Contacts of the strand formed by residues 244 - 251 (chain F) in PDB entry 1FZB
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 TYR 244 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152F ASP* 2.7 34.8 + - + +
192F THR* 5.0 0.7 - - + -
236F ILE* 3.1 33.1 - - + +
237F SER* 3.9 20.9 - - - +
239F GLN* 3.8 15.2 + - + +
240F SER* 5.3 2.0 - - - -
242F ILE 3.4 17.8 + - - -
243F PRO* 1.3 73.9 - - - +
245F ALA* 1.3 59.8 + - - +
264F MET* 3.1 8.9 + - - +
265F PHE* 2.8 42.6 + - + +
386F ILE* 4.2 17.7 - - + -
387F ILE* 3.4 24.2 - - - -
388F PRO* 3.6 26.6 - - + +
389F PHE* 4.3 0.4 - - - -
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Residues in contact with ALA 245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F TRP* 4.4 1.8 - - - -
244F TYR* 1.3 75.8 - - - +
246F LEU* 1.3 62.2 + - - +
247F ARG 4.0 0.2 + - - -
261F ASP* 6.0 0.9 - - + -
262F TYR 3.4 11.2 - - - +
263F ALA* 4.6 0.4 - - - +
265F PHE* 4.4 1.8 - - - -
386F ILE* 3.2 6.8 - - - -
387F ILE* 2.6 37.8 + - + +
389F PHE* 3.7 30.3 - - + +
392F LEU* 4.0 20.6 - - + -
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Residues in contact with LEU 246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F TRP* 5.6 0.2 - - - -
194F PHE* 3.7 28.0 - - + -
245F ALA* 1.3 75.5 - - - +
247F ARG* 1.3 76.4 - - - +
248F VAL* 4.3 8.7 - - + -
261F ASP* 3.2 8.0 - - - +
262F TYR* 2.9 44.1 + - + +
265F PHE* 3.6 41.7 - - + +
290F PHE* 4.0 26.9 - - + -
384F MET* 4.2 10.3 - - + -
385F LYS 3.4 13.2 - - - +
386F ILE* 3.9 2.7 - - + -
392F LEU* 6.1 0.2 - - - +
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Residues in contact with ARG 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F TRP* 3.6 42.6 - - + +
246F LEU* 1.3 76.2 - - - +
248F VAL* 1.3 74.9 + - - +
249F GLU* 3.8 18.0 + - + +
259F THR* 4.4 13.8 + - - +
260F ALA 3.6 3.1 - - - +
261F ASP* 2.7 32.7 + - - +
383F THR 3.4 4.0 - - - +
384F MET* 3.4 0.7 - - - -
385F LYS* 2.8 53.1 + - + +
392F LEU* 4.7 14.3 - - - +
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Residues in contact with VAL 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F LEU* 4.3 20.6 - - + -
247F ARG* 1.3 82.2 - - - +
249F GLU* 1.3 62.6 + - - +
250F LEU* 3.4 26.0 - - + -
259F THR* 3.1 24.5 - - - -
260F ALA* 2.9 24.8 + - + +
262F TYR* 4.6 3.6 - - + -
290F PHE* 5.0 0.9 - - + -
344F LEU* 3.8 28.7 - - + -
369F TRP* 4.3 23.3 - - + -
383F THR 3.3 5.4 - - - +
384F MET* 4.6 7.2 - - + +
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Residues in contact with GLU 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183F GLU* 4.9 1.0 - - - +
247F ARG* 3.8 21.5 + - + -
248F VAL* 1.3 79.9 - - - +
250F LEU* 1.3 66.2 + - - +
257F THR* 6.3 1.1 - - - -
258F SER 3.4 6.5 - - - +
259F THR* 4.6 9.2 - - + +
382F THR* 3.5 2.6 - - - -
383F THR* 2.9 57.5 + - + +
385F LYS* 2.8 36.0 + - - -
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Residues in contact with LEU 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F VAL* 3.4 24.7 - - + -
249F GLU* 1.3 82.9 - - - +
251F GLU* 1.3 64.0 + - - +
256F ARG 4.6 0.2 - - - -
257F THR* 3.2 25.4 - - - +
258F SER* 2.9 21.0 + - - +
286F ALA* 4.2 18.6 - - + -
344F LEU* 3.7 20.2 - - + -
369F TRP* 4.3 17.5 - - + -
372F TRP* 4.1 13.9 - - + -
379F MET* 4.0 19.3 - - + -
381F LYS 3.6 3.6 - - - -
382F THR* 3.2 26.2 - - - +
383F THR* 6.1 0.2 - - - -
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Residues in contact with GLU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F LEU* 1.3 79.6 - - - +
252F ASP* 1.3 63.6 + - - +
255F GLY* 3.5 23.1 - - - -
256F ARG 3.2 13.7 - - - +
257F THR* 3.8 16.5 - - + +
372F TRP* 4.4 2.7 - - - -
379F MET* 3.8 1.5 - - - +
380F LYS* 2.7 54.2 + - - +
381F LYS* 3.1 50.5 + - + +
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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