Contacts of the helix formed by residues 276 - 286 (chain C) in PDB entry 1FBA
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 276 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C SER* 1.3 74.6 - - - +
277C GLU* 1.3 59.4 + - - +
279C ALA* 3.7 3.6 + - - +
280C THR* 2.9 26.9 + - - -
304C ALA* 3.5 30.5 - - - +
305C LEU 4.3 2.3 - - - +
306C GLN 4.2 0.7 - - - -
307C ALA* 3.3 21.8 + - + +
308C SER* 2.7 45.8 + - - -
330C ARG* 3.5 25.2 + - - +
334C ASN* 5.2 0.5 + - - -
352C GLY* 3.1 10.9 - - - -
353C SER* 3.0 27.8 + - - +
356C LEU* 3.8 2.2 - - + +
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Residues in contact with GLU 277 (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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275C SER* 3.3 5.3 + - - +
276C GLU* 1.3 75.5 - - - +
278C GLU* 1.3 61.0 + - + +
280C THR* 3.1 3.8 + - - -
281C VAL* 2.9 48.7 + - + +
330C ARG* 3.2 17.1 + - - +
342C TYR* 2.7 25.1 + - - -
345C ALA* 3.8 0.9 - - - +
346C GLY* 2.8 32.9 + - - -
348C ALA 4.9 0.2 + - - -
349C GLY 5.5 0.4 - - - -
351C ALA* 3.5 31.4 + - - +
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Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LYS* 3.0 43.1 + - - +
273C GLY 4.7 0.3 - - - +
274C GLN* 3.3 21.5 - - - +
275C SER* 2.9 41.8 + - - +
277C GLU* 1.3 79.2 - - + +
279C ALA* 1.3 55.3 + - - +
281C VAL* 3.8 4.4 - - - +
282C ASN* 2.8 46.5 + - - +
354C GLY 5.1 0.8 - - - +
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Residues in contact with ALA 279 (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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232C MET* 3.9 1.7 - - - +
271C SER* 4.0 18.4 - - - -
274C GLN* 3.5 13.6 + - + +
275C SER 3.1 14.9 + - - +
276C GLU 3.8 5.2 - - - +
278C GLU* 1.3 80.2 - - - +
280C THR* 1.3 57.1 + - - +
283C LEU* 3.2 19.1 + - - +
301C TYR* 2.9 43.7 + - + +
304C ALA* 4.2 5.4 - - + -
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Residues in contact with THR 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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276C GLU 2.9 7.0 + - - -
277C GLU 3.1 5.5 + - - -
279C ALA* 1.3 76.2 - - - +
281C VAL* 1.3 59.4 + - - +
283C LEU 3.3 1.2 + - - -
284C SER* 3.0 24.9 + - - -
330C ARG* 2.7 31.6 + - - +
333C ALA 3.5 24.9 - - - +
334C ASN* 2.8 25.9 + - - +
337C ALA* 3.4 12.1 - - + +
342C TYR* 3.5 27.6 - - + -
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Residues in contact with VAL 281 (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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245C PRO* 3.8 27.6 - - + -
277C GLU* 2.9 41.5 + - + +
278C GLU* 3.9 5.4 - - - +
280C THR* 1.3 75.0 - - - +
282C ASN* 1.3 64.5 + - - +
284C SER* 3.2 7.4 + - - -
285C ALA* 3.0 23.2 + - - +
342C TYR* 4.0 14.8 - - + -
345C ALA* 4.3 16.4 - - + -
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Residues in contact with ASN 282 (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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232C MET* 3.6 21.3 - - + -
245C PRO* 3.3 32.8 - - - +
248C ILE* 3.8 27.8 - - + +
249C ALA* 4.8 0.7 - - - +
274C GLN* 2.7 26.2 + - - +
278C GLU* 2.8 29.8 + - - +
281C VAL* 1.3 73.1 - - - +
283C LEU* 1.3 61.7 + - - +
285C ALA* 3.2 5.4 + - - +
286C ILE* 3.0 30.0 + - - +
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Residues in contact with LEU 283 (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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232C MET* 4.0 5.5 - - + +
269C PHE* 4.0 17.3 - - + -
279C ALA 3.2 19.7 + - - +
280C THR 3.3 4.7 + - - +
282C ASN* 1.3 75.9 - - - +
284C SER* 1.3 63.3 + - - +
286C ILE* 3.4 5.8 + - + +
287C ASN* 3.2 31.4 + - - +
297C LEU 3.5 22.2 - - - +
298C THR 3.9 14.1 - - - +
299C PHE* 3.9 38.8 - - + -
301C TYR* 3.9 7.9 - - - +
334C ASN* 3.9 6.3 - - - +
337C ALA* 3.9 21.3 - - + +
338C ALA* 3.9 4.3 - - - +
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Residues in contact with SER 284 (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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280C THR 3.0 14.3 + - - -
281C VAL* 3.5 10.1 - - - -
282C ASN 3.1 0.2 - - - -
283C LEU* 1.3 77.3 - - - +
285C ALA* 1.3 63.5 + - - +
287C ASN 3.1 9.2 + - - -
288C ASN* 3.0 22.0 + - - -
337C ALA* 3.5 11.1 - - - +
340C GLY* 3.4 16.8 + - - -
341C LYS 3.7 0.2 + - - -
342C TYR* 3.1 42.9 + - - +
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Residues in contact with ALA 285 (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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245C PRO* 3.7 34.1 - - + +
246C GLU* 4.5 10.3 - - + +
249C ALA* 3.6 10.1 - - + +
281C VAL 3.0 15.8 + - - +
282C ASN 3.6 4.5 - - - +
284C SER* 1.3 75.0 - - - +
286C ILE* 1.3 65.3 + - - +
288C ASN* 3.0 19.5 + - - +
289C VAL* 3.4 9.2 + - - +
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Residues in contact with ILE 286 (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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232C MET* 3.9 29.8 - - + -
248C ILE* 5.3 1.3 - - + -
249C ALA* 3.8 24.9 - - - +
252C THR* 3.9 26.9 - - + +
253C VAL* 3.7 14.2 - - + +
269C PHE* 4.0 22.7 - - + -
282C ASN 3.0 18.3 + - - +
283C LEU* 3.5 10.3 - - - +
284C SER 3.2 0.2 - - - -
285C ALA* 1.3 75.6 - - - +
287C ASN* 1.3 58.6 + - - +
288C ASN 3.0 4.2 + - - -
289C VAL* 3.4 15.6 + - - +
293C ARG* 3.8 6.4 - - - -
297C LEU* 3.9 26.2 - - + -
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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