Contacts of the helix formed by residues 209 - 226 (chain C) in PDB entry 3TQI
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 THR 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C PRO 4.3 7.1 + - - -
207C ASN* 2.8 10.6 + - - -
208C TRP* 1.3 74.6 - - - +
210C THR* 1.3 73.3 + - + +
211C LYS* 3.5 22.7 - - + +
212C HIS* 3.1 27.5 + - + +
213C ILE* 2.9 26.6 + - - +
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Residues in contact with THR 210 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C TRP 4.4 0.2 + - - -
209C THR* 1.3 75.9 - - + +
211C LYS* 1.3 66.1 + - + +
213C ILE* 3.2 12.8 + - - +
214C ILE* 3.1 37.5 + - - +
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Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ILE* 4.6 10.9 - - - +
200A HIS* 3.9 29.7 + - - -
209C THR* 3.3 15.1 - - + +
210C THR* 1.3 80.5 + - + +
212C HIS* 1.3 67.0 + - + +
214C ILE* 3.6 11.5 + - + +
215C GLU* 3.3 32.1 + - - +
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Residues in contact with HIS 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.1 24.8 - - + +
207C ASN* 3.3 40.5 + - + +
209C THR* 3.1 27.8 + - + +
211C LYS* 1.3 79.2 - - + +
213C ILE* 1.3 66.0 + - - +
215C GLU* 3.3 19.8 + - - +
216C ASP* 3.0 24.6 + - - +
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Residues in contact with ILE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 5.8 1.3 - - + -
208C TRP* 3.4 57.7 - - + +
209C THR 2.9 22.0 + - - +
210C THR* 3.7 11.4 - - - +
212C HIS* 1.3 75.5 - - - +
214C ILE* 1.3 59.5 + - + +
216C ASP* 3.4 5.4 + - - +
217C SER* 2.8 35.1 + - - +
374C PRO 6.0 0.4 - - - +
378C LEU* 3.9 32.8 - - + -
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Residues in contact with ILE 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C THR* 3.1 28.8 + - - +
211C LYS* 3.7 12.1 - - + +
212C HIS 3.2 0.2 - - - -
213C ILE* 1.3 78.2 - - + +
215C GLU* 1.3 66.6 + - + +
217C SER* 3.2 5.7 + - - -
218C ILE* 3.0 42.0 + - + +
246C LEU* 4.4 16.2 - - + -
249C LYS* 5.7 5.6 - - + -
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Residues in contact with GLU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 6.1 2.0 - - + -
211C LYS* 3.3 20.9 + - - +
212C HIS* 3.3 24.1 + - - +
214C ILE* 1.3 80.0 - - + +
216C ASP* 1.3 61.7 + - - +
218C ILE* 3.6 8.4 + - + +
219C ARG* 3.2 27.9 + - - +
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Residues in contact with ASP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ILE* 4.4 24.3 + - + +
6C HIS* 3.9 30.8 + - - -
212C HIS 3.0 17.9 + - - +
213C ILE* 3.8 6.0 - - - +
215C GLU* 1.3 75.7 - - - +
217C SER* 1.3 61.4 + - - +
219C ARG* 3.4 7.0 + - - +
220C ASP* 2.9 32.7 + - - +
377C GLU* 5.4 1.4 - - - +
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Residues in contact with SER 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ILE* 2.8 25.0 + - - +
214C ILE* 3.2 4.5 + - - -
216C ASP* 1.3 78.1 + - - +
218C ILE* 1.3 64.6 + - - +
220C ASP* 3.4 6.1 + - - +
221C ILE* 3.0 30.3 + - - +
246C LEU* 3.7 26.6 - - - +
374C PRO* 3.7 25.8 + - - +
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Residues in contact with ILE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C ILE* 3.0 38.1 + - + +
215C GLU* 3.9 8.5 - - + +
217C SER* 1.3 73.3 - - - +
219C ARG* 1.3 67.4 + - + +
221C ILE* 3.1 4.2 + - - +
222C GLN* 3.0 37.0 + - - +
246C LEU* 4.4 16.6 - - + +
249C LYS* 4.4 22.7 - - + +
250C ALA* 3.5 34.8 - - + -
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Residues in contact with ARG 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C GLU* 3.2 15.7 + - + +
216C ASP* 3.6 10.1 - - - +
218C ILE* 1.3 79.2 - - + +
220C ASP* 1.3 54.4 + - - +
222C GLN* 3.1 19.4 + - - +
223C GLU* 2.8 51.3 + - - +
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Residues in contact with ASP 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ASP* 2.9 24.0 + - - +
217C SER* 3.7 8.3 - - - +
219C ARG* 1.3 76.6 - - - +
221C ILE* 1.3 63.2 + - - +
223C GLU* 3.6 14.9 + - - +
224C LYS* 3.2 54.5 + - - +
372C ILE* 4.3 5.0 - - - +
374C PRO* 6.1 1.2 - - - +
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Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C SER 3.0 20.0 + - - +
218C ILE* 3.1 6.3 + - - +
220C ASP* 1.3 76.6 - - - +
222C GLN* 1.3 60.0 + - - +
224C LYS* 3.3 3.2 + - - -
225C VAL* 2.9 40.6 + - + +
230C VAL* 5.6 0.9 - - + -
246C LEU* 4.4 7.9 - - + -
247C VAL* 3.7 45.3 - - + +
250C ALA* 3.9 17.3 - - + -
251C ILE* 4.1 13.5 - - + -
372C ILE* 4.5 19.3 - - + -
374C PRO* 4.2 19.5 - - + -
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Residues in contact with GLN 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C ILE* 3.0 33.2 + - - +
219C ARG* 3.6 25.7 + - - +
221C ILE* 1.3 74.3 - - - +
223C GLU* 1.3 66.4 + - - +
226C GLY* 2.9 29.5 + - - +
249C LYS 5.0 1.0 + - - -
250C ALA* 2.9 32.5 + - + +
251C ILE* 4.7 6.5 - - + -
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Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ARG* 2.8 34.9 + - + +
220C ASP* 3.8 17.9 + - - +
222C GLN* 1.3 74.9 - - - +
224C LYS* 1.3 62.8 + - + +
226C GLY* 4.1 3.8 + - - -
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Residues in contact with LYS 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ASP* 3.2 38.4 + - - +
221C ILE 3.9 2.2 - - - +
223C GLU* 1.3 82.0 - - + +
225C VAL* 1.3 64.6 + - + +
228C GLU* 5.3 0.5 - - - +
330C TRP* 3.3 33.2 - - + -
371C LEU 5.5 1.8 + - - +
372C ILE* 3.3 33.5 - - + +
373C GLU 5.4 2.2 + - - +
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Residues in contact with VAL 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ILE* 2.9 25.9 + - + +
224C LYS* 1.3 81.0 - - + +
226C GLY* 1.3 70.7 + - - +
227C LYS 3.0 3.5 + - - -
228C GLU* 3.1 45.2 - - + +
230C VAL* 3.5 28.3 - - + -
251C ILE* 4.1 8.7 - - + -
254C GLN* 3.9 4.5 - - - +
330C TRP* 3.9 26.7 - - + -
372C ILE* 5.2 6.7 - - + -
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Residues in contact with GLY 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C GLN* 2.9 20.9 + - - +
223C GLU 4.1 2.4 + - - -
224C LYS 3.5 2.2 - - - -
225C VAL* 1.3 77.8 - - - +
227C LYS* 1.3 61.4 + - - +
251C ILE* 4.6 5.7 - - - +
254C GLN* 3.5 11.3 + - - +
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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