Contacts of the helix formed by residues 190 - 200 (chain B) in PDB entry 1TW2
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 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187B GLY 3.1 13.3 + - - -
188B GLY 3.2 2.4 + - - -
189B LYS* 1.3 78.9 - - - +
191B GLY* 1.3 57.6 + - - +
192B PHE 3.4 2.7 - - - -
193B ALA* 3.5 2.5 + - - +
194B ALA* 2.9 28.8 + - - +
207B VAL* 3.9 22.9 - - - -
217B ALA* 4.2 0.4 - - - +
220B TYR* 4.3 2.5 - - - -
221B LEU* 3.7 14.4 - - - +
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Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLN* 3.1 34.5 + - - +
167B PHE* 3.4 21.0 - - - +
187B GLY 4.2 2.2 + - - -
189B LYS 4.6 0.2 - - - +
190B GLY* 1.3 74.8 - - - +
192B PHE* 1.3 59.4 + - - +
194B ALA* 3.4 7.3 + - - +
195B ALA* 3.1 24.4 + - - +
198B ARG* 4.5 0.9 + - - -
220B TYR* 4.3 2.9 - - - -
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Residues in contact with PHE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B PHE* 3.4 36.4 - + + -
170B PRO* 3.4 25.6 - - + -
171B ALA* 3.7 22.7 - - + -
176B TRP* 5.2 0.9 - + - -
184B ASP* 3.5 14.5 + - - +
187B GLY 5.0 1.5 + - - +
190B GLY 3.4 0.2 - - - -
191B GLY* 1.3 72.8 - - - +
193B ALA* 1.3 66.4 + - - +
194B ALA 3.1 0.2 - - - -
195B ALA* 3.2 1.6 + - - -
196B ILE* 3.1 42.5 + - + +
249B ILE* 3.5 39.5 - - + -
251B SER* 3.8 13.2 - - - -
282B HIS* 4.0 21.5 - + + -
345B LEU* 4.8 6.7 - - + -
1635B SAH 6.0 0.4 - - - +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B VAL* 6.2 0.9 - - + -
184B ASP* 4.2 11.9 + - + +
190B GLY 3.5 6.8 + - - +
192B PHE* 1.3 78.0 - - - +
194B ALA* 1.3 61.8 + - - +
196B ILE* 3.6 10.2 + - - +
197B ALA* 3.1 24.3 + - - +
205B ALA* 4.3 15.3 - - + +
207B VAL* 3.7 29.4 - - + -
230B VAL* 4.0 19.1 - - + +
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Residues in contact with ALA 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B GLY 2.9 17.9 + - - +
191B GLY 3.6 6.3 - - - +
192B PHE 3.1 0.4 - - - -
193B ALA* 1.3 74.7 - - - +
195B ALA* 1.3 64.2 + - - +
197B ALA* 3.2 10.6 + - - +
198B ARG* 3.2 32.2 + - - +
220B TYR* 4.0 17.9 - - + +
221B LEU* 4.3 5.3 - - + +
224B GLU* 5.0 0.2 - - + -
226B LEU* 3.7 26.1 - - + +
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B PHE* 3.7 29.4 - - + +
168B ASP* 3.9 18.2 - - - +
171B ALA* 3.8 9.1 - - + +
191B GLY 3.1 16.8 + - - +
192B PHE 3.2 3.5 + - - +
194B ALA* 1.3 76.0 - - - +
196B ILE* 1.3 62.1 + - - +
198B ARG* 3.7 16.8 + - - +
199B ARG* 3.3 24.4 + - - +
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ALA* 4.0 13.2 - - + -
176B TRP* 3.5 57.0 - - + +
182B VAL* 4.2 15.7 - - + -
184B ASP* 6.5 0.2 - - + -
192B PHE* 3.1 34.7 + - + +
193B ALA* 3.9 7.4 - - - +
195B ALA* 1.3 76.6 - - - +
197B ALA* 1.3 58.5 + - - +
199B ARG* 3.3 4.6 + - - +
200B ALA* 3.0 28.8 + - + +
203B VAL* 4.4 19.5 - - + -
205B ALA* 6.0 2.0 - - + -
249B ILE* 4.1 11.4 - - + -
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ALA 3.1 19.3 + - - +
194B ALA* 3.2 6.5 + - - +
196B ILE* 1.3 80.0 - - + +
198B ARG* 1.3 59.3 + - - +
200B ALA 3.4 6.0 - - - +
201B PRO 4.1 0.2 - - - -
203B VAL* 5.2 4.9 - - + +
205B ALA* 6.1 1.3 - - + -
226B LEU* 4.4 11.2 - - + -
229B ARG* 2.8 45.8 + - + +
230B VAL* 4.1 20.4 - - + -
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Residues in contact with ARG 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B GLN 4.5 2.6 + - - -
164B ASP* 3.4 27.7 + - - +
168B ASP* 3.9 8.9 + - - -
191B GLY 4.5 3.0 + - - -
194B ALA* 3.2 32.9 + - - +
195B ALA* 3.7 25.3 - - - +
197B ALA* 1.3 76.2 - - - +
199B ARG* 1.3 62.5 + - - +
200B ALA 3.5 0.4 - - - -
201B PRO* 5.3 2.4 - - - +
220B TYR* 4.2 3.6 + - - -
224B GLU* 3.3 26.9 + - - +
226B LEU* 4.7 14.3 - - + +
229B ARG* 4.7 2.7 - - - +
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ASP* 5.1 3.1 - - - +
171B ALA* 3.9 11.6 + - + +
172B ALA* 3.4 44.3 + - - +
174B TYR 4.9 1.8 + - - -
176B TRP* 4.8 12.0 - - + -
195B ALA 3.3 20.1 + - - +
196B ILE* 3.4 6.7 - - - +
198B ARG* 1.3 80.3 - - + +
200B ALA* 1.3 58.1 + - + +
201B PRO* 3.7 8.4 - - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B TRP* 3.8 33.4 - - + -
196B ILE* 3.0 14.8 + - + +
197B ALA 3.4 3.2 - - - +
198B ARG 3.5 0.2 - - - -
199B ARG* 1.3 78.5 - - - +
201B PRO* 1.3 65.9 - - - +
202B HIS* 3.1 10.9 + - + -
203B VAL* 3.2 20.3 + - + +
229B ARG* 2.8 17.2 + - - -
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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