Contacts of the helix formed by residues 184 - 196 (chain A) in PDB entry 1TQ6
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A GLY* 3.3 25.9 + - - -
80A SER 4.7 3.4 - - - -
157A ALA* 4.1 15.9 - - + +
158A THR* 4.5 6.0 - - + +
182A ARG* 3.8 2.2 - - - +
183A THR* 1.3 81.6 - - - +
185A VAL* 1.3 64.8 + - - +
186A ASP* 3.0 16.4 - - - -
187A SER* 2.8 30.1 + - - +
188A ASP* 3.5 5.2 - - - +
230A LEU 3.3 1.4 + - - -
500A GNP 2.9 70.4 + - + +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ARG* 4.0 16.6 - - - +
183A THR 3.1 0.2 + - - -
184A LYS* 1.3 77.6 - - - +
186A ASP* 1.3 62.0 + - - +
188A ASP* 3.1 20.7 + - - +
189A ILE* 3.2 14.9 + - + +
206A LEU* 3.4 33.9 - - + -
209A ILE* 4.2 9.0 - - + -
229A LEU* 3.5 38.1 - - + -
230A LEU 3.3 22.0 + - - +
238A TYR* 4.6 9.2 - - + -
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Residues in contact with ASP 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LYS* 3.0 9.5 - - - -
185A VAL* 1.3 79.4 + - - +
187A SER* 1.3 66.4 + - - -
189A ILE* 3.2 13.3 + - - +
190A THR* 3.0 34.3 + - + +
231A SER* 3.5 19.4 - - - +
233A LYS* 4.3 6.9 - - + +
234A ASN* 6.2 1.6 - - + -
238A TYR* 4.4 8.0 + - + +
500A GNP 2.8 45.4 + - - -
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 4.7 11.2 - - - -
184A LYS* 2.8 26.1 + - - +
186A ASP* 1.3 87.8 + - - +
188A ASP* 1.3 59.2 + - - +
190A THR* 2.7 14.9 + - - -
191A ASN* 2.7 29.7 + - - +
500A GNP 4.1 6.6 + - - -
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Residues in contact with ASP 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 3.6 15.8 - - - +
182A ARG* 2.6 47.2 + - - -
184A LYS 3.5 5.7 - - - +
185A VAL* 3.1 8.9 + - - +
187A SER* 1.3 78.5 - - - +
189A ILE* 1.3 59.1 + - - +
191A ASN* 3.5 7.2 + - - +
192A GLU* 3.3 23.6 + - - +
205A VAL* 4.1 6.5 - - + +
209A ILE* 3.6 19.0 - - + +
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 3.2 17.4 + - + +
186A ASP* 3.2 6.3 + - - +
188A ASP* 1.3 77.7 - - - +
190A THR* 1.3 62.3 + - + +
193A ALA* 3.3 8.8 + - - +
200A PHE* 3.1 41.7 - - + -
202A LYS* 3.6 21.8 - - + -
205A VAL* 4.3 12.8 - - + -
206A LEU* 3.6 30.1 - - + -
238A TYR* 3.2 28.7 - - + +
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Residues in contact with THR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASP* 3.0 18.8 + - + +
187A SER* 2.7 24.1 + - - -
189A ILE* 1.3 80.8 - - + +
191A ASN* 1.3 64.9 + - - +
193A ALA* 3.7 6.2 + - - +
194A ASP* 3.2 23.2 + - - +
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Residues in contact with ASN 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A SER* 2.7 28.0 + - - +
188A ASP* 3.8 8.1 - - - +
189A ILE 3.3 0.4 - - - -
190A THR* 1.3 80.4 + - - +
192A GLU* 1.3 64.5 + - - +
194A ASP* 3.4 5.5 + - - +
195A GLY* 3.3 19.2 + - - -
196A GLU* 4.3 1.7 - - - +
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASP 3.3 13.7 + - - +
191A ASN* 1.3 75.4 - - - +
193A ALA* 1.3 59.6 + - - +
196A GLU* 2.8 73.7 + - - +
199A THR 3.7 10.3 - - - +
200A PHE* 3.4 28.5 - - + -
205A VAL* 3.7 22.3 - - + +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ILE 3.3 18.2 + - - +
190A THR* 3.9 7.6 - - - +
191A ASN 3.3 0.2 - - - -
192A GLU* 1.3 79.0 - - - +
194A ASP* 1.3 62.5 + - - +
196A GLU 3.5 10.7 - - - +
197A PRO* 4.3 5.0 - - - +
200A PHE* 3.4 35.0 - - + -
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Residues in contact with ASP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A THR 3.2 16.5 + - - +
191A ASN* 3.6 7.9 - - - +
192A GLU 3.2 0.4 - - - -
193A ALA* 1.3 81.7 - - - +
195A GLY* 1.3 65.3 + - - +
197A PRO* 4.6 6.6 - - - +
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Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASN 3.3 8.1 + - - -
194A ASP* 1.3 83.4 + - - +
196A GLU* 1.3 75.5 + - - +
197A PRO* 3.2 10.9 - - - +
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Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A ASN 4.3 1.2 - - - +
192A GLU* 2.8 49.8 + - - +
193A ALA 3.5 5.9 - - - +
195A GLY* 1.3 84.9 - - - +
197A PRO* 1.3 70.8 - - - +
198A GLN 3.6 1.6 - - - -
199A THR* 3.0 32.8 - - - +
200A PHE* 3.0 15.8 - - - +
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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