Contacts of the helix formed by residues 335 - 355 (chain C) in PDB entry 5Y3R
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 LYS 335 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331C ALA* 2.9 28.5 + - - +
332C GLU 3.6 4.8 + - - +
333C MET 3.8 0.4 - - - -
334C HIS* 1.3 71.3 - - - +
336C ASN* 1.3 70.3 + - - +
338C LEU* 3.0 11.3 - - - +
339C GLN* 2.9 41.7 + - - +
378C ALA* 3.3 40.6 + - + +
379C LYS* 6.3 0.4 - - + -
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Residues in contact with ASN 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332C GLU 4.9 1.9 + - - +
335C LYS* 1.3 82.0 - - - +
337C LYS* 1.3 54.3 + - + +
339C GLN* 2.2 50.0 + - - +
340C TYR* 2.7 33.1 + - + -
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Residues in contact with LYS 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C THR 5.9 0.8 + - - -
287C LEU* 5.4 1.6 - - - +
288C ASP* 4.2 22.7 - - + +
332C GLU 4.9 1.9 + - - -
333C MET* 3.0 47.7 + - - +
334C HIS* 4.4 4.5 + - + +
335C LYS 3.6 0.4 - - - +
336C ASN* 1.3 78.2 - - + +
338C LEU* 1.3 63.7 + - - +
340C TYR* 3.0 30.2 - - + +
341C PHE* 3.0 20.6 + - - +
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C VAL* 3.7 31.0 - - + +
330C ASN 4.7 1.3 - - - +
334C HIS* 3.4 43.9 + - + +
335C LYS* 3.0 16.4 - - - +
337C LYS* 1.3 80.0 - - - +
339C GLN* 1.3 72.7 + - + +
341C PHE* 3.0 3.6 + - - +
342C MET* 2.8 52.3 + - + +
375C VAL* 4.5 12.1 - - + -
378C ALA* 5.2 8.3 - - + -
379C LYS* 3.6 24.5 - - + -
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Residues in contact with GLN 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C LYS* 2.9 25.6 + - - +
336C ASN* 2.2 37.7 + - - +
338C LEU* 1.3 82.3 - - + +
340C TYR* 1.3 57.2 + - + +
342C MET* 3.4 10.5 - - + +
343C GLU* 2.8 31.5 + - - +
378C ALA 5.1 2.0 + - - -
379C LYS* 3.7 32.0 - - + +
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Residues in contact with TYR 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ASP* 4.3 26.5 - - + -
336C ASN* 2.7 52.0 + - + +
337C LYS* 3.0 26.5 - - + +
338C LEU 2.9 0.4 + - - -
339C GLN* 1.3 71.8 - - + +
341C PHE* 1.3 67.8 + - - +
343C GLU* 3.6 2.3 - - - +
344C GLN* 2.8 32.5 + - + +
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Residues in contact with PHE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU* 3.6 26.9 - - + -
288C ASP* 5.7 0.8 - - - +
291C VAL* 3.3 37.2 - - + +
294C PHE* 4.5 15.3 - + - -
320C LEU* 3.4 34.5 - - + -
323C VAL* 3.5 33.7 - - + -
324C SER* 5.2 1.3 - - - -
327C VAL* 5.6 2.0 - - + -
334C HIS* 6.2 0.7 - - - +
337C LYS 3.0 7.5 + - - +
338C LEU* 3.7 5.4 - - - +
340C TYR* 1.3 76.6 - - - +
342C MET* 1.3 77.6 + - + +
344C GLN* 3.0 24.8 - - - +
345C PHE* 3.0 17.6 + + + +
370C ALA* 5.2 4.7 - - + -
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Residues in contact with MET 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C LEU* 2.8 50.2 + - + +
339C GLN* 3.4 10.1 - - + +
341C PHE* 1.3 84.5 - - + +
343C GLU* 1.3 58.6 + - - +
345C PHE* 3.2 7.9 + - - +
346C TYR* 2.7 33.9 + - + +
349C ILE* 5.1 3.9 - - + +
370C ALA 4.3 4.9 - - - +
371C GLY* 3.4 38.6 - - - +
375C VAL* 6.1 0.2 - - - -
379C LYS* 3.5 25.8 - - + +
384C MET* 4.9 8.5 - - + -
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Residues in contact with GLU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C GLN 2.8 21.8 + - - +
340C TYR* 3.8 2.5 - - - +
342C MET* 1.3 72.4 - - + +
344C GLN* 1.3 61.2 + - - +
346C TYR* 2.6 54.1 + - - +
347C GLY* 2.9 15.1 + - - -
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Residues in contact with GLN 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ASP 4.1 4.2 + - - -
291C VAL* 3.3 37.2 - - + +
292C SER* 3.3 23.8 + - - +
295C GLU* 3.6 16.8 + - - +
340C TYR* 2.8 28.3 + - + +
341C PHE* 3.0 17.5 - - - +
343C GLU* 1.3 78.7 - - - +
345C PHE* 1.3 62.7 + - - +
347C GLY* 3.6 3.6 + - - -
348C ILE* 3.2 14.7 - - - +
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Residues in contact with PHE 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL* 4.9 1.5 - - + +
294C PHE* 6.4 3.6 - + + -
295C GLU* 4.6 0.9 + - - -
298C LEU* 6.2 3.4 - - + -
316C LEU* 5.9 4.3 - - + -
320C LEU* 6.1 2.2 - - + -
341C PHE* 3.0 21.7 + + + +
342C MET* 3.7 7.0 - - - +
344C GLN* 1.3 79.3 - - - +
346C TYR* 1.3 56.6 + - - +
348C ILE* 2.4 63.6 + - + +
349C ILE* 2.9 42.0 + - + -
363C ILE* 4.1 14.8 - - + -
364C ARG* 3.4 33.2 - - + -
367C GLY* 3.3 36.6 - - - -
368C LEU 3.5 0.7 - - - -
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Residues in contact with TYR 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C MET* 2.7 20.2 + - + +
343C GLU* 2.6 49.1 + - - +
345C PHE* 1.3 71.2 - - - +
347C GLY* 1.3 55.4 + - - +
349C ILE* 2.6 64.4 + - + +
350C ARG* 3.0 50.8 + - + +
383C PHE* 4.7 12.0 - + - -
384C MET* 4.5 20.0 - - + -
391C ARG* 4.8 0.9 + - - -
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Residues in contact with GLY 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C GLU* 2.9 15.0 + - - -
344C GLN 4.2 4.0 - - - -
345C PHE 3.1 0.6 + - - -
346C TYR* 1.3 78.6 - - - +
348C ILE* 1.3 58.4 + - - +
350C ARG* 4.8 1.9 - - - +
351C ASN* 2.8 27.6 + - - +
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Residues in contact with ILE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295C GLU* 3.2 31.0 - - + +
298C LEU* 6.5 0.2 - - + -
299C LYS* 6.5 2.0 - - + -
344C GLN 3.2 15.0 - - - +
345C PHE* 2.4 43.5 + - + +
347C GLY* 1.3 73.9 - - - -
349C ILE* 1.3 62.4 + - - +
351C ASN* 2.8 16.2 + - - +
352C VAL* 3.0 0.7 + - - +
357C LYS* 2.4 50.5 + - + +
363C ILE* 5.2 7.0 - - + -
364C ARG* 5.4 2.8 - - + +
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Residues in contact with ILE 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342C MET* 5.1 8.7 - - + +
345C PHE* 2.9 44.6 + - + -
346C TYR* 2.6 56.3 + - + +
348C ILE* 1.3 69.8 - - - +
350C ARG* 1.3 58.4 + - - +
352C VAL* 3.0 25.6 - - - +
364C ARG* 5.2 2.0 - - - -
367C GLY 4.6 4.9 - - - +
368C LEU* 3.5 19.5 - - + -
371C GLY* 5.8 1.6 - - - -
384C MET* 5.7 4.3 - - + -
391C ARG* 3.3 33.3 + - - +
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Residues in contact with ARG 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346C TYR* 3.0 41.8 + - + +
347C GLY* 4.8 1.3 - - - +
349C ILE* 1.3 74.2 - - - +
351C ASN* 1.3 58.8 + - - +
352C VAL 3.0 2.7 - - - -
353C ASP* 2.4 68.7 + - - +
354C SER* 3.9 2.6 + - - -
383C PHE* 6.0 5.1 - - - -
387C GLU* 5.9 4.6 - - - +
391C ARG* 3.0 26.9 - - - +
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Residues in contact with ASN 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347C GLY 2.8 24.6 + - - +
348C ILE* 2.8 21.6 + - - +
350C ARG* 1.3 75.9 - - - +
352C VAL* 1.3 53.4 + - - +
353C ASP 3.3 0.5 + - - -
354C SER* 3.6 3.2 + - - -
355C ASN* 2.6 56.4 + - - +
357C LYS* 3.1 16.9 - - - +
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Residues in contact with VAL 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C ILE 3.0 1.2 + - - +
349C ILE 3.0 26.2 - - - +
351C ASN* 1.3 77.3 - - - +
353C ASP* 1.3 68.2 + - - +
355C ASN* 3.0 18.7 - - - +
357C LYS* 2.7 29.0 - - + +
361C ILE* 4.4 13.7 - - + -
364C ARG* 3.5 41.7 - - - +
391C ARG* 4.9 1.8 - - - +
1856C THR 3.1 10.0 + - - -
1858C LEU* 3.6 19.5 - - + +
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Residues in contact with ASP 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ARG* 2.4 66.6 + - + +
352C VAL* 1.3 77.5 - - - +
354C SER* 1.3 57.1 + - - +
391C ARG* 3.9 10.4 + - - -
1856C THR 2.4 31.9 + - - +
1857C LYS 3.3 1.7 + - - -
1858C LEU* 3.1 37.5 + - + +
1859C ASN* 5.0 4.9 + - + +
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Residues in contact with SER 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350C ARG 3.9 1.9 + - - -
351C ASN* 3.6 4.8 + - - -
352C VAL 3.2 0.2 - - - -
353C ASP* 1.3 79.1 - - - +
355C ASN* 1.3 59.0 + - - +
1856C THR* 2.9 25.2 - - - +
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Residues in contact with ASN 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C ASN* 2.6 45.3 + - - +
352C VAL* 3.0 17.8 - - - +
354C SER* 1.3 80.4 - - - +
356C ASN* 1.3 63.1 + - - +
357C LYS* 3.1 32.4 + - - +
1856C THR* 2.6 32.8 + - - +
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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
------------------------------------------------------------
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