Contacts of the helix formed by residues 240 - 250 (chain C) in PDB entry 2I6A
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 ASP 240 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238C THR* 3.2 13.2 + - - +
239C LYS* 1.3 76.5 - - - +
241C ILE* 1.3 59.6 + - - +
242C LYS* 4.1 10.4 + - - +
243C GLU* 3.0 24.9 + - + +
244C ILE* 2.7 36.4 + - - +
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Residues in contact with ILE 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C GLU* 4.1 21.5 - - + +
227C ALA* 4.0 15.0 - - + -
239C LYS 3.5 5.5 + - - -
240C ASP* 1.3 74.6 + - - +
242C LYS* 1.3 66.9 + - + +
244C ILE* 3.1 11.5 + - + +
245C ALA* 2.7 32.9 + - - +
264C PHE* 3.7 36.3 - - + -
266C GLN* 4.0 25.4 - - + +
272C ILE* 4.0 24.2 - - + -
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Residues in contact with LYS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C ASP* 3.4 10.6 + - - +
241C ILE* 1.3 92.5 - - + +
243C GLU* 1.3 59.1 + - - +
245C ALA* 3.3 3.1 + - - +
246C LYS* 2.9 28.4 + - - +
272C ILE* 4.2 11.2 - - + -
279C VAL* 3.6 41.2 + - + +
280C THR* 5.6 0.4 - - - +
281C ALA* 4.6 21.8 - - + +
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Residues in contact with GLU 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C THR* 3.7 11.7 - - - +
240C ASP* 3.0 30.3 + - + +
242C LYS* 1.3 76.1 - - - +
244C ILE* 1.3 58.5 + - - +
246C LYS* 3.3 22.3 + - - +
247C LYS* 2.8 74.2 + - - +
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Residues in contact with ILE 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227C ALA* 3.5 25.8 - - + +
228C ALA* 4.0 11.9 - - + -
230C PHE* 5.1 1.3 - - + -
231C ALA* 3.4 33.9 - - + +
236C PHE* 3.8 8.8 - - + -
238C THR* 3.6 23.8 - - + +
239C LYS* 4.2 6.3 - - - +
240C ASP 2.7 26.9 + - - +
241C ILE* 3.1 11.0 + - + +
243C GLU* 1.3 70.6 - - - +
245C ALA* 1.3 59.6 + - - +
247C LYS* 3.5 0.8 + - - -
248C THR* 2.7 42.5 + - - +
264C PHE* 4.1 13.9 - - + -
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Residues in contact with ALA 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C ILE 2.7 19.6 + - - +
242C LYS 3.5 5.2 - - - +
243C GLU 3.3 0.2 - - - -
244C ILE* 1.3 73.2 - - - +
246C LYS* 1.3 57.7 + - - +
248C THR* 3.4 0.5 + - - -
249C GLN* 2.9 31.5 + - - +
262C VAL* 3.7 9.1 - - + +
264C PHE* 3.5 22.0 - - + -
272C ILE* 3.9 18.4 - - + -
274C ALA* 3.5 21.9 - - + +
279C VAL* 4.5 0.2 - - + -
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Residues in contact with LYS 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C LYS 2.9 16.2 + - - +
243C GLU* 3.6 23.6 - - - +
244C ILE 3.2 0.2 - - - -
245C ALA* 1.3 74.8 - - - +
247C LYS* 1.3 69.5 + - + +
249C GLN* 3.6 8.6 + - - +
250C ALA* 3.3 21.9 + - + +
274C ALA* 4.1 3.8 - - - +
279C VAL* 3.9 18.4 - - + -
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Residues in contact with LYS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C PHE* 3.6 49.5 - - + +
237C GLU 5.2 0.4 - - - -
238C THR* 3.6 16.8 - - + -
243C GLU* 2.8 53.9 + - - +
246C LYS* 1.3 78.9 - - + +
248C THR* 1.3 61.5 + - - +
250C ALA* 3.3 14.6 + - - +
251C LEU* 3.4 14.7 + - - +
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Residues in contact with THR 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C MET* 4.4 2.0 - - + -
220C LEU* 3.6 31.6 - - + -
230C PHE* 3.5 15.0 - - + -
236C PHE* 3.1 15.2 - - - -
244C ILE* 2.7 25.5 + - - +
245C ALA* 3.7 4.5 - - - -
247C LYS* 1.3 73.8 - - - +
249C GLN* 1.3 66.7 + - - +
250C ALA 3.0 2.5 + - - -
251C LEU* 3.2 40.1 + - + +
260C ARG* 3.4 6.8 + - - -
262C VAL* 4.2 12.3 - - + -
264C PHE* 4.5 2.5 - - + -
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Residues in contact with GLN 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ALA 2.9 13.3 + - - +
246C LYS* 3.7 11.2 - - + +
247C LYS 3.4 0.2 - - - -
248C THR* 1.3 76.1 - - - +
250C ALA* 1.3 62.5 + - + +
251C LEU 3.2 0.8 - - - +
259C GLN* 3.8 12.8 - - - +
260C ARG* 2.8 62.6 + - - +
262C VAL* 3.4 23.2 - - + +
274C ALA* 4.3 7.4 - - + +
275C THR* 3.8 21.6 - - - +
276C GLU* 3.3 19.8 - - - +
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Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246C LYS* 3.3 15.4 + - + +
247C LYS* 3.7 9.2 - - - +
248C THR 3.0 1.4 - - - -
249C GLN* 1.3 82.0 - - + +
251C LEU* 1.3 65.6 + - - +
252C PRO* 3.8 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