Contacts of the helix formed by residues 276 - 286 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D GLN 4.0 0.4 + - - -
275D SER* 1.3 71.9 - - - +
277D GLU* 1.3 61.1 + - - +
279D ALA* 3.5 3.3 + - - +
280D THR* 3.0 25.3 + - - -
303D ARG 4.3 1.6 - - - +
304D ALA* 3.2 39.3 - - - +
305D LEU 4.2 2.8 - - - +
306D GLN 4.0 2.6 + - - -
307D ALA* 3.3 15.1 + - - -
308D SER* 2.8 50.2 + - - -
330D ARG* 3.8 23.5 + - - +
334D ASN* 5.4 0.3 + - - -
352D GLY* 3.4 3.8 - - - -
353D SER* 2.9 34.5 + - - +
356D LEU* 4.1 1.2 - - + +
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Residues in contact with GLU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D SER* 3.3 5.6 + - - +
276D GLU* 1.3 75.7 - - - +
278D GLU* 1.3 61.7 + - + +
280D THR* 3.2 3.3 + - - -
281D VAL* 2.8 50.1 + - + +
330D ARG* 2.9 23.9 + - - +
342D TYR* 2.5 26.6 + - - -
345D ALA* 3.9 0.5 - - - +
346D GLY* 2.9 26.1 + - - -
349D GLY 3.3 20.8 - - - +
351D ALA* 3.5 20.0 + - - +
352D GLY* 5.2 0.2 - - - -
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Residues in contact with GLU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D LYS* 2.8 42.1 + - - +
273D GLY 4.8 0.3 - - - +
274D GLN* 3.5 19.9 - - + +
275D SER* 3.0 37.7 + - - +
277D GLU* 1.3 79.8 - - - +
279D ALA* 1.3 54.5 + - - +
281D VAL* 4.0 4.4 - - - +
282D ASN* 2.8 47.4 + - - +
355D SER* 5.9 1.6 - - - -
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Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D MET* 4.0 2.2 - - - +
271D SER* 3.9 19.7 - - - -
274D GLN* 3.5 13.7 + - + +
275D SER 3.0 17.0 + - - +
276D GLU 3.8 4.7 - - - +
278D GLU* 1.3 76.6 - - - +
280D THR* 1.3 57.1 + - - +
283D LEU* 3.2 18.7 + - - +
301D TYR* 2.8 43.7 + - + +
304D ALA* 4.1 5.2 - - + -
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Residues in contact with THR 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D GLU 3.0 6.4 + - - -
277D GLU 3.2 5.3 + - - -
279D ALA* 1.3 76.4 - - - +
281D VAL* 1.3 65.8 + - - +
283D LEU 3.2 1.6 + - - -
284D SER* 3.0 19.8 + - - -
330D ARG* 2.9 27.6 + - - +
333D ALA 3.3 31.6 - - - +
334D ASN* 3.1 22.9 + - - +
337D ALA* 3.4 7.8 - - + +
342D TYR* 3.5 27.6 - - + -
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Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D PRO* 3.8 29.4 - - + -
277D GLU* 2.8 44.6 + - + +
278D GLU* 4.0 4.9 - - - +
280D THR* 1.3 72.5 - - - +
282D ASN* 1.3 64.8 + - - +
284D SER* 3.2 6.4 + - - -
285D ALA* 3.0 21.0 + - - +
342D TYR* 4.0 14.8 - - + -
345D ALA* 4.1 17.5 - - + -
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Residues in contact with ASN 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D MET* 3.7 20.0 - - + -
245D PRO* 3.4 32.3 - - - +
248D ILE* 3.8 30.4 - - + +
249D ALA* 4.8 0.5 + - - +
274D GLN* 2.8 25.2 + - - +
278D GLU* 2.8 26.5 + - - +
281D VAL* 1.3 77.6 - - - +
283D LEU* 1.3 61.1 + - - +
285D ALA* 3.2 6.8 + - - +
286D ILE* 3.0 29.1 + - - +
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Residues in contact with LEU 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D MET* 4.0 5.0 - - + +
269D PHE* 3.9 19.5 - - + -
279D ALA 3.2 20.0 + - - +
280D THR* 3.2 4.7 + - - +
282D ASN* 1.3 75.9 - - - +
284D SER* 1.3 62.9 + - - +
286D ILE* 3.3 6.8 + - + +
287D ASN* 3.2 25.2 + - - +
297D LEU 3.7 20.2 - - - +
298D THR 3.9 16.4 - - - +
299D PHE* 3.9 29.2 - - + -
301D TYR* 3.8 7.6 - - - +
334D ASN* 4.0 22.9 - - - +
337D ALA* 4.0 13.2 - - + +
338D ALA* 4.0 4.3 - - - +
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Residues in contact with SER 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D THR 3.0 14.0 + - - -
281D VAL* 3.2 9.2 + - - -
283D LEU* 1.3 77.1 - - - +
285D ALA* 1.3 61.9 + - - +
287D ASN* 3.2 9.9 + - - -
288D ASN* 3.1 23.2 + - - -
337D ALA* 3.4 11.5 + - - +
340D GLY* 3.4 14.0 + - - -
341D LYS 3.6 0.2 + - - -
342D TYR* 3.0 44.9 + - - +
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Residues in contact with ALA 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D PRO* 3.7 33.2 - - + +
246D GLU* 4.6 10.3 - - + +
249D ALA* 3.6 6.0 - - + +
281D VAL* 3.0 12.4 + - + +
282D ASN 3.6 8.3 - - - +
284D SER* 1.3 74.3 - - - +
286D ILE* 1.3 64.7 + - - +
288D ASN* 3.0 18.2 + - - +
289D VAL* 3.4 13.9 + - - +
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Residues in contact with ILE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D MET* 3.9 36.6 - - + -
248D ILE* 5.3 1.3 - - + -
249D ALA* 3.6 25.5 - - - +
252D THR* 4.0 11.4 - - + +
253D VAL* 3.7 13.5 - - + +
269D PHE* 3.9 33.4 - - + -
282D ASN 3.0 18.4 + - - +
283D LEU* 3.4 10.3 - - + +
284D SER 3.3 0.2 - - - -
285D ALA* 1.3 77.4 - - - +
287D ASN* 1.3 57.2 + - - +
288D ASN 3.2 3.8 + - - -
289D VAL* 3.5 14.2 + - - +
293D ARG* 3.6 14.6 - - - -
297D LEU* 4.0 16.4 - - + -
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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