Contacts of the helix formed by residues 227 - 239 (chain D) in PDB entry 2W93
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 VAL 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D CYS* 3.1 27.0 + - - +
225D HIS 3.5 9.6 - - - +
226D ASP* 1.3 81.5 - - - +
228D LYS* 1.3 55.5 + - - +
229D ALA 3.3 2.2 - - - -
230D GLU* 3.3 10.9 + - - +
231D THR* 2.6 40.2 + - + +
285D VAL* 3.8 20.2 - - + -
326D MET* 3.9 17.5 - - + -
327D LYS* 3.9 32.1 - - + -
330D LEU* 3.9 15.9 - - + -
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Residues in contact with LYS 228 (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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222D CYS* 3.6 16.8 + - - +
223D SER* 4.0 22.5 + - - +
226D ASP* 3.7 4.4 + - - +
227D VAL* 1.3 77.4 - - - +
229D ALA* 1.3 57.3 + - - +
231D THR* 3.8 1.3 - - - -
232D LYS* 2.9 31.5 + - - +
250D GLY 4.2 11.6 + - - -
251D SER* 3.5 41.9 - - - +
404D THR 5.1 1.4 + - - -
405D TYR* 3.3 36.5 - - + +
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Residues in contact with ALA 229 (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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228D LYS* 1.3 75.8 - - - +
230D GLU* 1.3 74.5 + - - +
232D LYS* 3.4 11.3 + - - +
233D LYS* 3.1 22.7 + - - +
327D LYS* 5.8 0.9 - - - +
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Residues in contact with GLU 230 (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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226D ASP 3.7 0.2 - - - +
227D VAL* 3.3 20.6 - - + +
229D ALA* 1.3 83.4 - - - +
231D THR* 1.3 58.2 + - - +
233D LYS* 3.3 3.8 + - - +
234D LEU* 2.9 27.3 + - - +
327D LYS* 2.8 37.0 + - - +
330D LEU* 3.9 30.0 - - + +
331D GLN* 3.1 39.4 + - + +
334D LEU* 3.8 17.8 - - + +
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Residues in contact with THR 231 (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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216D ILE* 4.7 6.8 - - - +
218D ALA* 4.8 1.0 - - - +
222D CYS* 3.6 23.5 - - - -
227D VAL* 2.6 28.8 + - + +
228D LYS* 3.8 3.6 - - - -
230D GLU* 1.3 74.9 - - - +
232D LYS* 1.3 67.3 + - - +
234D LEU* 3.1 11.1 + - - +
235D ILE* 3.0 28.6 + - - +
252D ILE* 4.0 17.7 - - - +
285D VAL* 3.7 27.2 - - + +
330D LEU* 4.5 5.6 - - + -
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Residues in contact with LYS 232 (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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228D LYS 2.9 18.2 + - - +
229D ALA* 3.5 10.1 - - - +
231D THR* 1.3 77.1 - - - +
233D LYS* 1.3 62.6 + - - +
235D ILE* 3.3 13.4 + - - +
236D ASP* 3.1 37.0 + - - +
252D ILE* 5.5 4.2 - - - +
253D ASP* 3.7 26.5 + - + +
256D HIS* 5.6 6.1 - - + -
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Residues in contact with LYS 233 (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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229D ALA 3.1 10.0 + - - +
230D GLU 3.6 7.6 - - - +
232D LYS* 1.3 77.3 - - - +
234D LEU* 1.3 66.7 + - - +
236D ASP* 3.4 27.3 + - + +
237D LEU* 2.9 54.5 + - + +
334D LEU* 3.7 23.8 - - + -
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Residues in contact with LEU 234 (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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216D ILE* 3.9 33.9 - - + -
230D GLU 2.9 14.0 + - - +
231D THR* 3.1 12.5 + - - +
233D LYS* 1.3 77.8 - - - +
235D ILE* 1.3 54.9 + - - +
237D LEU* 4.3 1.2 - - - +
238D THR* 2.8 41.9 + - - +
283D LEU* 4.4 13.7 - - + -
285D VAL* 4.7 9.9 - - + -
309D PHE* 5.4 2.0 - - + -
330D LEU* 4.2 23.8 - - + -
333D LEU* 4.9 7.6 - - + -
334D LEU* 3.5 12.1 - - + +
337D ILE* 3.8 35.2 - - + -
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Residues in contact with ILE 235 (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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216D ILE* 3.8 26.2 - - + -
231D THR* 3.0 22.6 + - - +
232D LYS* 3.6 9.6 - - - +
233D LYS 3.2 0.2 - - - -
234D LEU* 1.3 75.7 - - - +
236D ASP* 1.3 53.2 + - - +
238D THR* 4.1 0.4 - - - -
239D GLN* 2.8 33.3 + - - -
240D PHE 4.2 13.5 - - - +
242D ALA* 3.7 24.9 - - + -
252D ILE* 3.8 29.8 - - + -
253D ASP 5.8 0.4 - - - +
256D HIS* 3.7 33.0 - - + +
258D ARG* 4.3 3.4 - - + -
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Residues in contact with ASP 236 (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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232D LYS* 3.1 33.8 + - - +
233D LYS* 3.2 31.0 + - + +
235D ILE* 1.3 74.8 - - - +
237D LEU* 1.3 62.9 + - - +
238D THR 3.1 1.4 + - - -
239D GLN* 2.7 29.8 + - - +
256D HIS* 2.7 36.5 + - - -
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Residues in contact with LEU 237 (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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233D LYS* 2.9 51.4 + - + +
234D LEU 4.4 0.4 - - - +
236D ASP* 1.3 73.8 - - - +
238D THR* 1.3 59.2 + - - +
239D GLN* 5.0 1.8 - - - +
334D LEU* 3.3 50.0 - - + +
337D ILE* 4.2 14.6 - - + -
338D ALA* 4.0 34.4 - - + +
341D ALA* 4.8 2.1 - - - +
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Residues in contact with THR 238 (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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216D ILE* 3.7 12.1 - - + -
234D LEU* 2.8 26.6 + - - +
235D ILE 3.8 1.8 - - - +
237D LEU* 1.3 80.9 - - - +
239D GLN* 1.3 67.9 + - - +
240D PHE* 3.0 74.0 + - + +
337D ILE* 4.0 16.5 - - - +
341D ALA* 3.9 14.0 - - - +
344D TYR* 4.0 5.0 - - - -
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Residues in contact with GLN 239 (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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235D ILE 2.8 21.7 + - - -
236D ASP* 2.7 32.3 + - - +
237D LEU 5.0 1.6 - - - +
238D THR* 1.3 74.1 - - - +
240D PHE* 1.3 60.9 + - - +
256D HIS* 4.5 9.0 + - - -
257D PRO* 5.9 0.7 - - - +
258D ARG* 2.8 51.5 + - - +
344D TYR* 3.4 11.1 - - + -
346D PRO* 4.9 10.0 - - + +
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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