Contacts of the helix formed by residues 211 - 222 (chain D) in PDB entry 2POZ
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 THR 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A GLY 4.9 0.2 - - - -
301A ASN* 3.4 21.5 - - - +
302A MSE 4.1 3.6 - - - +
303A ARG* 3.5 42.0 + - + +
327A ASN* 6.2 1.1 - - + -
174D ARG 5.7 0.2 - - - +
175D ARG* 3.6 24.1 + - + +
176D SER* 5.6 1.3 - - - +
210D LEU* 1.3 79.8 - - - +
212D THR* 1.3 68.0 + - - +
213D ASP* 2.8 22.2 + - - -
214D GLU* 3.3 9.2 + - - +
215D THR* 3.0 22.2 + - - -
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Residues in contact with THR 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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274A CYS 5.8 1.3 - - - -
275A GLY* 5.5 6.3 - - - -
300A TYR 4.5 2.4 + - - -
301A ASN* 2.7 40.8 + - - +
211D THR* 1.3 73.1 - - - +
213D ASP* 1.3 63.0 + - - +
215D THR* 3.4 5.8 + - - -
216D ILE* 3.0 42.5 + - + +
241D ALA* 3.6 10.4 - - + +
244D VAL* 4.2 16.6 - - + -
245D ILE* 3.9 16.2 - - + -
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Residues in contact with ASP 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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252A PRO* 3.7 33.4 - - + +
275A GLY* 4.1 22.0 - - - +
276A ILE* 3.7 11.1 - - - +
303A ARG* 2.6 31.4 + - - -
211D THR* 2.8 27.7 + - - -
212D THR* 1.3 76.2 - - - +
214D GLU* 1.3 68.8 + - - +
216D ILE* 3.3 11.0 + - - +
217D ARG* 3.1 21.3 + - - +
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Residues in contact with GLU 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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228A CYS* 5.0 3.5 - - - +
303A ARG* 2.8 40.4 + - - +
182D ILE* 4.1 20.6 - - + +
210D LEU* 3.7 23.6 - - + +
211D THR* 3.3 9.8 + - - +
213D ASP* 1.3 81.1 + - - +
215D THR* 1.3 60.6 + - - +
217D ARG* 2.6 45.9 + - - +
218D PHE* 3.0 29.6 + - - +
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Residues in contact with THR 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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301A ASN* 5.4 0.2 + - - -
206D LEU* 4.3 7.8 - - + +
210D LEU* 3.0 34.6 + - - +
211D THR 3.0 16.0 + - - -
212D THR* 3.7 7.2 - - - -
214D GLU* 1.3 75.8 - - - +
216D ILE* 1.3 66.5 + - - +
218D PHE* 3.3 5.1 + - - +
219D CYS* 2.9 33.6 + - - -
233D PRO* 3.2 37.3 + - + +
245D ILE* 4.1 11.2 - - + -
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Residues in contact with ILE 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 THR* 3.0 36.3 + - + +
213D ASP* 3.3 10.5 + - - +
215D THR* 1.3 75.0 - - - +
217D ARG* 1.3 64.7 + - - +
219D CYS* 3.3 1.2 + - - +
220D ARG* 3.0 60.2 + - - +
244D VAL* 4.5 4.3 - - + -
245D ILE* 4.3 16.2 - - + -
248D GLN* 3.7 34.1 - - + +
249D ILE* 4.0 14.4 - - + -
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Residues in contact with ARG 217 (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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226A ASP* 5.0 9.9 + - - -
227A ILE 2.8 30.3 + - - -
228A CYS* 3.4 21.3 + - - +
250A PRO 5.6 1.0 + - - -
251A LEU* 5.9 0.8 - - - +
252A PRO* 3.7 19.8 - - + +
182D ILE* 6.3 3.8 - - + -
213D ASP 3.1 14.1 + - - +
214D GLU* 2.6 51.5 + - - +
215D THR 3.2 0.2 - - - -
216D ILE* 1.3 80.1 - - - +
218D PHE* 1.3 63.9 + - - +
220D ARG* 3.4 7.9 + - - +
221D LYS* 3.0 25.5 + - + +
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Residues in contact with PHE 218 (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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160D PRO* 4.2 11.4 - - + -
161D LEU* 4.4 9.2 - - + -
182D ILE* 4.3 23.6 - - + -
185D ALA* 3.7 25.4 - - + -
186D TYR* 3.6 31.2 - - + -
189D VAL* 4.3 2.0 - - + -
206D LEU* 4.2 34.5 - - + -
210D LEU* 5.4 4.9 - - + -
214D GLU 3.0 16.3 + - - +
215D THR* 3.3 4.9 + - - +
217D ARG* 1.3 78.9 - - - +
219D CYS* 1.3 65.3 + - - +
221D LYS* 3.0 21.2 + - + +
222D ILE* 3.1 43.8 + - + +
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Residues in contact with CYS 219 (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 LEU* 4.3 7.6 - - - -
215D THR* 2.9 35.4 + - - +
218D PHE* 1.3 78.0 - - - +
220D ARG* 1.3 61.8 + - - +
222D ILE* 3.3 13.7 - - - +
223D GLY* 3.2 17.0 + - - -
230D VAL* 4.3 16.8 - - - -
233D PRO* 4.9 1.1 - - - -
249D ILE* 3.6 35.9 - - + -
250D PRO* 4.8 0.9 - - - -
251D LEU* 3.6 25.6 - - + +
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Residues in contact with ARG 220 (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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249A ILE 5.0 1.2 + - - -
250A PRO* 3.7 38.0 + - - +
216D ILE* 3.0 34.2 + - - +
217D ARG* 3.7 7.1 - - - +
219D CYS* 1.3 76.3 - - - +
221D LYS* 1.3 60.6 + - - +
223D GLY* 3.1 5.4 + - - -
224D GLU* 3.0 23.9 - - - +
248D GLN* 2.8 51.4 + - - +
249D ILE* 4.7 0.9 - - - -
250D PRO* 4.1 23.6 - - + +
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Residues in contact with LYS 221 (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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182D ILE* 6.3 2.2 - - + -
183D GLU* 4.2 12.6 + - - +
186D TYR* 3.6 58.8 + - + -
187D ARG* 5.8 1.6 - - - +
217D ARG* 3.0 17.8 + - + +
218D PHE* 3.0 16.6 + - + +
220D ARG* 1.3 78.3 - - - +
222D ILE* 1.3 56.5 + - + +
224D GLU* 2.5 20.9 - - - +
225D LEU* 5.0 0.7 - - - +
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Residues in contact with ILE 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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186D TYR* 3.9 21.1 - - + -
189D VAL* 4.3 10.8 - - + -
204D VAL* 4.6 16.6 - - + -
218D PHE* 3.1 47.3 + - + +
219D CYS* 3.3 16.6 - - - +
221D LYS* 1.3 73.1 - - - +
223D GLY* 1.3 59.2 + - - +
224D GLU 3.2 3.1 - - - -
225D LEU* 2.8 39.8 + - + +
227D ILE* 3.7 20.3 - - + +
230D VAL* 5.9 1.3 - - + -
251D LEU* 3.8 20.6 - - + -
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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