Contacts of the helix formed by residues 184 - 191 (chain X) in PDB entry 1T6B
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 PRO 184 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22X TYR* 3.7 25.6 - - + -
32X PRO* 4.4 16.2 - - + -
35X VAL* 3.9 19.5 - - + -
175X VAL 6.2 0.2 - - - -
176X PRO* 3.6 17.5 - - + +
177X ASP* 4.8 4.3 - - + -
182X GLY 3.6 6.5 - - - +
183X ILE* 1.3 91.1 - - + +
185X ASP* 1.3 66.8 + - - +
186X SER* 4.4 12.8 - - - +
187X LEU* 2.9 20.6 + - + +
188X GLU* 3.4 7.6 + - - +
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Residues in contact with ASP 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176X PRO* 2.9 27.5 + - + +
177X ASP* 3.4 2.4 - - - -
178X ARG* 3.0 59.0 + - - +
183X ILE 3.3 1.1 + - - -
184X PRO* 1.3 70.6 - - - +
186X SER* 1.3 62.8 + - - +
187X LEU 3.3 0.7 + - - -
188X GLU* 3.5 3.8 + - - +
189X VAL* 3.3 27.1 + - + +
223X PRO* 3.8 26.6 - - + +
800X CA 3.8 6.6 - - - -
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Residues in contact with SER 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X GLN 4.7 4.2 + - - -
32X PRO* 3.9 27.5 - - - +
176X PRO* 4.8 1.0 + - - +
184X PRO* 3.0 4.3 + - - +
185X ASP* 1.3 78.2 - - - +
187X LEU* 1.3 61.3 + - - +
189X VAL* 3.5 2.4 + - - -
190X GLU* 2.7 50.6 + - - +
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Residues in contact with LEU 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X PRO* 4.3 15.7 - - + +
35X VAL* 4.2 17.3 - - + -
183X ILE* 4.1 7.0 - - + -
184X PRO* 2.9 19.3 + - + +
186X SER* 1.3 84.6 + - - +
188X GLU* 1.3 59.6 + - - +
189X VAL 3.1 1.8 - - - -
190X GLU* 5.1 1.3 - - + -
191X GLY* 2.6 37.8 + - - +
192X TYR* 3.2 11.4 - - + -
203X LEU* 3.1 38.4 - - + +
204X SER* 4.4 3.6 - - - -
205X PRO* 3.6 36.6 - - + -
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Residues in contact with GLU 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179X ASP* 3.1 2.8 - - - +
181X ASP* 3.1 5.6 - - - +
183X ILE* 3.7 17.9 - - + +
184X PRO 3.4 13.6 + - - +
185X ASP* 3.9 5.6 - - - +
187X LEU* 1.3 77.2 - - - +
189X VAL* 1.3 60.8 + - - +
192X TYR* 3.7 10.1 - - - -
220X LYS* 3.5 10.7 - - - +
221X SER* 2.8 54.6 + - - +
222X SER 3.0 8.8 - - - +
223X PRO* 3.6 9.5 - - + +
235X ASP* 3.2 1.0 - - - +
519X PRO* 5.2 0.3 - - - +
800X CA 2.3 30.9 - - - -
801X CA 2.5 28.7 - - - -
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Residues in contact with VAL 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178X ARG* 5.8 0.9 - - - +
185X ASP* 3.3 13.3 + - + +
186X SER* 4.1 3.4 - - - +
187X LEU 3.1 0.8 - - - -
188X GLU* 1.3 77.8 - - - +
190X GLU* 1.3 69.9 + - + +
220X LYS* 3.8 16.7 + - - +
221X SER 4.6 0.7 - - - -
223X PRO* 3.5 36.3 - - + -
517X THR* 4.3 10.8 - - - +
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Residues in contact with GLU 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186X SER* 2.7 41.9 + - - +
187X LEU* 5.1 1.3 - - + -
189X VAL* 1.3 86.3 - - + +
191X GLY* 1.3 63.2 + - - +
205X PRO* 6.5 0.7 - - + -
206X TRP* 4.5 4.5 - - - +
218X LYS* 3.7 17.5 + - - -
220X LYS* 4.0 4.8 - - - +
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Residues in contact with GLY 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187X LEU* 2.6 25.6 + - - +
189X VAL 3.5 1.0 - - - -
190X GLU* 1.3 79.6 - - - +
192X TYR* 1.3 58.9 + - - +
205X PRO* 3.6 7.1 - - - +
206X TRP* 3.0 24.5 + - - +
218X LYS* 4.5 2.5 - - - -
219X TYR 3.2 15.3 - - - -
220X LYS* 4.1 8.5 - - - -
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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