Contacts of the helix formed by residues 201 - 216 (chain D) in PDB entry 2IHU
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 GLY 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199D ALA 3.4 0.2 + - - -
200D ASP* 1.3 82.2 + - - +
202D TRP* 1.3 65.7 + - - +
203D GLN* 3.2 12.0 + - - -
204D LYS* 3.1 24.6 + - - +
205D ALA* 3.1 11.8 + - - +
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Residues in contact with TRP 202 (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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198D VAL* 3.2 31.3 - - + +
199D ALA* 3.3 19.4 + - + +
200D ASP* 3.6 0.4 + - - -
201D GLY* 1.3 78.4 - - - +
203D GLN* 1.3 89.0 + - + +
205D ALA* 3.2 10.3 + - - +
206D ALA* 2.8 34.5 + - + +
335D VAL* 3.6 11.8 - - + +
336D VAL 3.6 16.6 - - - +
337D THR* 3.4 26.9 + - + -
341D ALA* 3.5 30.1 - - + -
342D PHE* 3.8 14.8 - - - -
345D HIS* 3.8 29.6 - + + -
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Residues in contact with GLN 203 (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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201D GLY* 4.1 7.3 + - - -
202D TRP* 1.3 125.6 + - + +
204D LYS* 1.3 59.0 + - - +
206D ALA* 3.3 1.0 + - - -
207D ASP* 2.9 35.3 + - - +
345D HIS* 3.4 30.1 + - + +
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Residues in contact with LYS 204 (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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201D GLY* 3.1 16.1 + - - +
203D GLN* 1.3 74.3 - - - +
205D ALA* 1.3 65.7 + - - +
207D ASP* 3.1 14.1 + - + +
208D GLN* 3.0 34.9 + - + +
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Residues in contact with ALA 205 (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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201D GLY 3.1 11.2 + - - +
202D TRP* 3.2 12.1 + - - +
204D LYS* 1.3 76.4 - - - +
206D ALA* 1.3 55.9 + - - +
208D GLN* 3.1 14.9 + - - +
209D ALA 2.9 23.2 + - - -
333D VAL* 3.2 20.8 - - + +
334D ASP 3.8 23.1 - - - +
335D VAL* 4.1 4.9 - - + -
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Residues in contact with ALA 206 (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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202D TRP* 2.8 20.3 + - + +
203D GLN* 3.3 9.8 + - - +
205D ALA* 1.3 72.6 - - - +
207D ASP* 1.3 57.5 + - - +
209D ALA* 3.2 10.4 + - - +
210D ALA* 2.9 26.9 + - - +
335D VAL* 4.1 6.0 - - + +
342D PHE* 4.0 24.9 - - + -
345D HIS* 3.6 21.5 - - + -
346D PHE* 3.9 5.9 - - + -
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Residues in contact with ASP 207 (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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203D GLN* 2.9 19.3 + - - +
204D LYS* 3.1 14.5 + - + +
206D ALA* 1.3 71.7 - - - +
208D GLN* 1.3 61.7 + - + +
210D ALA* 3.3 8.7 + - - +
211D ALA* 3.0 26.2 + - - +
345D HIS* 2.8 29.1 + - - -
349D ALA* 4.0 10.8 - - - +
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Residues in contact with GLN 208 (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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204D LYS* 3.0 27.1 + - + +
205D ALA* 3.5 18.6 + - - +
207D ASP* 1.3 74.1 - - + +
209D ALA* 1.3 65.6 + - - +
211D ALA* 3.3 8.5 + - - +
212D LEU* 3.1 26.2 + - - +
333D VAL* 4.2 18.2 - - + +
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Residues in contact with ALA 209 (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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205D ALA 2.9 12.2 + - - +
206D ALA* 3.4 12.8 - - - +
208D GLN* 1.3 76.1 - - - +
210D ALA* 1.3 55.9 + - - +
212D LEU* 3.3 6.2 + - - +
213D LEU* 3.0 26.7 + - - +
290D LEU* 4.8 2.6 - - - +
292D LEU* 4.8 2.0 - - + +
316D VAL* 3.6 41.7 - - + +
333D VAL* 4.2 3.7 - - + +
335D VAL* 4.8 1.3 - - + -
342D PHE* 4.8 2.0 - - + -
346D PHE* 3.8 13.8 - - + -
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Residues in contact with ALA 210 (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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206D ALA 2.9 13.3 + - - +
207D ASP* 3.4 9.4 - - - +
209D ALA* 1.3 73.8 - - - +
211D ALA* 1.3 58.8 + - - +
213D LEU* 3.2 2.5 + - - +
214D ALA 3.0 24.3 + - - -
346D PHE* 3.4 13.4 - - + -
349D ALA* 3.9 17.7 - - + +
350D THR* 3.8 21.8 - - + -
353D PHE* 3.2 17.9 - - + -
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Residues in contact with ALA 211 (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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207D ASP 3.0 13.3 + - - +
208D GLN* 3.3 12.1 + - - +
210D ALA* 1.3 75.3 - - - +
212D LEU* 1.3 63.5 + - + +
214D ALA* 3.4 8.5 + - - +
215D GLU* 3.3 30.6 + - - +
353D PHE* 5.3 1.1 - - - -
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Residues in contact with LEU 212 (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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208D GLN 3.1 15.6 + - - +
209D ALA* 3.3 7.4 + - - +
211D ALA* 1.3 76.8 - - + +
213D LEU* 1.3 57.3 + - - +
215D GLU* 3.4 14.5 + - - +
216D ALA* 3.1 26.7 + - - +
290D LEU* 3.7 13.9 - - + +
314D LYS* 4.1 47.6 - - + +
316D VAL* 4.2 14.6 - - + -
332D ASP* 4.5 6.5 - - + -
333D VAL* 3.8 27.1 - - + -
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Residues in contact with LEU 213 (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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209D ALA 3.0 13.2 + - - +
210D ALA* 3.2 8.7 + - - +
212D LEU* 1.3 74.9 - - - +
214D ALA* 1.3 55.4 + - - +
216D ALA* 3.1 8.7 + - - +
219D PRO* 3.6 37.0 - - + -
243D LEU* 3.8 25.6 - - + -
245D ILE* 4.0 13.5 - - + -
290D LEU* 3.6 10.9 - - + +
292D LEU* 4.8 5.2 - - + -
346D PHE* 3.6 31.2 - - + -
350D THR* 3.9 8.5 - - + -
353D PHE* 4.2 6.1 - - + -
356D LYS* 2.7 39.2 + - - -
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Residues in contact with ALA 214 (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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210D ALA 3.0 8.4 + - - +
211D ALA* 3.6 12.3 - - - +
213D LEU* 1.3 74.7 - - - +
215D GLU* 1.3 60.6 + - + +
353D PHE* 3.5 31.5 - - + -
356D LYS* 3.1 17.3 + - - +
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Residues in contact with GLU 215 (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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211D ALA* 3.3 19.9 + - - +
212D LEU* 3.8 14.9 - - - +
213D LEU 3.1 0.8 - - - -
214D ALA* 1.3 77.5 - - + +
216D ALA* 1.3 63.6 + - - +
217D LYS 3.8 1.2 + - - -
289D ASP* 4.5 1.6 - - - +
314D LYS* 5.5 3.5 + - - -
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Residues in contact with ALA 216 (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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212D LEU 3.1 15.6 + - - +
213D LEU 3.1 8.9 + - - +
215D GLU* 1.3 77.1 - - - +
217D LYS* 1.3 60.4 + - - +
219D PRO* 4.3 10.3 - - + -
289D ASP* 3.6 19.7 - - - +
290D LEU* 3.9 23.1 - - + -
356D LYS* 2.7 33.5 + - - +
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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