Contacts of the helix formed by residues 278 - 289 (chain X) in PDB entry 2FSL
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 ASN 278 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124X ASP* 2.9 42.6 + - - +
128X GLN* 4.1 4.8 - - - +
276X GLY 3.8 1.0 + - - -
277X ALA* 1.3 70.4 - - - +
279X PRO* 1.3 73.0 - - - +
280X LEU* 2.9 36.9 + - - +
281X ALA* 3.0 17.7 + - + +
282X VAL* 3.1 10.6 + - - +
307X TYR* 3.8 12.3 - - - -
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Residues in contact with PRO 279 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277X ALA 3.2 8.3 - - - +
278X ASN* 1.3 88.0 - - - +
280X LEU* 1.3 57.5 + - + +
282X VAL* 3.4 9.3 + - + +
283X ASP* 3.0 27.4 + - - +
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Residues in contact with LEU 280 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278X ASN* 2.9 23.0 + - - +
279X PRO* 1.3 73.9 - - + +
281X ALA* 1.3 63.0 + - - +
283X ASP* 3.5 5.2 + - + +
284X LEU* 3.1 18.7 + - - +
305X HIS* 3.3 20.6 - - + +
306X ALA* 3.7 43.7 - - + +
307X TYR* 3.8 18.7 - - + +
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Residues in contact with ALA 281 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X ASP* 4.1 1.8 - - - +
213X MET* 3.6 22.3 - - + +
217X LEU* 4.0 13.7 - - + -
277X ALA* 5.0 1.6 - - + -
278X ASN* 3.0 17.9 + - + +
280X LEU* 1.3 76.7 - - - +
282X VAL* 1.3 59.1 + - - +
284X LEU* 3.2 1.5 + - - +
285X LEU* 2.9 35.3 + - - +
307X TYR* 3.4 30.6 - - + +
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Residues in contact with VAL 282 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270X PHE* 3.6 28.9 - - + +
271X ALA* 3.7 20.0 - - + +
274X PHE* 4.1 16.8 - - + +
277X ALA* 4.0 24.5 - - + +
278X ASN 3.1 13.3 + - - +
279X PRO* 3.7 9.4 - - + +
281X ALA* 1.3 75.3 - - - +
283X ASP* 1.3 64.3 + - - +
285X LEU* 3.2 9.2 + - + +
286X GLU* 2.9 30.8 + - - +
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Residues in contact with ASP 283 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279X PRO 3.0 16.9 + - - +
280X LEU* 3.6 12.1 - - + +
282X VAL* 1.3 78.4 - - - +
284X LEU* 1.3 61.4 + - - +
286X GLU* 3.3 25.4 + - - +
287X LYS* 2.8 46.0 + - - +
305X HIS* 2.9 18.5 + - + +
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Residues in contact with LEU 284 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213X MET* 4.0 14.6 - - + -
280X LEU 3.1 17.4 + - - +
281X ALA 3.2 5.3 + - - +
283X ASP* 1.3 73.6 - - - +
285X LEU* 1.3 64.9 + - - +
287X LYS* 2.9 16.0 + - + +
288X MET* 3.0 45.7 + - + +
297X ILE* 4.1 20.6 - - + -
302X ALA* 4.1 7.0 - - + -
305X HIS* 3.9 28.0 + - + -
307X TYR* 4.1 9.4 - - + -
308X PHE* 3.5 34.8 - - + -
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Residues in contact with LEU 285 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210X GLY* 3.5 32.3 - - - +
213X MET* 4.0 21.8 - - + -
214X ALA* 4.0 4.5 - - + +
217X LEU* 3.8 24.7 - - + -
270X PHE* 3.8 14.1 - - + -
274X PHE* 4.2 29.4 - - + -
281X ALA 2.9 23.8 + - - +
282X VAL* 3.6 6.3 - - + +
284X LEU* 1.3 76.6 - - - +
286X GLU* 1.3 60.8 + - - +
288X MET* 3.2 3.8 + - - +
289X LEU* 3.0 37.5 + - + +
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Residues in contact with GLU 286 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267X LYS* 3.6 33.8 + - - +
269X ASN* 4.7 6.2 + - - -
270X PHE* 3.5 41.2 + - + +
282X VAL* 2.9 15.5 + - - +
283X ASP* 3.5 29.3 + - - +
285X LEU* 1.3 75.2 - - - +
287X LYS* 1.3 60.2 + - + +
289X LEU 4.2 3.5 + - - +
290X VAL* 3.2 19.8 - - - +
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Residues in contact with LYS 287 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283X ASP* 2.8 40.6 + - - +
284X LEU* 2.9 9.7 + - - +
286X GLU* 1.3 80.5 - - + +
288X MET* 1.3 58.7 + - - +
290X VAL* 3.6 6.5 - - - +
295X LYS 4.2 1.4 - - - +
296X ARG* 3.5 8.5 - - - -
297X ILE* 3.0 55.7 + - + +
305X HIS* 4.4 10.5 - - + -
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Residues in contact with MET 288 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X ILE* 4.8 1.6 - - + -
135X LEU* 4.3 18.6 - - + -
206X ILE* 3.8 21.3 - - + +
207X TRP* 4.1 7.3 - - - -
209X VAL* 3.9 21.8 - - + -
210X GLY* 3.8 30.3 - - - -
213X MET* 4.6 7.6 - - - +
284X LEU* 3.0 46.8 + - + +
285X LEU* 3.2 4.9 + - - +
287X LYS* 1.3 78.1 - - - +
289X LEU* 1.3 57.7 + - - +
290X VAL 3.2 8.4 + - - -
296X ARG* 3.4 22.9 + - - +
297X ILE* 3.7 13.7 - - + -
302X ALA* 4.6 4.0 - - + -
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Residues in contact with LEU 289 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207X TRP* 3.7 52.5 - - + +
210X GLY* 4.0 7.4 - - - +
211X CYS* 4.0 14.6 - - - +
222X LEU* 3.7 23.3 - - + -
223X PHE* 4.5 2.7 - - + -
238X LEU* 4.4 3.8 - - + -
239X VAL* 3.3 23.3 - - + +
270X PHE* 4.0 25.1 - - + -
274X PHE* 5.1 2.7 - - + -
285X LEU* 3.0 36.3 + - + +
286X GLU 4.4 2.3 - - - +
287X LYS 3.7 0.2 - - - -
288X MET* 1.3 74.7 - - - +
290X VAL* 1.3 60.7 + - - +
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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