Contacts of the helix formed by residues 221 - 235 (chain D) in PDB entry 3EDC
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 SER 221 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277C GLU* 5.7 9.2 - - - -
73D LEU* 4.9 6.1 - - - -
219D ASP* 2.5 28.0 + - - -
220D TRP* 1.3 79.2 - - - +
222D ALA* 1.3 65.2 + - - +
223D MET* 3.7 8.3 + - - +
224D SER* 2.7 34.5 + - - -
225D GLY 3.2 4.7 + - - -
248D GLN* 4.7 3.8 - - - +
249D MET* 3.3 8.5 - - - +
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Residues in contact with ALA 222 (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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277C GLU* 5.4 1.8 - - - +
278C ASP* 3.8 25.7 + - - +
281C CYS* 3.8 24.1 - - + -
221D SER* 1.3 73.2 - - - +
223D MET* 1.3 63.1 + - - +
225D GLY 2.9 3.3 + - - -
226D PHE 2.9 18.7 + - - -
248D GLN* 3.1 29.2 + - - +
251D LEU* 4.2 8.7 - - + -
252D GLY* 3.3 8.6 - - - +
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Residues in contact with MET 223 (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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280C SER* 3.3 31.6 - - - +
281C CYS* 3.8 12.2 - - - -
221D SER* 3.4 8.1 + - - +
222D ALA* 1.3 77.9 - - - +
224D SER* 1.3 56.8 + - - +
226D PHE* 3.3 22.6 + - - +
227D GLN* 2.8 58.5 + - - +
255D ARG* 4.5 6.7 - - - +
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Residues in contact with SER 224 (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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218D GLY* 3.6 10.2 - - - -
219D ASP* 3.0 46.1 + - - -
221D SER* 2.7 26.3 + - - -
223D MET* 1.3 75.7 - - - +
225D GLY* 1.3 56.7 + - - +
227D GLN* 4.2 11.9 - - - +
228D GLN* 2.8 41.1 + - - +
249D MET* 3.7 2.8 - - - +
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Residues in contact with GLY 225 (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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185D LEU* 3.8 15.2 - - - +
221D SER 3.2 2.9 + - - -
222D ALA 2.9 7.9 + - - -
224D SER* 1.3 83.3 + - - +
226D PHE* 1.3 59.8 + - - +
229D THR* 2.6 32.2 + - - -
249D MET* 3.5 20.4 - - - -
252D GLY 3.6 6.7 - - - -
253D ALA 3.7 0.2 - - - -
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Residues in contact with PHE 226 (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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281C CYS* 4.0 12.1 - - - -
222D ALA 2.9 10.9 + - - +
223D MET* 3.5 20.4 - - - +
225D GLY* 1.3 74.9 - - - +
227D GLN* 1.3 64.3 + - + +
230D MET* 2.8 73.9 + - + +
252D GLY 3.3 14.3 - - - +
255D ARG* 3.4 47.6 - - + -
256D ALA* 3.8 19.8 - - - +
259D GLU* 3.6 6.3 - - - -
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Residues in contact with GLN 227 (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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223D MET* 2.8 53.2 + - - +
224D SER* 4.1 8.3 - - - +
226D PHE* 1.3 79.7 - - + +
228D GLN* 1.3 69.2 + - - +
230D MET* 3.9 3.5 - - - +
231D GLN* 3.0 25.3 + - - +
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Residues in contact with GLN 228 (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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185D LEU* 3.8 18.8 - - + -
216D ARG* 3.5 35.8 + - + +
217D GLU 3.5 31.7 + - - +
218D GLY* 4.4 1.1 - - - -
224D SER* 2.8 25.3 + - - +
225D GLY 4.3 0.2 - - - +
227D GLN* 1.3 83.5 - - - +
229D THR* 1.3 61.0 + - - +
231D GLN* 3.3 5.6 + - - +
232D MET* 3.1 22.5 + - - +
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Residues in contact with THR 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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185D LEU* 3.9 4.9 - - - +
225D GLY 2.6 23.2 + - - -
228D GLN* 1.3 73.6 - - - +
230D MET* 1.3 59.1 + - - +
232D MET* 3.2 12.0 + - - +
233D LEU* 2.9 43.6 + - + +
242D MET* 3.7 30.4 - - + +
253D ALA* 3.4 24.5 - - - +
256D ALA* 3.7 20.2 - - + -
257D ILE* 4.4 1.8 - - + -
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Residues in contact with MET 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 PHE* 2.8 60.8 + - + +
227D GLN* 3.9 4.9 - - - +
229D THR* 1.3 78.4 - - - +
231D GLN* 1.3 55.9 + - - +
233D LEU* 3.8 3.0 - - - -
234D ASN* 2.8 53.3 + - - +
256D ALA* 3.5 22.6 - - + +
259D GLU* 3.9 19.7 - - + +
260D SER* 3.7 17.7 - - - +
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Residues in contact with GLN 231 (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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216D ARG* 3.6 7.2 - - - +
227D GLN 3.0 18.8 + - - +
228D GLN* 3.8 6.7 - - - +
229D THR 3.2 0.2 - - - -
230D MET* 1.3 73.6 - - - +
232D MET* 1.3 66.0 + - - +
234D ASN* 4.1 15.7 + - - +
235D GLU* 3.0 44.3 + - - +
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Residues in contact with MET 232 (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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183D ALA* 3.7 33.0 - - + -
184D LEU 4.8 3.4 - - - +
185D LEU* 6.2 0.7 - - + -
214D ALA* 4.0 17.3 - - + -
216D ARG* 3.5 39.8 - - + +
228D GLN 3.1 12.3 + - - +
229D THR* 3.5 11.9 - - - +
231D GLN* 1.3 75.9 - - - +
233D LEU* 1.3 64.4 + - - +
235D GLU* 3.0 15.3 + - - +
237D ILE* 3.2 45.8 + - + +
239D PRO* 4.3 9.9 - - - -
242D MET* 4.4 18.4 - - + +
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Residues in contact with LEU 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 THR* 2.9 34.6 + - + +
230D MET* 4.0 3.8 - - - +
232D MET* 1.3 77.8 - - + +
234D ASN* 1.3 59.7 + - - +
236D GLY* 3.1 17.5 + - - -
237D ILE 3.5 18.4 - - - +
238D VAL* 4.2 18.5 - - + +
239D PRO* 4.3 3.6 - - + -
256D ALA* 3.9 10.5 - - + +
257D ILE* 4.1 16.8 - - + -
260D SER* 3.4 29.8 - - - +
262D LEU* 4.6 4.7 - - + -
268D ILE* 4.0 23.1 - - + -
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Residues in contact with ASN 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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230D MET* 2.8 47.5 + - - +
231D GLN* 3.7 18.2 + - - +
232D MET 3.2 0.2 - - - -
233D LEU* 1.3 78.2 - - - +
235D GLU* 1.3 60.3 + - - +
236D GLY 3.2 1.2 + - - -
260D SER* 5.6 0.2 + - - -
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Residues in contact with GLU 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 ARG* 2.7 36.6 + - - -
231D GLN* 3.0 32.3 + - - +
232D MET 3.0 9.3 + - - +
234D ASN* 1.3 75.6 - - - +
236D GLY* 1.3 59.2 + - - +
237D ILE* 3.3 24.4 + - + +
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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