Contacts of the helix formed by residues 194 - 203 (chain B) in PDB entry 1T8U
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 LYS 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191B SER* 2.9 36.2 + - - +
193B ASP* 1.3 79.7 - - + +
195B GLY* 1.3 61.8 - - - +
197B ALA* 5.6 0.7 - - - +
198B TRP* 3.3 66.3 + - + +
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Residues in contact with GLY 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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187B PHE* 3.4 13.8 - - - -
192B TYR 3.0 13.3 + - - -
193B ASP 3.2 2.9 - - - -
194B LYS* 1.3 83.0 - - - +
196B LEU* 1.3 65.2 + - - -
197B ALA* 3.2 4.6 + - - -
198B TRP 3.3 0.2 + - - -
199B TYR 3.2 15.1 + - - -
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Residues in contact with LEU 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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152B LEU* 3.9 15.1 - - + +
187B PHE* 3.8 23.9 - - + -
188B PHE* 4.8 1.6 - - + -
192B TYR* 5.2 5.6 - - + +
195B GLY* 1.3 69.2 - - - -
197B ALA* 1.3 56.0 + - - +
199B TYR* 3.4 9.5 - - + +
200B ARG* 2.7 35.9 + - - +
231B ALA 5.4 0.9 - - - +
232B MET* 3.9 50.7 - - + +
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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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194B LYS 5.6 0.9 - - - +
195B GLY* 3.2 1.7 - - - -
196B LEU* 1.3 75.2 - - - +
198B TRP* 1.3 67.1 + - - +
200B ARG* 3.3 21.3 + - - +
201B ASP* 3.0 33.7 + - - +
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Residues in contact with TRP 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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185B PRO 4.5 7.6 - - - -
187B PHE* 3.7 32.5 - + + -
191B SER* 4.0 20.6 - - - -
194B LYS* 3.3 56.6 + - + +
195B GLY 3.3 2.0 + - - +
197B ALA* 1.3 78.9 - - - +
199B TYR* 1.3 78.8 + - - +
201B ASP* 3.3 18.9 + - + +
202B LEU* 3.3 47.8 + - + +
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Residues in contact with TYR 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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152B LEU* 3.7 20.0 - - + -
153B PRO* 3.3 37.2 - - + +
156B ILE* 3.7 1.7 - - - +
185B PRO* 4.1 5.2 - - + -
187B PHE* 3.5 43.1 - + + -
188B PHE* 3.4 28.3 - + - -
195B GLY 3.2 10.1 + - - +
196B LEU* 3.4 11.2 - - + +
198B TRP* 1.3 86.1 - - - +
200B ARG* 1.3 62.1 + - - +
202B LEU* 3.0 26.3 + - + +
203B MET* 3.4 25.3 - - + +
214B GLU* 2.6 31.8 + - - +
232B MET* 3.9 3.4 - - - -
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Residues in contact with ARG 200 (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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150B LYS* 3.6 37.2 - - + +
151B GLN* 4.4 7.0 - - - +
152B LEU* 4.0 16.6 - - + +
196B LEU 2.7 21.6 + - - +
197B ALA* 3.3 17.6 + - - +
199B TYR* 1.3 73.2 - - - +
201B ASP* 1.3 83.1 + - - +
203B MET* 3.0 31.2 + - - +
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Residues in contact with ASP 201 (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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150B LYS* 2.9 38.4 + - - +
197B ALA* 3.0 25.0 + - - +
198B TRP* 3.7 10.5 - - + +
199B TYR 3.2 0.4 - - - -
200B ARG* 1.3 102.0 + - - +
202B LEU* 1.3 59.2 + - - +
203B MET 3.2 0.4 - - - +
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Residues in contact with LEU 202 (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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181B VAL* 3.9 21.5 - - + +
185B PRO* 4.2 24.9 - - + -
198B TRP* 3.3 59.0 + - + +
199B TYR* 3.0 13.7 + - + +
201B ASP* 1.3 75.6 - - - +
203B MET* 1.3 69.0 + - + +
204B PRO* 3.9 1.0 - - - +
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Residues in contact with MET 203 (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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150B LYS* 3.4 23.7 + - + +
151B GLN 3.3 26.2 - - - +
153B PRO* 3.8 16.6 - - + -
181B VAL* 3.4 30.3 - - + -
185B PRO* 4.7 1.6 - - + -
199B TYR* 3.4 47.6 - - + +
200B ARG* 3.0 18.5 + - - +
201B ASP 3.8 0.5 - - - +
202B LEU* 1.3 86.2 - - + +
204B PRO* 1.3 74.2 - - + +
212B THR* 3.6 20.2 - - + -
213B MET 4.7 2.2 - - - +
214B GLU* 4.7 3.6 - - + -
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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