Contacts of the helix formed by residues 240 - 250 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238D THR* 3.2 6.3 - - - +
239D LYS* 1.3 76.0 - - - +
241D ILE* 1.3 74.1 + - - +
242D LYS* 3.7 12.1 + - - +
243D GLU* 2.8 38.4 + - + +
244D ILE* 2.8 14.5 + - - +
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Residues in contact with ILE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D GLU* 4.0 14.8 - - + +
227D ALA* 5.0 5.6 - - + -
239D LYS 3.3 7.2 + - - +
240D ASP* 1.3 75.7 + - - +
242D LYS* 1.3 59.9 + - + +
244D ILE* 2.9 15.5 + - - +
245D ALA* 2.8 33.8 + - - +
264D PHE* 3.9 32.7 - - + -
266D GLN* 2.8 59.2 - - + +
272D ILE* 4.2 15.7 - - + -
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Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D ASP* 3.4 10.9 + - - +
241D ILE* 1.3 79.5 - - + +
243D GLU* 1.3 57.2 + - - +
245D ALA* 3.7 7.6 - - - -
246D LYS* 3.0 27.5 + - - +
272D ILE* 3.9 19.3 - - + -
279D VAL* 3.2 40.5 + - + +
280D THR* 4.7 0.6 - - - +
281D ALA* 4.0 32.8 - - - +
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Residues in contact with GLU 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D THR* 3.2 28.7 - - + +
240D ASP* 2.8 27.7 + - + +
242D LYS* 1.3 73.5 - - - +
244D ILE* 1.3 60.6 + - - +
246D LYS* 3.4 21.3 + - - +
247D LYS* 2.9 51.9 + - + +
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Residues in contact with ILE 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ALA* 4.0 21.8 - - + +
228D ALA* 4.4 10.5 - - - +
230D PHE* 5.1 1.3 - - + -
231D ALA* 3.2 27.4 - - + +
236D PHE* 3.8 11.4 - - + -
238D THR* 3.3 29.2 - - + +
239D LYS* 3.8 8.5 - - - +
240D ASP 2.8 25.3 + - - +
241D ILE* 3.3 9.0 - - - +
243D GLU* 1.3 78.9 - - - +
245D ALA* 1.3 53.7 + - - +
248D THR* 2.6 48.2 + - - +
264D PHE* 3.9 15.3 - - + -
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Residues in contact with ALA 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D ILE 2.8 18.6 + - - +
242D LYS 3.7 4.0 - - - +
244D ILE* 1.3 72.9 - - - +
246D LYS* 1.3 61.9 + - - +
249D GLN* 3.2 18.5 + - - +
262D VAL* 3.8 9.1 - - + +
264D PHE* 3.6 21.1 - - + -
272D ILE* 3.6 27.6 - - + -
274D ALA* 3.3 25.4 - - + +
279D VAL* 4.7 0.4 - - + -
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Residues in contact with LYS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D LYS 3.0 18.6 + - - +
243D GLU* 3.7 23.5 + - - +
244D ILE 3.2 0.2 - - - -
245D ALA* 1.3 77.4 - - - +
247D LYS* 1.3 70.3 + - + +
249D GLN* 3.4 9.7 + - - +
250D ALA* 3.4 18.9 + - - +
274D ALA* 4.0 3.1 - - - +
279D VAL* 3.8 15.7 - - + -
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Residues in contact with LYS 247 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236D PHE* 3.7 53.2 + - + +
237D GLU 5.0 0.4 - - - -
238D THR* 3.8 20.9 - - + -
243D GLU* 2.9 42.3 + - + +
246D LYS* 1.3 75.5 - - + +
248D THR* 1.3 64.4 + - - +
250D ALA* 3.1 16.3 + - - +
251D LEU* 3.3 15.8 + - - +
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Residues in contact with THR 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D MET* 4.8 3.4 - - - -
220D LEU* 3.7 30.5 - - + -
230D PHE* 3.8 10.5 - - + -
236D PHE* 3.3 13.3 - - - -
244D ILE* 2.6 29.8 + - - +
245D ALA 4.0 3.8 - - - -
246D LYS 3.3 0.2 - - - -
247D LYS* 1.3 76.7 - - - +
249D GLN* 1.3 62.0 + - - +
250D ALA 3.1 1.1 + - - -
251D LEU* 3.2 29.5 - - + +
260D ARG* 3.1 17.0 + - - -
262D VAL* 3.9 16.2 - - + -
264D PHE* 4.4 2.1 - - + -
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Residues in contact with GLN 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245D ALA 3.2 16.8 + - - +
246D LYS* 3.7 10.1 - - - +
247D LYS 3.3 0.6 - - - -
248D THR* 1.3 77.1 - - - +
250D ALA* 1.3 63.7 + - + +
251D LEU 4.3 0.3 - - - +
259D GLN* 3.5 18.3 - - - +
260D ARG* 2.8 57.4 + - + +
262D VAL* 3.5 17.9 - - + +
274D ALA* 4.1 9.9 - - + +
275D THR* 3.6 22.1 - - - +
276D GLU* 3.5 18.6 - - - +
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Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D LYS* 3.4 11.2 + - + +
247D LYS* 3.1 12.2 + - - +
248D THR 3.1 0.6 - - - -
249D GLN* 1.3 82.7 - - + +
251D LEU* 1.3 69.5 + - - +
252D PRO* 3.5 3.6 - - - +
259D GLN* 5.9 0.2 - - - -
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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