Contacts of the helix formed by residues 206 - 215 (chain A) in PDB entry 1TUB
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 ASN 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ILE* 3.3 13.8 - - + +
172A TYR 4.2 10.7 + - - +
204A VAL 3.3 3.2 + - - -
205A ASP* 1.3 72.8 - - - +
207A GLU* 1.3 58.4 + - - +
208A ALA 3.3 0.2 - - - -
209A ILE* 3.4 5.4 - - - +
210A TYR* 2.3 43.8 + - + -
224A TYR* 3.1 11.3 + - - +
227A LEU* 2.0 44.4 - - - +
500A GTP 2.5 39.8 + - - +
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Residues in contact with GLU 207 (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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172A TYR 5.4 0.2 + - - -
174A ALA* 3.6 23.5 - - + +
175A PRO* 3.5 25.1 - - + +
176A GLN* 3.5 52.2 + - - +
205A ASP* 3.0 0.8 - - + -
206A ASN* 1.3 81.9 - - - +
208A ALA* 1.3 52.2 + - - +
210A TYR* 4.7 4.3 - - - +
211A ASP* 2.8 38.3 - - - +
304A LYS* 5.2 7.7 - - + +
330B GLU* 6.1 0.5 - - - +
333B LEU* 5.1 1.0 - - - +
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Residues in contact with ALA 208 (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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205A ASP* 3.2 2.6 - - - +
207A GLU* 1.3 77.1 - - - +
209A ILE* 1.3 49.1 + - - +
210A TYR 3.5 0.2 - - - -
211A ASP* 3.1 7.2 - - - +
212A ILE* 2.7 41.1 + - - +
301A GLN 3.6 3.5 - - - +
302A MET 1.3 49.6 - - - +
303A VAL* 2.9 21.7 - - - +
304A LYS* 5.0 1.1 - - - +
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Residues in contact with ILE 209 (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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204A VAL* 2.1 43.5 - - + -
205A ASP 2.9 11.8 + - - +
206A ASN* 3.4 5.6 - - - +
207A GLU 3.6 0.2 - - - -
208A ALA* 1.3 71.7 - - - +
210A TYR* 1.3 51.0 + - - +
211A ASP 2.8 5.2 - - - -
212A ILE* 3.0 4.1 - - - +
213A CYS* 2.6 41.9 + - - -
227A LEU* 1.2 91.3 - - + -
230A LEU* 3.1 29.6 - - + -
231A ILE* 2.9 10.3 - - + -
302A MET* 3.3 10.5 - - + -
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Residues in contact with TYR 210 (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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206A ASN* 2.3 38.6 - - + +
207A GLU* 4.7 5.4 - - - +
208A ALA 3.5 0.2 - - - -
209A ILE* 1.3 73.5 - - - +
211A ASP* 1.3 66.2 + - - +
213A CYS* 3.8 9.6 - - - +
214A ARG* 3.6 19.9 + - - +
220A GLU* 6.1 0.3 - - - -
224A TYR* 2.8 45.3 - + - -
227A LEU* 2.2 30.7 - - + +
325B MET 4.5 0.7 - - - -
326B LYS* 1.8 72.7 - - + -
329B ASP* 5.8 1.1 - - + -
330B GLU* 3.5 20.4 - - + +
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Residues in contact with ASP 211 (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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207A GLU* 2.8 32.9 - - - +
208A ALA* 3.1 12.3 - - - +
209A ILE 2.8 0.4 - - - -
210A TYR* 1.3 80.6 - - - +
212A ILE* 1.3 58.3 + - + +
213A CYS 2.9 4.3 - - - -
214A ARG* 2.5 56.0 + - - +
215A ARG* 2.9 34.3 + - - +
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Residues in contact with ILE 212 (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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208A ALA 2.7 22.6 + - - +
209A ILE* 3.0 11.6 + - - +
211A ASP* 1.3 76.0 - - - +
213A CYS* 1.3 60.5 + - - +
214A ARG 3.1 1.1 - - - -
215A ARG* 4.3 1.1 - - - +
216A ASN* 2.9 48.5 + - + +
217A LEU* 3.3 3.1 + - - +
230A LEU* 2.0 54.1 - - + -
275A VAL* 4.9 7.7 - - + +
299A ALA 3.4 11.4 - - - +
300A ASN* 3.6 6.1 - - - +
301A GLN 3.2 21.5 - - - +
302A MET* 4.1 5.8 - - - -
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Residues in contact with CYS 213 (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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209A ILE* 2.6 37.1 + - - +
210A TYR* 4.0 9.4 - - - +
211A ASP 2.9 0.6 - - - -
212A ILE* 1.3 85.1 - - - +
214A ARG* 1.3 57.6 - - - +
215A ARG 3.6 0.2 - - - -
217A LEU* 3.4 15.9 - - + -
218A ASP 3.4 34.1 + - - +
219A ILE 3.5 11.0 + - - +
220A GLU* 5.7 0.7 - - - -
222A PRO* 5.0 2.7 - - + -
226A ASN 5.9 0.2 - - - -
227A LEU* 5.5 0.2 - - - -
230A LEU* 4.6 4.0 - - - -
326B LYS* 3.4 27.6 - - - +
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Residues in contact with ARG 214 (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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210A TYR 3.6 14.0 + - - +
211A ASP* 2.5 48.6 + - - +
213A CYS* 1.3 82.8 - - - +
215A ARG* 1.3 79.3 + - + +
217A LEU 4.5 4.0 - - - +
218A ASP* 5.6 0.4 - - - +
220A GLU* 4.7 35.4 - - + +
330B GLU* 5.7 6.2 + - - -
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Residues in contact with ARG 215 (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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211A ASP* 2.9 30.1 + - - +
212A ILE* 5.7 0.2 - - - +
214A ARG* 1.3 105.3 - - + +
216A ASN* 1.3 70.9 + - - +
217A LEU 4.4 1.6 - - - -
280A LYS* 5.9 0.2 + - - -
299A ALA* 5.3 14.4 - - + +
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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