Contacts of the helix formed by residues 207 - 221 (chain C) in PDB entry 1JXQ
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 207 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C LEU* 1.3 74.8 - - - +
208C ALA* 1.3 67.1 + - - +
209C LYS* 3.9 6.4 + - - +
210C LYS* 2.9 43.3 + - + +
211C MET* 2.9 9.9 + - - +
246C THR* 3.4 21.5 - - + +
247C ASP* 3.3 27.1 - - + +
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Residues in contact with ALA 208 (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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207C THR* 1.3 71.5 - - - +
209C LYS* 1.3 62.4 + - - +
211C MET* 3.1 12.3 + - - +
212C VAL* 3.1 19.4 + - - +
245C GLY* 3.3 9.8 - - - -
247C ASP* 2.9 16.1 + - - +
254C CYS* 3.4 41.3 - - + +
255C PRO 4.4 1.6 - - - +
256C VAL* 3.7 18.4 - - + +
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Residues in contact with LYS 209 (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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207C THR* 3.0 9.5 + - - +
208C ALA* 1.3 79.6 - - - +
210C LYS* 1.3 62.9 + - + +
212C VAL* 3.5 7.1 + - - +
213C LEU* 3.1 49.0 + - + +
247C ASP* 4.2 2.5 + - - +
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Residues in contact with LYS 210 (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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205C ASP 5.5 0.9 - - - +
206C LEU* 4.0 30.2 - - + +
207C THR* 2.9 29.9 + - + +
209C LYS* 1.3 72.4 - - + +
211C MET* 1.3 56.4 + - - +
213C LEU* 3.1 17.3 + - + +
214C ALA* 2.7 36.4 + - - +
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Residues in contact with MET 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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168C ILE* 4.2 26.9 - - + -
170C ASN* 3.7 9.6 - - - +
206C LEU* 3.8 16.8 - - + +
207C THR 2.9 12.8 + - - +
208C ALA* 3.1 7.8 + - - +
210C LYS* 1.3 78.3 - - - +
212C VAL* 1.3 64.7 + - - +
214C ALA* 3.0 2.9 + - - +
215C LEU* 2.9 31.4 + - + +
234C ILE* 4.2 23.8 - - + -
236C SER* 5.5 0.4 - - - -
243C VAL* 4.0 27.4 - - + -
244C TYR 4.5 2.0 - - - +
245C GLY* 3.5 32.3 - - - -
256C VAL* 4.1 14.6 - - + -
261C ILE* 5.1 1.6 - - + -
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Residues in contact with VAL 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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208C ALA 3.1 13.3 + - - +
209C LYS* 3.7 9.0 - - - +
211C MET* 1.3 77.4 - - - +
213C LEU* 1.3 54.8 + - + +
215C LEU* 3.2 10.6 + - + +
216C LEU* 2.7 53.7 + - + +
256C VAL* 4.2 22.4 - - + -
260C LYS* 4.2 28.0 - - + +
264C ILE* 4.3 11.4 - - + -
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Residues in contact with LEU 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C LYS* 3.1 45.5 + - + +
210C LYS* 3.1 22.4 + - + +
212C VAL* 1.3 77.0 - - + +
214C ALA* 1.3 64.1 + - - +
216C LEU* 3.0 17.4 + - + +
217C GLU* 2.9 25.6 + - - +
220C ARG* 5.1 2.1 + - - +
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Residues in contact with ALA 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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166C LEU* 4.3 15.5 - - + +
168C ILE* 4.6 3.1 - - + -
203C LYS* 4.2 33.0 + - + +
206C LEU* 4.6 9.6 - - + -
210C LYS 2.7 15.8 + - - +
211C MET 3.4 7.6 - - - +
213C LEU* 1.3 73.4 - - - +
215C LEU* 1.3 62.8 + - - +
217C GLU* 3.3 7.7 + - - +
218C LEU* 3.1 22.2 + - - +
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Residues in contact with LEU 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LEU* 3.9 20.0 - - + -
168C ILE* 4.5 9.0 - - + -
211C MET* 2.9 23.3 + - + +
212C VAL* 3.6 4.0 - - - +
214C ALA* 1.3 79.1 - - - +
216C LEU* 1.3 61.1 + - - +
218C LEU* 3.3 6.3 + - - +
219C ALA 3.2 18.0 + - - -
232C VAL* 4.1 20.0 - - + -
234C ILE* 4.9 4.0 - - + -
256C VAL* 5.4 0.9 - - + -
261C ILE* 3.5 41.3 - - + -
264C ILE* 3.6 28.7 - - + +
265C PHE* 3.8 23.3 - - + -
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Residues in contact with LEU 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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212C VAL* 2.7 40.4 + - + +
213C LEU* 3.0 17.5 + - + +
215C LEU* 1.3 71.8 - - - +
217C GLU* 1.3 58.3 + - - +
219C ALA* 3.5 2.3 + - - +
220C ARG* 3.0 51.4 + - - +
264C ILE* 4.2 22.2 - - + -
269C SER* 5.5 4.7 - - - +
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Residues in contact with GLU 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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201C GLU* 5.6 1.2 - - - +
203C LYS* 4.3 17.0 + - - -
213C LEU 2.9 11.1 + - - +
214C ALA* 3.6 10.1 - - - +
216C LEU* 1.3 73.9 - - - +
218C LEU* 1.3 66.9 + - - +
220C ARG* 3.0 35.3 + - + +
221C GLN* 3.2 28.1 + - + +
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Residues in contact with LEU 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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164C HIS* 3.8 27.4 - - + -
166C LEU* 3.6 37.0 - - + +
201C GLU* 5.7 4.5 - - - +
214C ALA 3.1 12.4 + - - +
215C LEU 3.4 9.2 - - - +
217C GLU* 1.3 76.6 - - - +
219C ALA* 1.3 61.3 + - - +
221C GLN* 3.3 23.7 + - - +
224C HIS* 2.8 34.1 + - + -
230C CYS* 4.2 9.2 - - - -
231C VAL 4.8 1.1 - - - +
232C VAL* 4.0 9.9 - - + -
265C PHE* 3.8 24.2 - - + -
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Residues in contact with ALA 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 LEU 3.2 2.9 + - - +
216C LEU 3.9 2.9 - - - +
218C LEU* 1.3 75.6 - - - +
220C ARG* 1.3 58.5 + - - +
221C GLN 2.9 13.5 + - - +
224C HIS* 4.1 0.4 - - - -
264C ILE* 3.6 34.5 - - + +
265C PHE* 3.7 21.5 - - + -
269C SER* 4.4 7.0 - - - +
270C CYS* 3.2 36.7 - - + +
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Residues in contact with ARG 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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213C LEU* 5.1 2.0 + - - +
216C LEU* 3.0 52.6 + - - +
217C GLU* 3.0 23.2 + - - +
219C ALA* 1.3 75.0 - - - +
221C GLN* 1.3 60.0 + - - +
269C SER 5.5 2.2 - - - -
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Residues in contact with GLN 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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164C HIS* 4.0 23.8 + - - +
201C GLU* 5.5 4.8 + - - -
217C GLU* 3.2 25.6 + - + +
218C LEU* 3.4 35.1 - - - +
219C ALA 2.9 12.7 - - - +
220C ARG* 1.3 82.6 - - + +
222C ASP* 1.3 61.8 - - - +
224C HIS* 3.5 18.8 + - + +
272C SER* 4.0 6.1 - - - -
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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