Contacts of the strand formed by residues 257 - 265 (chain B) in PDB entry 1FIC
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 THR 257 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249B GLU* 5.3 13.9 - - + +
250B LEU 3.1 8.3 - - - +
251B GLU* 3.7 28.0 - - + +
255B GLY 4.0 4.4 + - - +
256B ARG* 1.3 78.8 - - - +
258B SER* 1.3 65.7 + - - +
259B THR* 6.4 0.2 - - - -
285B ASP* 4.1 7.8 - - - +
372B TRP* 4.3 2.9 - - - -
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Residues in contact with SER 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B VAL 3.8 0.3 - - - +
249B GLU* 3.5 2.8 - - - +
250B LEU* 2.8 33.6 + - - +
257B THR* 1.3 77.7 - - - +
259B THR* 1.3 66.0 + - - +
285B ASP* 3.5 17.3 - - - -
286B ALA* 3.3 16.8 - - - +
372B TRP* 3.2 45.3 - - - -
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Residues in contact with THR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ARG* 3.8 38.4 + - - +
248B VAL 3.2 9.4 - - - +
249B GLU* 4.2 14.1 - - + -
257B THR* 6.4 0.4 - - - -
258B SER* 1.3 78.7 - - - +
260B ALA* 1.3 61.5 + - - +
261B ASP* 4.6 2.6 + - - -
284B GLY* 3.2 15.1 - - - -
285B ASP* 3.0 11.7 + - - -
286B ALA* 2.9 25.8 + - - +
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Residues in contact with ALA 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B LEU 3.7 0.9 - - - +
247B ARG* 3.6 0.5 - - - -
248B VAL* 2.9 33.2 + - + +
259B THR* 1.3 80.3 - - - +
261B ASP* 1.3 62.9 + - - +
262B TYR* 3.9 6.7 - - + -
281B PHE* 4.0 7.9 - - + -
283B GLY 3.6 6.9 + - - -
286B ALA* 4.1 4.0 - - + -
287B GLY 3.6 24.0 - - - +
369B TRP* 3.8 19.5 - - + -
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Residues in contact with ASP 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246B LEU 3.2 7.0 - - - +
247B ARG* 2.9 48.0 + - - +
259B THR* 4.6 2.3 - - - -
260B ALA* 1.3 79.6 + - - +
262B TYR* 1.3 59.2 + - - +
281B PHE* 3.3 12.5 - - - -
282B ALA* 2.7 47.4 + - + +
283B GLY 2.8 18.5 + - - +
284B GLY* 5.8 0.2 - - - -
392B LEU* 4.4 17.2 - - + +
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Residues in contact with TYR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ALA* 3.4 3.8 - - - -
246B LEU* 2.9 50.9 + - + +
248B VAL* 4.7 1.6 - - + -
260B ALA* 3.9 25.8 - - + -
261B ASP* 1.3 76.4 - - - +
263B ALA* 1.3 63.1 + - - +
265B PHE* 4.2 3.4 - - + +
278B TYR* 3.4 48.9 - + + -
280B TYR 3.4 2.2 - - - -
281B PHE* 3.6 15.7 - + + -
282B ALA* 4.7 0.9 - - - -
288B ASP* 2.6 44.8 + - - -
289B ALA 3.6 1.0 + - - -
290B PHE* 3.4 30.7 + + + +
369B TRP* 3.6 10.2 - + - -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B TYR 4.4 0.9 - - - -
245B ALA* 4.5 1.1 - - - +
261B ASP 4.2 0.4 - - - -
262B TYR* 1.3 71.6 - - - +
264B MET* 1.3 65.6 + - + +
278B TYR* 3.7 1.2 - - - +
279B ALA 2.8 24.9 + - - -
280B TYR* 2.8 48.0 + - + +
282B ALA* 4.3 5.2 - - + +
389B PHE* 3.5 30.7 - - + -
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Residues in contact with MET 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B PRO* 4.0 23.8 - - + -
244B TYR 3.0 14.4 + - - -
263B ALA* 1.3 76.6 - - + +
265B PHE* 1.3 62.3 + - - +
266B LYS* 3.9 9.5 + - - +
277B THR 3.5 1.6 - - - +
278B TYR* 3.1 16.3 + - - -
279B ALA* 3.5 17.4 + - + +
280B TYR* 3.4 40.2 - - + +
389B PHE* 3.9 25.4 - - + -
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Residues in contact with PHE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B PHE* 3.8 23.6 - + - -
233B ILE* 4.2 6.3 - - + -
237B SER* 4.0 19.7 - - - +
244B TYR* 2.9 21.2 + - + +
245B ALA 4.5 0.2 - - - -
246B LEU* 3.8 42.6 - - + +
262B TYR* 4.2 3.6 - - + +
263B ALA 3.5 0.2 - - - -
264B MET* 1.3 75.7 - - - +
266B LYS* 1.3 69.0 + - - +
267B VAL* 3.5 27.4 - - + -
276B LEU* 3.2 34.1 - - + -
277B THR 3.3 7.0 - - - -
278B TYR* 4.3 7.0 - + + +
335B TRP* 5.0 4.7 - + - -
384B MET* 5.5 0.2 - - + -
386B ILE* 3.8 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