Contacts of the helix formed by residues 165 - 182 (chain D) in PDB entry 2J3T
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 GLY 165 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ALA* 1.3 79.3 - - - +
166D ILE* 1.3 62.5 + - - +
167D ASP* 3.4 4.5 + - - -
168D SER* 3.9 12.6 + - - -
169D LEU* 3.6 16.1 + - - +
209D ALA* 4.6 8.3 - - - +
212D ALA* 4.1 14.1 - - - +
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Residues in contact with ILE 166 (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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3D ILE* 4.7 5.6 - - + -
145D HIS* 3.3 53.6 - - + +
157D VAL* 4.4 9.2 - - + -
159D ALA* 4.3 13.0 - - + -
163D GLN* 3.8 33.2 - - + +
164D ALA* 3.9 8.5 - - - +
165D GLY* 1.3 78.3 - - - +
167D ASP* 1.3 68.4 + - - +
168D SER 3.2 0.4 - - - -
169D LEU* 3.2 19.8 + - + +
170D LEU* 3.0 28.4 + - + +
209D ALA* 5.6 0.9 - - + -
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Residues in contact with ASP 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* 3.4 1.3 - - - -
166D ILE* 1.3 81.3 + - - +
168D SER* 1.3 58.9 + - - +
170D LEU* 3.5 12.0 + - - +
171D ARG* 3.0 42.2 + - - +
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Residues in contact with SER 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D GLY* 3.9 14.0 + - - -
166D ILE 3.2 0.2 - - - -
167D ASP* 1.3 76.6 - - - +
169D LEU* 1.3 55.5 + - - +
171D ARG* 3.5 29.1 + - - +
172D LYS* 2.7 36.8 + - - +
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Residues in contact with LEU 169 (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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3D ILE* 3.8 18.4 - - + -
157D VAL* 3.6 40.6 - - + -
165D GLY 3.6 10.9 + - - +
166D ILE* 3.2 15.6 + - + +
168D SER* 1.3 79.0 - - - +
170D LEU* 1.3 52.5 + - - +
172D LYS* 3.1 4.0 + - - +
173D ILE* 2.8 56.5 + - + +
205D ALA* 4.1 25.4 - - + +
206D LEU* 4.2 13.0 - - + -
209D ALA* 3.7 18.6 - - + -
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D HIS* 4.1 23.3 - - + +
146D CYS 4.3 8.5 - - - +
147D TYR* 4.0 29.0 - - + -
155D PHE* 3.5 35.9 - - + +
157D VAL* 3.5 26.5 - - + -
166D ILE* 3.0 25.0 + - + +
167D ASP* 3.7 11.0 - - - +
169D LEU* 1.3 76.1 - - - +
171D ARG* 1.3 58.0 + - - +
173D ILE* 3.3 6.6 + - + +
174D TYR* 3.0 28.1 + - - +
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Residues in contact with ARG 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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147D TYR* 5.8 4.9 - - + -
167D ASP* 3.0 24.6 + - - +
168D SER* 3.5 39.4 + - - +
170D LEU* 1.3 76.9 - - - +
172D LYS* 1.3 62.2 + - - +
174D TYR* 3.4 12.5 - - + +
175D GLU* 3.2 26.6 + - + +
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Residues in contact with LYS 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 SER 2.7 23.6 + - - +
169D LEU* 3.3 7.6 - - - +
171D ARG* 1.3 73.2 - - - +
173D ILE* 1.3 64.2 + - - +
175D GLU* 3.1 26.1 + - - +
176D ILE* 3.0 40.8 + - + +
201D ASN* 5.7 1.6 - - - -
205D ALA* 3.6 28.0 - - + +
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Residues in contact with ILE 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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6D VAL* 4.3 11.4 - - + -
8D VAL* 4.9 4.3 - - + -
155D PHE* 3.7 30.1 - - + -
157D VAL* 4.1 21.5 - - + -
169D LEU* 2.8 46.5 + - + +
170D LEU* 3.3 8.0 + - + +
172D LYS* 1.3 71.9 - - + +
174D TYR* 1.3 53.6 + - - +
176D ILE* 3.3 7.9 + - - +
177D TYR* 2.7 33.4 + - - +
198D PHE* 4.6 7.8 - - + -
202D LEU* 3.5 34.1 - - + -
205D ALA* 5.2 2.5 - - + -
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Residues in contact with TYR 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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147D TYR* 3.9 30.5 - + + -
149D THR* 3.4 30.9 - - + +
150D LEU* 5.0 11.4 + - - +
155D PHE* 3.6 28.7 - + + -
170D LEU 3.0 13.0 + - - +
171D ARG* 3.4 16.4 - - + +
173D ILE* 1.3 78.0 - - - +
175D GLU* 1.3 58.8 + - + +
177D TYR* 3.3 6.2 + + - +
178D SER* 2.8 46.6 + - - -
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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 ARG* 3.2 15.9 + - + +
172D LYS* 3.1 36.6 + - + +
174D TYR* 1.3 81.2 - - + +
176D ILE* 1.3 64.6 + - + +
178D SER* 3.0 11.8 + - - -
179D ASP* 3.0 31.0 + - - +
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Residues in contact with ILE 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 LYS* 3.0 37.9 + - + +
173D ILE* 3.6 10.8 - - + +
175D GLU* 1.3 75.5 - - + +
177D TYR* 1.3 63.2 + - - +
179D ASP* 3.2 21.8 + - + +
180D PHE* 3.3 8.1 + - - +
198D PHE* 3.4 43.3 - - + +
201D ASN* 3.4 48.5 - - + +
202D LEU* 3.5 9.4 - - + +
205D ALA* 4.3 3.1 - - + -
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Residues in contact with TYR 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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8D VAL* 5.1 0.2 - - + -
16D ILE* 4.8 6.8 - - + +
149D THR* 5.3 2.5 - - + -
151D THR* 5.5 2.5 - - - -
153D ILE* 3.9 37.8 - - + +
155D PHE* 3.7 30.5 - + + -
173D ILE 2.7 21.8 + - - +
174D TYR* 3.5 11.4 - + - +
176D ILE* 1.3 73.2 - - - +
178D SER* 1.3 62.1 + - - +
180D PHE* 2.9 22.5 + + - +
181D ALA* 2.9 40.5 + - + +
189D LEU* 5.1 8.8 - - - +
193D ILE* 3.9 30.1 - - + -
198D PHE* 3.5 14.8 - + + -
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Residues in contact with SER 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 TYR* 2.8 35.8 + - - -
175D GLU* 3.0 16.6 + - - -
177D TYR* 1.3 79.3 - - - +
179D ASP* 1.3 58.7 + - - +
181D ALA* 3.1 6.8 + - - -
182D LEU* 2.8 48.1 + - - +
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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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175D GLU* 3.0 18.2 + - - +
176D ILE* 3.5 13.8 - - - +
177D TYR 3.2 0.4 - - - -
178D SER* 1.3 78.9 - - - +
180D PHE* 1.3 58.5 + - - +
182D LEU* 4.0 8.3 - - - +
183D LYS* 3.0 42.2 + - - +
201D ASN* 5.3 7.1 + - - +
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Residues in contact with PHE 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 ILE 3.3 8.0 + - - +
177D TYR* 2.9 27.7 + + - +
179D ASP* 1.3 78.3 - - - +
181D ALA* 1.3 62.3 + - - +
183D LYS* 4.4 4.0 - - - +
184D ASN* 3.0 55.4 + - + +
187D TYR* 3.5 47.1 - + + -
193D ILE* 4.0 28.9 - - + -
194D ARG 5.2 0.2 - - - -
195D CYS* 3.6 36.1 - - + -
198D PHE* 4.3 12.8 - - + -
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Residues in contact with ALA 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 TYR* 2.9 31.5 + - + +
178D SER* 3.7 10.5 - - - +
180D PHE* 1.3 79.0 - - - +
182D LEU* 1.3 61.7 + - + +
183D LYS 3.1 4.7 - - - -
184D ASN 3.2 27.4 - - - +
185D PRO* 3.2 8.5 - - - +
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Residues in contact with LEU 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 SER* 2.8 37.0 + - - +
179D ASP* 4.0 7.4 - - - +
181D ALA* 1.3 75.4 - - + +
183D LYS* 1.3 57.9 + - - +
185D PRO* 4.5 6.8 - - - +
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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