Contacts of the strand formed by residues 278 - 283 (chain F) in PDB entry 1LE9
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 ILE 278 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248F LEU* 3.4 33.4 - - + -
273F VAL* 3.8 28.5 - - + -
274F GLN* 3.6 23.6 - - - +
275F LYS 4.2 6.8 - - - +
276F ASP 3.8 0.4 - - - -
277F ASP* 1.3 81.0 - - - +
279F GLN* 1.3 65.8 + - - +
298F PHE* 3.1 29.9 - - + -
303F VAL* 4.3 3.4 - - + -
309F ILE* 3.6 15.0 - - + -
331F LEU* 4.2 14.4 - - + -
332F ARG 3.5 14.1 - - - +
333F ARG* 4.2 1.1 - - - -
334F LYS* 4.9 1.1 - - - +
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Residues in contact with GLN 279 (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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278F ILE* 1.3 77.7 - - - +
280F ILE* 1.3 65.6 + - - +
281F ARG 3.9 0.2 + - - -
295F PHE* 4.1 31.3 - - + +
296F GLY 6.0 0.2 - - - +
298F PHE* 3.9 9.6 - - + -
331F LEU* 3.7 6.6 - - - +
332F ARG* 2.6 81.6 + - + +
334F LYS* 3.7 31.4 - - + +
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Residues in contact with ILE 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F LEU* 4.6 9.6 - - + -
279F GLN* 1.3 75.3 - - - +
281F ARG* 1.3 60.0 + - - +
282F PHE* 4.0 5.1 - - + -
294F GLY 3.8 0.2 - - - +
295F PHE* 3.2 17.4 - - - +
296F GLY 3.4 18.4 + - - +
298F PHE* 3.7 15.4 - - + -
309F ILE* 3.8 19.3 - - + -
311F PHE* 3.2 66.9 - - + -
329F VAL* 3.9 20.9 - - + -
330F GLN 3.7 4.3 - - - +
331F LEU* 4.5 12.1 - - + -
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Residues in contact with ARG 281 (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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279F GLN 3.9 0.6 + - - -
280F ILE* 1.3 74.1 - - - +
282F PHE* 1.3 68.8 + - - +
283F TYR* 3.4 40.0 + - - +
290F GLY 5.8 1.4 + - - -
291F VAL 4.8 4.2 + - - -
293F GLU* 3.8 24.6 + - + +
294F GLY 3.5 1.8 - - - +
295F PHE* 3.4 22.4 - - + -
328F PHE 3.8 0.2 - - - +
329F VAL* 3.3 3.2 - - - -
330F GLN* 2.8 70.0 + - + +
332F ARG* 3.9 36.6 - - + +
339F THR* 5.3 1.4 - - - +
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Residues in contact with PHE 282 (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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280F ILE* 4.0 10.5 - - + -
281F ARG* 1.3 76.7 - - - +
283F TYR* 1.3 61.4 + - - +
292F TRP* 4.4 12.3 - - + -
293F GLU* 2.9 6.6 - - - +
294F GLY* 2.6 51.4 + - - +
296F GLY 4.6 2.0 - - - -
311F PHE* 3.6 35.9 - + - -
313F THR* 4.1 13.5 - - + -
314F PRO* 3.8 17.5 - - + -
327F VAL* 4.1 9.2 - - + -
328F PHE 2.9 15.5 - - - +
329F VAL* 3.5 22.4 - - + -
345F PHE* 3.6 24.9 - + - -
347F TYR* 3.5 18.4 - - - -
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Residues in contact with TYR 283 (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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281F ARG* 3.4 48.2 - - - +
282F PHE* 1.3 77.6 - - - +
284F GLU* 1.3 65.9 + - - +
285F GLU 5.8 0.2 - - - -
291F VAL 4.6 1.6 - - - +
292F TRP 3.2 10.8 - - - +
293F GLU* 4.3 0.9 - - + -
327F VAL* 2.7 24.3 - - - +
328F PHE* 2.9 47.6 + + + +
330F GLN* 3.1 37.5 + - + -
342F PRO* 2.9 29.3 - - - +
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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