Contacts of the helix formed by residues 242 - 248 (chain B) in PDB entry 1L8A
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 242 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281A ILE* 4.3 10.5 - - + -
202B ILE* 4.0 8.5 - - + -
238B SER 3.8 6.7 - - - +
239B LYS* 3.3 30.9 + - + +
240B GLY 3.7 0.2 - - - -
241B ALA* 1.3 77.4 - - - +
243B THR* 1.3 63.6 + - - +
245B ALA* 3.1 10.4 + - - +
255B PHE* 4.1 5.8 - - + -
281B ILE* 4.1 9.4 - - + +
282B PHE* 3.5 53.6 - - + -
285B ALA* 3.5 25.8 - - + -
287B TRP* 2.7 35.7 + - + +
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Residues in contact with THR 243 (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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239A LYS* 4.0 17.1 + - - -
277A GLU* 3.0 41.6 + - + +
281A ILE* 3.7 31.2 - - + -
241B ALA* 3.1 2.3 + - - -
242B ILE* 1.3 77.1 - - + +
244B ILE* 1.3 63.2 + - - +
246B THR* 3.1 6.6 + - - -
247B ARG* 2.9 33.4 + - - +
285B ALA* 4.0 20.6 - - + -
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Residues in contact with ILE 244 (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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234A ASP* 4.1 7.6 - - - +
202B ILE* 4.9 6.5 - - + -
203B TYR* 3.9 24.5 - - + +
206B LYS* 4.3 13.5 - - + -
241B ALA* 3.1 16.9 + - + +
243B THR* 1.3 81.1 - - - +
245B ALA* 1.3 56.6 + - - +
247B ARG* 2.8 51.1 - - + +
248B GLU* 2.8 45.7 + - + +
250B LEU* 4.1 1.5 - - + +
567B GLU* 5.5 1.6 - - - +
570B ASN* 5.0 3.8 - - - +
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Residues in contact with ALA 245 (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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202B ILE* 4.7 4.8 - - + +
241B ALA 4.2 1.0 + - - -
242B ILE 3.1 13.9 + - - +
243B THR 3.1 1.0 - - - -
244B ILE* 1.3 78.9 - - - +
246B THR* 1.3 57.5 + - - +
249B LYS* 3.1 4.7 + - - -
250B LEU* 2.8 48.7 + - + +
253B LEU* 4.2 4.9 - - + -
287B TRP* 3.4 26.2 - - + -
383B ALA* 3.8 18.2 + - + -
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Residues in contact with THR 246 (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 THR* 3.1 8.6 + - - -
245B ALA* 1.3 77.1 - - - +
247B ARG* 1.3 67.7 + - + +
248B GLU 3.1 1.6 - - - -
249B LYS* 3.1 17.5 + - - +
285B ALA 2.6 28.7 + - - +
286B GLY* 3.4 26.4 + - - +
287B TRP* 3.6 8.7 + - - -
381B GLY 4.7 1.4 - - - +
382B LYS* 5.1 9.0 - - + +
383B ALA 5.6 0.3 + - - -
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Residues in contact with ARG 247 (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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234A ASP* 2.8 43.9 + - - +
239A LYS* 5.3 1.4 - - - +
268A VAL* 4.2 11.1 + - - +
269A THR* 3.4 30.3 - - + +
274A ILE* 4.3 2.6 - - - +
277A GLU* 2.8 42.4 + - - +
243B THR* 2.9 19.8 + - - +
244B ILE* 2.8 32.7 + - - +
246B THR* 1.3 80.1 - - + +
248B GLU* 1.3 71.9 + - + +
249B LYS* 3.7 6.9 + - - +
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Residues in contact with GLU 248 (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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206B LYS* 3.3 37.8 + - + +
209B LYS* 5.0 3.6 - - - +
244B ILE* 2.8 30.5 + - + +
247B ARG* 1.3 86.3 - - + +
249B LYS* 1.3 70.7 + - - +
250B LEU* 3.2 24.6 + - + +
538B TYR* 4.2 13.7 - - - -
540B PRO* 4.2 21.4 - - + +
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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