
376R PRO* 3.6 16.7 - - + +
393R ILE 5.2 2.0 + - - -
394R PHE* 2.8 32.7 + - - +
397R ASP* 2.8 47.6 + - - +
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Residues in contact with ASP 351 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319R ARG* 2.8 25.3 + - - -
347R ASP* 2.9 48.3 + - - +
350R ARG* 1.3 87.1 + - - +
352R ASP* 1.3 60.0 + - - +
353R TYR 3.5 7.8 - - - +
354R VAL* 3.9 12.9 - - + +
368R TRP* 3.3 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
------------------------------------------------------------
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