Contacts of the helix formed by residues 276 - 286 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A SER* 1.3 73.8 - - - +
277A GLU* 1.3 61.4 + - - +
279A ALA* 3.6 3.5 + - - +
280A THR* 2.9 27.4 + - - -
303A ARG 4.3 0.2 - - - +
304A ALA* 3.3 36.6 - - - +
305A LEU 4.2 1.6 - - - -
306A GLN 4.0 3.6 + - - -
307A ALA* 3.4 9.8 + - - -
308A SER* 2.6 50.0 + - - -
309A VAL* 5.7 0.3 - - - +
330A ARG* 3.7 24.5 + - - +
334A ASN* 5.2 0.2 + - - -
352A GLY* 3.7 3.5 - - - -
353A SER* 3.1 31.8 + - - +
356A LEU* 3.9 4.8 - - + +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A SER* 3.2 6.1 + - - +
276A GLU* 1.3 77.1 - - - +
278A GLU* 1.3 60.9 + - - +
280A THR* 3.1 3.8 + - - -
281A VAL* 2.9 47.6 + - + +
330A ARG* 3.1 19.3 + - - +
342A TYR* 2.7 21.7 + - - -
345A ALA* 4.5 0.3 - - - +
346A GLY* 2.7 30.9 + - - -
349A GLY 3.3 13.5 - - - +
351A ALA* 3.4 27.0 + - - +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS* 2.9 43.4 + - - +
273A GLY 5.0 0.5 - - - +
274A GLN* 3.6 21.7 - - + +
275A SER* 3.2 35.3 + - - +
277A GLU* 1.3 78.8 - - - +
279A ALA* 1.3 54.5 + - - +
281A VAL* 4.5 4.9 - - - +
282A ASN* 2.7 46.3 + - - +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A MET* 4.0 1.5 - - - +
271A SER* 4.1 17.5 - - - -
274A GLN* 3.4 13.4 + - + +
275A SER 3.1 15.7 + - - +
276A GLU 3.6 6.1 - - - +
277A GLU 3.2 0.2 - - - -
278A GLU* 1.3 79.4 - - - +
280A THR* 1.3 60.1 + - - +
283A LEU* 3.3 14.4 + - - +
301A TYR* 2.8 43.7 + - + +
304A ALA* 4.1 5.6 - - + -
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Residues in contact with THR 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLU 2.9 14.4 + - - -
277A GLU 3.1 5.7 + - - -
279A ALA* 1.3 77.0 - - - +
281A VAL* 1.3 65.3 + - - +
283A LEU 3.3 1.4 + - - -
284A SER* 3.0 19.4 + - - -
330A ARG* 3.0 21.3 + - - +
333A ALA 3.5 28.5 - - - +
334A ASN* 2.9 25.1 + - - +
337A ALA* 3.4 8.4 - - + +
342A TYR* 3.5 26.9 - - + -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 3.7 29.4 - - + -
277A GLU* 2.9 43.9 + - + +
278A GLU* 4.0 5.6 - - - +
280A THR* 1.3 75.5 - - - +
282A ASN* 1.3 63.6 + - - +
284A SER* 3.3 5.3 + - - -
285A ALA* 3.1 23.1 + - + +
342A TYR* 4.0 15.5 - - + -
345A ALA* 4.1 19.1 - - + -
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Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A MET* 3.6 23.0 - - + -
234A THR* 5.2 0.2 - - - +
245A PRO* 3.5 30.3 - - - +
248A ILE* 3.7 29.3 - - + +
249A ALA* 4.8 0.7 - - - +
274A GLN* 2.8 27.1 + - - +
278A GLU* 2.7 28.3 + - - +
281A VAL* 1.3 74.8 - - - +
283A LEU* 1.3 61.2 - - - +
285A ALA* 3.3 7.2 + - - +
286A ILE* 3.0 26.8 + - - +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A MET* 3.8 5.9 - - + +
269A PHE* 3.9 18.8 - - + -
279A ALA 3.3 15.8 + - - +
280A THR 3.7 3.6 - - - +
282A ASN* 1.3 77.4 - - - +
284A SER* 1.3 62.2 + - - +
286A ILE* 3.3 6.3 + - + +
287A ASN* 3.2 29.6 + - - +
297A LEU 3.7 20.6 - - - +
298A THR* 3.7 16.4 - - - +
299A PHE* 3.8 38.6 - - + -
301A TYR* 3.7 10.5 - - + +
334A ASN* 4.2 6.7 - - - +
337A ALA* 3.9 20.2 - - + -
338A ALA 4.2 2.2 - - - +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A THR 3.0 16.1 + - - -
281A VAL* 3.7 6.3 - - - -
282A ASN 3.2 0.2 - - - -
283A LEU* 1.3 78.1 - - - +
285A ALA* 1.3 61.7 + - - +
287A ASN* 3.2 11.4 + - - +
288A ASN* 2.9 24.1 + - - -
337A ALA* 3.5 17.0 - - - +
340A GLY* 3.3 13.3 + - - -
341A LYS 3.5 0.3 + - - -
342A TYR* 3.0 40.1 + - - +
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PRO* 3.7 34.8 - - + +
246A GLU* 4.6 9.9 - - + +
249A ALA* 3.5 9.7 - - + +
281A VAL 3.1 12.4 + - - +
282A ASN 3.6 8.3 - - - +
284A SER* 1.3 74.1 - - - +
286A ILE* 1.3 65.6 + - - +
288A ASN* 3.0 19.4 + - - +
289A VAL* 3.4 9.0 + - - +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A MET* 3.9 31.9 - - + -
248A ILE* 5.2 1.3 - - + -
249A ALA* 3.7 26.7 - - - +
252A THR* 3.8 24.5 - - + +
253A VAL* 3.7 8.7 - - + +
269A PHE* 4.0 19.7 - - + -
282A ASN 3.0 18.4 + - - +
283A LEU* 3.4 10.1 - - + +
284A SER 3.2 0.2 - - - -
285A ALA* 1.3 76.2 - - - +
287A ASN* 1.3 59.5 + - - +
288A ASN 3.2 3.8 + - - -
289A VAL* 3.4 15.0 + - - +
293A ARG* 3.5 14.9 - - - -
297A LEU* 3.9 26.5 - - + -
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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