Contacts of the helix formed by residues 166 - 182 (chain D) in PDB entry 2CEA
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 ALA 166 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D VAL* 3.9 24.8 - - + +
164D GLY 3.4 2.8 - - - +
165D GLY* 1.3 77.4 - - - +
167D GLU* 1.3 67.5 + - - +
168D GLU* 3.2 7.2 - - - -
169D ALA* 3.0 25.8 + - + +
170D ILE* 3.1 17.9 + - + +
210D LEU* 4.8 8.3 - - + -
328D VAL* 5.0 9.6 - - + -
1608D ADP 5.0 2.7 - - - +
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Residues in contact with GLU 167 (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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165D GLY* 3.5 15.6 + - - +
166D ALA* 1.3 85.2 + - - +
168D GLU* 1.3 76.5 + - + +
170D ILE* 3.6 11.4 + - + +
171D GLU* 3.2 27.4 + - - +
335D GLY* 5.6 1.6 - - - -
338D LYS* 5.1 12.6 - - - +
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Residues in contact with GLU 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D GLY 5.0 0.3 - - - +
166D ALA* 3.5 5.2 - - - -
167D GLU* 1.3 96.2 + - + +
169D ALA* 1.3 61.8 + - - +
171D GLU* 3.0 23.2 + - - +
172D GLU* 3.2 13.4 + - + +
327D VAL 6.0 2.2 - - - +
329D ASP* 5.4 4.2 - - - +
442D ARG* 4.6 19.5 + - - +
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Residues in contact with ALA 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ALA* 3.0 14.5 + - + +
168D GLU* 1.3 75.3 - - - +
170D ILE* 1.3 68.4 + - - +
172D GLU* 3.1 14.4 + - - +
173D LEU* 3.1 19.3 + - + +
210D LEU* 4.0 22.9 - - + -
326D ILE* 3.8 29.3 - - + +
327D VAL 4.8 7.3 + - - +
328D VAL* 5.1 2.9 - - + -
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Residues in contact with ILE 170 (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 PHE* 3.8 49.5 - - + +
163D VAL* 4.4 24.2 - - + +
166D ALA* 3.1 25.5 + - - +
167D GLU* 3.8 11.0 - - + +
169D ALA* 1.3 74.3 - - - +
171D GLU* 1.3 69.1 + - - +
173D LEU* 2.8 20.3 + - - +
174D LYS* 2.9 30.1 + - - +
210D LEU* 4.3 8.7 - - + +
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Residues in contact with GLU 171 (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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167D GLU 3.2 12.1 + - - +
168D GLU* 3.0 14.6 + - - +
170D ILE* 1.3 86.5 - - - +
172D GLU* 1.3 64.0 + - + +
174D LYS* 3.3 37.3 + - - +
175D GLU* 4.5 1.9 + - - +
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Residues in contact with GLU 172 (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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168D GLU* 3.2 14.3 + - + +
169D ALA* 3.1 9.5 + - - +
171D GLU* 1.3 78.9 - - + +
173D LEU* 1.3 60.9 + - - +
174D LYS 3.7 0.2 + - - -
175D GLU* 3.8 10.9 - - - +
176D VAL* 4.2 0.3 - - - +
324D LYS* 3.0 40.9 + - - +
325D LYS 4.5 6.1 - - - +
326D ILE* 4.3 24.2 - - + +
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Residues in contact with LEU 173 (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 PHE* 4.4 5.8 - - + -
169D ALA* 3.1 16.4 + - + +
170D ILE* 2.8 7.6 + - - +
172D GLU* 1.3 75.6 - - - +
174D LYS* 1.3 66.7 + - - +
175D GLU 3.2 2.5 - - - -
176D VAL* 2.8 18.8 + - + +
177D VAL* 3.0 14.9 + - - +
197D ILE* 4.1 13.7 - - + -
199D LEU* 5.1 0.9 - - + -
210D LEU* 3.9 36.1 - - + -
214D VAL* 4.0 24.7 - - + -
303D MET* 3.5 28.7 - - + -
324D LYS* 5.9 0.2 - - - +
326D ILE* 3.5 24.2 - - + -
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Residues in contact with LYS 174 (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 PHE* 4.1 22.7 - - + +
170D ILE* 2.9 33.3 + - - +
171D GLU* 3.3 31.3 + - - +
173D LEU* 1.3 75.6 - - - +
175D GLU* 1.3 62.5 - - - +
177D VAL* 3.0 12.7 + - + +
178D GLU* 3.0 26.2 + - - +
217D GLU* 5.5 3.4 + - - +
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Residues in contact with GLU 175 (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 GLU 4.5 1.7 + - - +
172D GLU* 3.8 14.0 + - - +
174D LYS* 1.3 75.6 - - - +
176D VAL* 1.3 68.9 + - - +
178D GLU* 3.2 9.9 + - - +
179D PHE* 2.9 23.0 + - - +
186D PHE* 4.0 11.7 - - + -
193D MET* 4.0 23.7 - - + +
324D LYS* 3.4 20.5 + - - +
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Residues in contact with VAL 176 (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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172D GLU 4.2 5.6 - - - +
173D LEU* 2.8 23.6 + - + +
175D GLU* 1.3 77.3 - - - +
177D VAL* 1.3 62.2 + - - +
179D PHE* 3.1 5.4 + - - +
180D LEU* 3.0 25.6 + - + +
193D MET* 3.7 20.0 - - + -
194D PRO* 5.4 2.0 - - + -
197D ILE* 3.7 33.7 - - + -
214D VAL* 4.1 18.2 - - + -
301D ILE* 4.2 23.1 - - + -
303D MET* 5.8 0.7 - - - -
324D LYS* 4.4 8.3 - - - +
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Residues in contact with VAL 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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160D PHE* 4.2 18.4 - - + -
173D LEU 3.0 9.3 + - - +
174D LYS* 3.0 10.2 + - + +
176D VAL* 1.3 76.6 - - - +
178D GLU* 1.3 66.7 + - - +
180D LEU* 3.1 3.2 + - - +
181D LYS* 3.0 46.0 + - + +
214D VAL* 3.6 35.4 - - + +
217D GLU* 4.0 26.5 - - + +
218D ALA* 4.0 5.8 - - + +
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Residues in contact with GLU 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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174D LYS* 3.0 12.5 + - - +
175D GLU* 3.6 11.4 - - - +
177D VAL* 1.3 82.9 - - - +
179D PHE* 1.3 64.1 + - - +
181D LYS* 3.4 33.9 + - - +
182D ASP* 3.4 16.6 + - - +
185D LYS* 5.4 0.2 - - - +
186D PHE* 3.7 21.4 - - + -
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Residues in contact with PHE 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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175D GLU 2.9 12.5 + - - +
176D VAL 3.3 9.4 - - - +
178D GLU* 1.3 76.9 - - - +
180D LEU* 1.3 67.4 + - + +
182D ASP 3.0 1.6 + - - -
183D PRO* 2.7 61.2 - - + +
186D PHE* 3.4 39.2 - + + -
187D ASN* 3.7 13.7 - - - -
191D ALA 4.8 2.0 - - - -
193D MET* 3.6 35.2 - - + -
296D SER* 3.7 33.7 - - - -
297D LYS* 4.6 0.4 - - - -
299D GLY* 4.1 13.2 - - - -
300D ILE 5.5 0.2 - - - -
301D ILE* 4.8 10.1 - - + -
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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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176D VAL* 3.0 25.3 + - + +
177D VAL 3.1 2.4 + - - +
179D PHE* 1.3 79.0 - - + +
181D LYS* 1.3 62.0 + - - +
182D ASP 3.3 0.7 + - - -
183D PRO* 3.3 12.7 - - - +
214D VAL* 4.2 11.9 - - + -
218D ALA* 3.7 21.4 - - + +
220D VAL* 4.8 8.1 - - + +
254D PRO* 4.1 20.1 - - + +
255D CYS 4.5 6.7 - - - +
256D ILE* 3.7 34.5 - - + -
299D GLY* 3.5 33.2 - - - +
301D ILE* 4.5 13.0 - - + -
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Residues in contact with LYS 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 VAL* 3.0 38.5 + - + +
178D GLU* 3.4 32.7 + - - +
179D PHE 3.2 0.4 - - - -
180D LEU* 1.3 77.0 - - - +
182D ASP* 1.3 64.3 + - + +
183D PRO* 3.8 1.1 - - - +
217D GLU* 3.9 15.6 + - - +
218D ALA* 4.0 19.3 - - - +
219D ASN* 6.1 0.9 - - - +
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Residues in contact with ASP 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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178D GLU 3.4 7.0 + - - +
179D PHE 3.0 5.9 + - - +
181D LYS* 1.3 84.4 - - + +
183D PRO* 1.3 57.2 - - - +
184D SER* 2.6 25.4 + - - -
185D LYS* 2.6 51.2 + - + +
186D PHE* 4.1 1.6 + - - -
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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