Contacts of the helix formed by residues 200 - 215 (chain A) in PDB entry 1T0R
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 PHE 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ALA 3.3 19.3 - - - -
196A PHE* 2.9 16.5 + - + +
198A THR 3.6 0.4 - - - -
199A GLY* 1.3 83.1 - - - +
201A THR* 1.3 61.0 + - - +
202A ASN 3.4 1.8 - - - -
203A MET 3.4 4.0 + - - -
204A GLN* 2.9 27.8 + - - +
262A ILE* 4.1 12.3 - - + -
265A SER* 3.5 22.4 - - - -
266A TRP* 3.8 26.9 - - + -
269A PHE* 3.6 43.9 - + + -
294A MET* 4.0 23.6 - - + -
298A ILE* 3.9 17.1 - - + +
302A PHE* 3.4 26.2 - + - -
320A PHE* 4.9 2.7 - + - -
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Residues in contact with THR 201 (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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196A PHE* 3.0 53.3 + - + +
197A GLU* 3.4 15.4 + - - +
200A PHE* 1.3 70.9 - - + +
202A ASN* 1.3 68.2 + - - +
204A GLN* 3.8 20.4 - - - +
205A PHE* 2.9 39.3 + - + +
231A GLU* 3.6 17.6 + - - -
502A AZI 4.9 4.8 + - - +
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Residues in contact with ASN 202 (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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197A GLU 3.0 18.1 + - - +
198A THR* 4.4 11.5 + - - +
200A PHE 3.4 0.4 - - - -
201A THR* 1.3 80.0 + - - +
203A MET* 1.3 77.2 + - - +
206A LEU* 3.9 4.9 + - - +
228A GLN* 2.6 54.7 + - - +
231A GLU* 3.5 24.6 - - + +
232A SER* 4.2 13.2 + - - -
235A ALA* 5.7 0.9 - - + -
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Residues in contact with MET 203 (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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198A THR 5.5 1.9 + - - +
199A GLY 6.0 0.6 - - - -
200A PHE 3.4 6.6 + - - +
202A ASN* 1.3 99.7 - - + +
204A GLN* 1.3 67.5 + - - +
205A PHE 3.3 0.4 - - - -
206A LEU* 3.0 38.5 + - + +
207A GLY* 3.0 18.5 + - - -
228A GLN* 5.2 0.7 - - - +
293A PHE* 4.1 6.1 - - + -
297A TRP* 3.7 61.5 - - + +
298A ILE* 4.3 6.5 - - + -
301A GLN* 5.3 4.5 - - - -
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Residues in contact with GLN 204 (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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96A HIS* 5.3 5.5 + - - -
196A PHE* 5.5 0.7 - - - -
200A PHE 2.9 11.1 + - - +
201A THR* 3.7 11.7 - - - +
203A MET* 1.3 75.8 - - - +
205A PHE* 1.3 76.6 + - + +
207A GLY* 2.8 4.7 + - - -
208A LEU* 2.6 44.2 + - + +
269A PHE* 3.3 38.1 - - + -
272A LEU* 5.8 2.0 - - - +
273A THR* 3.3 28.9 + - + +
293A PHE* 4.0 14.1 - - - -
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Residues in contact with PHE 205 (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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96A HIS* 3.7 26.5 - + - -
100A ILE* 4.9 7.6 - - + -
104A GLU* 4.2 16.2 - - - -
141A GLN* 4.8 2.7 - - - -
201A THR* 2.9 28.3 + - + +
204A GLN* 1.3 104.4 - - + +
206A LEU* 1.3 56.6 + - - +
208A LEU* 3.9 5.2 - - + -
209A ALA* 2.9 14.9 + - - +
224A ILE* 2.9 53.5 - - + +
227A ILE* 3.8 31.0 - - + -
228A GLN* 4.1 17.4 - - + +
231A GLU* 5.5 5.4 - - - -
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Residues in contact with LEU 206 (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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202A ASN 3.9 3.1 + - - +
203A MET* 3.0 50.7 + - + +
205A PHE* 1.3 79.8 - - - +
207A GLY* 1.3 59.1 + - - +
209A ALA* 3.4 7.1 + - + +
210A ALA* 3.1 21.5 + - - +
225A SER* 6.1 0.7 - - - -
228A GLN* 3.2 36.8 - - + +
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Residues in contact with GLY 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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203A MET 3.0 8.9 + - - -
204A GLN 2.8 6.7 + - - -
206A LEU* 1.3 75.8 - - - +
208A LEU* 1.3 63.5 + - - +
210A ALA* 3.1 7.6 + - - +
211A ASP* 2.9 32.1 + - - +
293A PHE* 4.8 13.5 - - - -
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Residues in contact with LEU 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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89A TRP* 4.3 15.0 - - + -
92A THR* 4.7 11.2 - - + -
96A HIS* 3.6 35.2 - - + +
204A GLN* 2.6 28.0 + - + +
205A PHE* 3.8 13.9 - - + +
207A GLY* 1.3 73.0 - - - +
209A ALA* 1.3 56.7 + - - +
211A ASP* 3.2 9.6 + - + +
212A ALA* 2.9 27.4 + - - +
220A PHE* 3.7 28.5 - - + -
224A ILE* 3.9 12.1 - - + -
276A ILE* 6.1 2.2 - - + -
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Residues in contact with ALA 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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205A PHE 2.9 19.3 + - - +
206A LEU* 3.6 7.9 - - + +
208A LEU* 1.3 76.9 - - - +
210A ALA* 1.3 63.0 + - - +
212A ALA* 3.5 7.1 + - - +
213A ALA* 3.3 21.1 + - - +
221A ALA* 3.8 7.5 - - - +
224A ILE* 3.9 15.2 - - + +
225A SER* 3.5 29.6 - - - +
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Residues in contact with ALA 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 LEU 3.1 13.7 + - - +
207A GLY* 3.1 12.5 + - - +
209A ALA* 1.3 77.6 - - - +
211A ASP* 1.3 65.3 + - - +
213A ALA* 3.4 7.4 + - - +
214A GLU* 3.3 20.6 + - - +
287A ASN* 5.4 6.3 - - - +
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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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89A TRP* 4.4 13.5 - - + -
207A GLY 2.9 20.7 + - - +
208A LEU* 3.6 12.7 - - + +
210A ALA* 1.3 79.1 - - - +
212A ALA* 1.3 66.3 + - - +
214A GLU* 3.2 8.6 + - - +
215A ALA* 3.1 23.0 + - - +
276A ILE* 6.0 1.2 - - - +
277A MET* 4.9 14.4 - - - +
281A THR* 4.8 19.8 - - + +
285A SER 4.7 10.2 - - - +
287A ASN* 4.9 7.6 - - - +
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Residues in contact with ALA 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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89A TRP* 3.4 16.3 - - + -
208A LEU 2.9 16.5 + - - +
209A ALA 3.7 1.3 - - - +
210A ALA 3.4 0.2 - - - -
211A ASP* 1.3 76.6 - - - +
213A ALA* 1.3 59.7 + - - +
215A ALA* 3.3 4.2 + - - +
217A ASP* 3.0 30.6 + - - +
220A PHE* 3.7 18.6 - - + -
221A ALA* 3.4 33.9 - - + +
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Residues in contact with ALA 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 ALA 3.3 10.0 + - - +
210A ALA* 3.5 10.8 - - - +
211A ASP 3.1 0.2 - - - -
212A ALA* 1.3 76.4 - - - +
214A GLU* 1.3 61.3 + - - +
216A GLY* 2.8 22.5 + - - -
218A HIS* 3.9 22.9 - - + +
221A ALA* 3.7 12.5 - - + +
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Residues in contact with GLU 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 ALA 3.3 10.1 + - - +
211A ASP* 3.2 12.2 + - - +
213A ALA* 1.3 77.7 - - - +
215A ALA* 1.3 60.1 + - - +
216A GLY 3.2 0.9 + - - -
284A GLU* 4.4 6.4 - - - +
285A SER* 3.5 43.9 + - - +
287A ASN* 5.8 2.9 - - - +
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Residues in contact with ALA 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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81A PHE* 3.1 19.6 - - - -
86A ASP* 6.4 0.9 - - + -
89A TRP* 4.1 34.1 - - + -
211A ASP 3.1 10.8 + - - +
212A ALA 3.6 9.4 - - - +
213A ALA 3.1 1.0 - - - -
214A GLU* 1.3 76.6 - - - +
216A GLY* 1.3 57.7 + - - +
217A ASP 4.4 0.9 - - - +
282A PRO* 6.2 4.3 - - + -
285A SER* 5.7 1.8 - - - -
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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