Contacts of the helix formed by residues 279 - 294 (chain C) in PDB entry 4UC5
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 ARG 279 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C SER* 3.7 25.1 - - - +
274C ARG* 3.9 13.7 - - - +
276C ASP* 2.8 33.2 + - + +
278C THR* 1.3 112.9 + - - +
280C GLN* 1.3 66.9 + - - +
281C MET 3.0 2.5 - - - -
282C GLU* 2.9 49.7 + - + +
283C VAL* 2.9 14.7 + - - +
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Residues in contact with GLN 280 (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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268C CYS* 3.4 29.6 - - + +
269C SER* 3.4 28.2 + - - +
273C SER* 4.1 5.1 - - - +
276C ASP 3.9 0.6 + - - -
277C TYR* 3.1 25.5 + - - +
279C ARG* 1.3 76.6 - - - +
281C MET* 1.3 57.5 + - - +
283C VAL* 3.4 3.5 + - - +
284C ALA* 3.0 28.6 + - - +
303C VAL* 3.4 13.7 - - - +
304C GLU* 2.8 47.3 + - - +
325C ALA 4.3 2.6 + - - -
327C ILE* 4.0 13.9 - - + +
335C LEU* 4.2 8.6 - - + +
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Residues in contact with MET 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C TYR 4.5 0.4 + - - -
278C THR* 3.8 13.3 + - - +
279C ARG 3.0 0.2 - - - -
280C GLN* 1.3 78.3 - - - +
282C GLU* 1.3 64.1 + - - +
284C ALA* 3.4 1.7 + - - +
285C GLN* 3.0 23.0 + - + +
327C ILE* 5.4 4.8 - - + +
331C ALA* 4.5 10.8 - - + +
334C GLU* 4.1 23.1 - - + +
335C LEU* 4.0 40.1 - - + +
338C LEU* 3.5 32.3 - - + -
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C TYR* 4.3 9.4 + - - +
274C ARG* 3.0 31.4 + - - +
278C THR 4.3 1.0 + - - +
279C ARG* 2.9 44.0 + - + +
281C MET* 1.3 74.9 - - - +
283C VAL* 1.3 70.3 + - + +
285C GLN* 3.1 10.6 + - + +
286C ASP* 3.0 21.0 + - - +
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Residues in contact with VAL 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C TYR* 3.7 41.7 - - + -
266C ILE* 4.6 0.2 - - + -
267C ASP 4.6 1.3 - - - +
268C CYS* 3.7 32.3 - - + +
272C ASN 3.8 21.5 - - - +
273C SER* 4.7 0.7 - - - -
274C ARG* 4.8 0.9 - - - +
279C ARG 2.9 18.8 + - - +
280C GLN 3.6 6.3 - - - +
282C GLU* 1.3 78.4 - - + +
284C ALA* 1.3 63.3 + - - +
286C ASP* 3.0 14.2 + - - +
287C ILE* 3.0 29.2 + - + +
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Residues in contact with ALA 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C CYS* 4.4 8.1 - - - -
280C GLN 3.0 16.3 + - - +
281C MET* 3.8 4.3 - - - +
282C GLU 3.3 0.2 - - - -
283C VAL* 1.3 77.1 - - - +
285C GLN* 1.3 52.7 + - - +
287C ILE* 3.2 12.8 + - - +
288C ALA* 2.7 35.7 + - - +
335C LEU* 3.9 28.9 - - + -
338C LEU* 4.1 9.9 - - + -
339C LEU* 3.9 12.1 - - + +
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Residues in contact with GLN 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C MET* 3.0 14.5 + - + +
282C GLU* 3.1 14.1 + - - +
284C ALA* 1.3 77.2 - - - +
286C ASP* 1.3 56.7 + - - +
288C ALA* 3.3 4.1 + - - +
289C ALA* 2.9 28.9 + - - +
338C LEU* 4.0 15.6 - - + +
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Residues in contact with ASP 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C TYR* 3.9 28.4 - - + -
244C ASP* 3.8 15.0 - - - +
245C ALA* 4.2 1.0 + - - +
282C GLU 3.0 9.9 + - - +
283C VAL 3.0 10.4 + - - +
285C GLN* 1.3 76.6 - - - +
287C ILE* 1.3 58.2 + - - +
289C ALA* 3.2 10.1 + - - +
290C GLN* 3.0 44.7 + - - +
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Residues in contact with ILE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C TYR 4.6 1.8 - - - +
266C ILE* 3.8 32.8 - - + -
268C CYS* 3.9 16.6 - - - -
283C VAL* 3.0 33.5 + - + +
284C ALA* 3.5 7.9 - - - +
286C ASP* 1.3 75.4 - - + +
288C ALA* 1.3 66.1 + - - +
290C GLN* 3.2 13.5 + - - +
291C LEU* 2.9 38.6 + - + +
298C ILE* 4.5 13.0 - - + -
301C VAL* 4.0 24.2 - - + -
339C LEU* 4.3 5.2 - - + -
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Residues in contact with ALA 288 (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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284C ALA 2.7 20.2 + - - +
285C GLN 3.6 5.2 - - - +
287C ILE* 1.3 72.4 - - - +
289C ALA* 1.3 63.5 + - - +
291C LEU* 3.1 6.8 + - - +
292C GLU* 2.9 29.4 + - - +
338C LEU* 3.8 27.6 - - + -
339C LEU* 4.4 4.2 - - + +
342C ALA* 3.7 27.0 - - + +
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C GLN 2.9 14.8 + - - +
286C ASP* 3.3 13.2 - - - +
288C ALA* 1.3 77.4 - - - +
290C GLN* 1.3 56.4 + - - +
292C GLU* 3.4 12.1 + - - +
293C GLN* 3.0 29.5 + - - +
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Residues in contact with GLN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C TYR 2.9 26.5 + - - -
245C ALA* 3.2 37.6 - - + +
248C VAL* 3.6 17.6 - - - +
266C ILE* 4.6 0.8 - - - +
286C ASP* 3.0 32.9 + - - +
287C ILE* 3.2 18.6 + - - +
289C ALA* 1.3 77.7 - - + +
291C LEU* 1.3 54.1 + - - +
293C GLN* 3.3 3.1 + - - -
294C ASP 2.7 32.1 + - - -
295C GLY* 2.9 12.9 + - - +
298C ILE* 3.9 18.3 - - + +
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 4.1 22.2 - - + -
287C ILE* 2.9 35.4 + - + +
288C ALA* 3.6 10.1 - - - +
290C GLN* 1.3 76.3 - - - +
292C GLU* 1.3 57.4 + - - +
294C ASP 4.4 0.2 - - - -
295C GLY* 3.9 10.1 - - - +
298C ILE* 4.4 14.1 - - + -
339C LEU* 4.6 3.8 - - + +
342C ALA* 4.2 22.8 - - + +
343C ASN* 3.7 10.8 - - + +
346C ARG* 3.5 50.1 - - + +
349C ARG* 3.1 27.0 + - - -
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Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ALA* 2.9 18.3 + - - +
289C ALA* 3.5 13.1 - - - +
291C LEU* 1.3 74.1 - - - +
293C GLN* 1.3 58.7 + - - +
338C LEU* 5.8 2.1 - - - +
341C GLY 5.3 0.2 - - - -
342C ALA* 4.0 23.6 + - - +
345C LYS* 4.1 37.2 + - + +
349C ARG* 2.7 23.1 + - - +
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Residues in contact with GLN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C ALA 3.0 16.9 + - - +
290C GLN* 4.0 3.8 - - - +
292C GLU* 1.3 80.7 - - - +
294C ASP* 1.3 63.6 + - + +
349C ARG* 3.6 10.0 + - - -
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Residues in contact with ASP 294 (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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290C GLN 2.7 12.0 + - - -
291C LEU 4.2 0.2 - - - -
292C GLU 3.7 0.2 - - - -
293C GLN* 1.3 78.0 - - + +
295C GLY* 1.3 64.9 + - - +
296C GLY* 3.0 14.6 + - - -
346C ARG* 3.7 6.2 - - - -
349C ARG* 2.7 25.7 + - - +
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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