Contacts of the helix formed by residues 176 - 186 (chain D) in PDB entry 2X7O
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 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C ARG* 3.5 43.4 + - - +
174D GLY 4.1 2.0 - - - +
175D THR* 1.3 78.0 - - - +
177D LEU* 1.4 64.5 + - - +
178D LYS* 3.3 3.0 + - - +
179D ASP* 2.7 36.3 + - - +
180D LEU* 3.2 24.4 + - - +
224D TRP* 3.8 7.4 - - - -
225D ARG* 5.2 8.1 - - + +
227D GLU* 3.4 22.5 + - - +
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Residues in contact with LEU 177 (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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176D THR* 1.4 70.8 - - - +
178D LYS* 1.4 59.8 + - - +
180D LEU* 3.3 15.4 + - + +
181D ILE* 3.2 37.4 + - + +
201D ILE* 4.8 4.3 - - + -
224D TRP* 3.6 33.5 - - + +
227D GLU* 2.8 30.1 + - + +
228D GLU 4.1 13.2 - - - +
229D VAL* 4.0 25.4 - - + -
263D ILE* 4.3 33.7 - - + -
281D ASP* 4.9 3.4 - - - +
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Residues in contact with LYS 178 (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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365C ILE 5.7 2.0 - - - +
366C ASP* 4.0 24.6 - - - +
367C ILE 4.3 15.3 - - - +
368C ALA* 4.5 17.5 - - + +
369C PRO* 5.9 0.7 - - - -
176D THR* 3.3 4.2 - - - +
177D LEU* 1.4 76.2 - - - +
179D ASP* 1.3 62.3 + - - +
181D ILE* 3.7 23.1 + - + +
182D TYR* 3.7 11.1 + - - +
227D GLU* 3.2 17.0 + - + +
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Residues in contact with ASP 179 (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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240C ARG* 5.3 2.8 - - - -
243C PHE* 3.6 34.7 - - + -
244C ARG* 3.9 23.5 + - - +
247C GLU* 6.1 1.1 - - + -
357C ARG* 4.6 13.6 + - - +
366C ASP* 4.7 8.8 - - - +
174D GLY 4.4 1.0 - - - +
175D THR* 4.8 2.5 - - + -
176D THR* 2.7 30.3 + - - +
178D LYS* 1.3 77.8 - - - +
180D LEU* 1.4 61.5 + - - +
182D TYR* 3.4 10.7 + - - +
183D ASP* 3.0 29.2 + - - +
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Residues in contact with LEU 180 (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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171D ILE* 5.1 6.3 - - + -
175D THR* 4.2 15.9 - - + -
176D THR 3.2 19.1 + - - +
177D LEU* 3.3 16.8 + - + +
179D ASP* 1.4 74.2 - - - +
181D ILE* 1.4 62.8 + - + +
183D ASP* 3.4 20.4 + - + +
184D MET* 3.4 16.7 + - - +
193D LEU* 3.9 35.5 - - + +
197D VAL* 4.4 14.1 - - + -
201D ILE* 4.4 13.2 - - + -
224D TRP* 3.7 32.3 - - + -
263D ILE* 6.3 0.7 - - + -
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Residues in contact with ILE 181 (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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177D LEU* 3.2 27.9 + - + +
178D LYS* 3.8 22.7 - - + +
179D ASP 3.3 0.2 - - - -
180D LEU* 1.4 75.3 - - + +
182D TYR* 1.3 56.5 + - - +
184D MET* 3.4 10.3 - - - +
185D THR* 2.7 40.8 + - - +
255D ARG* 3.5 26.0 - - - +
263D ILE* 5.1 9.9 - - + -
281D ASP* 3.9 23.1 - - - +
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Residues in contact with TYR 182 (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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247C GLU* 6.0 0.2 - - - -
251C THR 5.7 0.9 - - - -
327C PRO* 3.8 27.9 - - - +
357C ARG* 3.5 49.6 + - + +
358C HIS 6.1 0.4 - - - -
359C ASP* 5.0 12.0 - - + +
364C THR* 5.8 11.7 - - + -
366C ASP* 5.1 16.2 - - + -
178D LYS 3.7 9.0 + - - +
179D ASP* 3.4 11.6 + - - +
180D LEU 3.3 0.4 - - - -
181D ILE* 1.3 79.9 - - - +
183D ASP* 1.4 63.9 + - - +
185D THR* 4.7 3.1 - - - +
186D THR* 2.6 67.7 + - + +
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Residues in contact with ASP 183 (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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243C PHE* 5.6 2.6 - - - -
247C GLU* 4.1 19.4 - - - +
175D THR* 5.5 3.6 - - - +
179D ASP* 3.0 27.1 + - - +
180D LEU* 3.6 18.7 - - + +
181D ILE 3.3 0.4 - - - -
182D TYR* 1.4 81.9 - - - +
184D MET* 1.3 55.6 + - - +
186D THR* 4.9 0.4 - - - -
187D SER* 3.4 21.4 + - - -
193D LEU* 5.0 8.5 - - + -
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Residues in contact with MET 184 (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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180D LEU 3.5 8.7 - - - +
181D ILE* 3.4 17.3 - - - +
183D ASP* 1.3 79.8 - - - +
185D THR* 1.3 62.0 + - - +
186D THR 3.6 0.2 - - - -
187D SER* 3.7 13.5 - - - -
189D SER 3.9 4.9 - - - +
190D GLY* 4.4 5.2 - - - +
191D SER 3.7 22.9 - - - +
192D GLY* 3.8 22.0 - - - +
193D LEU* 3.8 40.6 - - + +
255D ARG* 3.4 40.7 - - - +
262D PHE* 3.7 16.2 - - + +
263D ILE* 5.1 2.7 - - - +
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Residues in contact with THR 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362C THR* 5.3 14.1 - - + +
181D ILE* 2.7 28.9 + - - +
182D TYR* 4.5 2.5 - - - -
184D MET* 1.3 78.2 - - - +
186D THR* 1.3 65.4 + - + +
187D SER 3.3 5.9 + - - +
190D GLY* 5.2 5.3 - - - -
255D ARG* 3.4 42.9 + - + +
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Residues in contact with THR 186 (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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323C THR* 5.2 8.5 - - - +
359C ASP* 4.8 16.6 - - + +
362C THR* 5.0 6.7 - - - +
182D TYR* 2.6 63.4 + - + +
183D ASP* 4.9 0.7 - - - -
185D THR* 1.3 79.8 - - + +
187D SER* 1.3 65.6 + - - +
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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