Contacts of the helix formed by residues 240 - 245 (chain F) in PDB entry 1I43
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 ALA 240 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208F SER 3.8 0.4 - - - +
209F PRO* 3.7 15.6 - - + +
237F GLY* 3.1 5.0 + - - +
239F PHE* 1.3 80.4 - - - +
241F THR* 1.3 77.7 + - - +
244F ASN* 3.1 29.3 + - + +
245F GLN* 3.2 42.0 - - + +
355F MET* 5.0 3.8 - - + -
358F PHE 6.2 0.4 - - - -
359F GLY* 5.7 0.9 - - - +
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Residues in contact with THR 241 (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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237F GLY 2.8 17.4 + - - -
238F THR 3.7 1.4 + - - -
239F PHE 3.6 1.0 - - - -
240F ALA* 1.3 84.1 - - - +
242F PRO* 1.3 73.6 - - + +
243F LEU* 2.8 41.5 + - + +
244F ASN 3.2 6.5 + - - +
245F GLN 3.4 8.8 + - - +
257F HIS* 3.8 5.6 - - - -
262F PHE* 3.4 35.2 - - - +
263F LEU* 5.8 0.7 - - - +
310F LEU* 4.7 5.0 - - + +
314F VAL* 4.2 18.8 - - + +
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Residues in contact with PRO 242 (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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123F ILE* 6.1 3.4 - - + -
126F LEU* 4.2 29.3 - - + +
127F GLU* 3.5 35.2 - - + +
241F THR* 1.3 90.5 - - + +
243F LEU* 1.3 57.8 + - - +
245F GLN 3.7 9.9 - - - +
246F LYS* 3.0 32.2 + - - +
257F HIS* 3.3 19.0 - - + +
263F LEU* 4.3 19.7 - - + -
310F LEU* 4.7 1.8 - - + -
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Residues in contact with LEU 243 (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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57F ASP* 3.3 47.6 - - + +
61F ALA* 5.4 1.1 - - + -
126F LEU* 4.2 14.8 - - + -
241F THR* 2.8 13.0 + - + +
242F PRO* 1.3 81.3 - - - +
244F ASN* 1.3 65.6 + - - +
245F GLN 3.4 0.8 + - - -
246F LYS* 4.7 2.6 - - - -
310F LEU* 3.6 12.6 - - + -
311F HIS* 3.3 40.2 - - + +
314F VAL* 3.5 26.5 - - + -
356F THR* 3.7 13.3 + - - +
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Residues in contact with ASN 244 (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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240F ALA* 3.1 28.8 + - + +
241F THR* 3.2 1.6 + - - -
243F LEU* 1.3 79.8 - - - +
245F GLN* 1.3 61.9 + - - +
314F VAL* 4.1 11.3 - - - +
318F ASN* 2.8 43.6 + - - +
355F MET* 3.3 5.0 - - + -
356F THR* 2.9 37.8 + - - +
357F GLY* 3.4 19.8 + - - +
359F GLY* 3.3 18.0 - - - +
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Residues in contact with GLN 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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127F GLU* 4.3 2.6 - - - +
208F SER 2.9 23.3 + - - +
219F ILE* 4.1 15.5 - - + +
235F ILE* 4.6 5.1 - - - +
237F GLY* 4.0 11.7 - - - -
240F ALA* 3.2 19.6 - - + +
241F THR 3.4 10.4 + - - +
242F PRO* 3.6 14.3 - - - +
243F LEU 3.4 1.8 + - - -
244F ASN* 1.3 84.3 - - - +
246F LYS* 1.3 66.0 + - - +
247F ALA* 3.8 14.8 + - + +
250F LEU* 5.5 0.4 - - + -
354F GLN* 3.6 25.7 + - - +
355F MET* 3.3 29.5 - - + +
356F THR* 5.4 1.6 - - - -
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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