Contacts of the helix formed by residues 207 - 221 (chain C) in PDB entry 1F9E
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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175C LYS* 5.8 1.8 - - + +
206C CYS* 1.3 76.0 - - - +
208C VAL* 1.3 62.9 + - - +
209C GLU* 3.4 11.1 - - - +
210C GLN* 2.8 48.6 + - - +
211C ILE* 2.8 22.6 + - - +
245C GLY* 4.3 1.3 - - - -
246C THR* 3.3 19.5 - - + +
247C ASP* 3.0 33.4 - - + +
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C THR* 1.3 72.8 - - - +
209C GLU* 1.3 66.4 + - - +
211C ILE* 3.0 11.0 + - + +
212C TYR* 3.0 52.6 + - + -
245C GLY* 3.7 11.7 - - - +
247C ASP* 3.0 5.7 + - - -
254C GLN* 3.0 53.4 - - + +
255C GLU 3.7 15.3 - - - +
256C ALA* 4.2 8.7 - - + +
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Residues in contact with GLU 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* 3.4 10.3 + - - +
208C VAL* 1.3 82.7 - - - +
210C GLN* 1.3 66.1 + - + +
212C TYR* 3.4 11.9 + - - +
213C GLU* 3.1 42.1 + - - +
247C ASP* 5.5 1.1 + - - +
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Residues in contact with GLN 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C HIS 5.1 1.7 - - - +
205C ASP 4.2 5.9 + - - +
206C CYS* 3.9 16.7 - - + +
207C THR* 2.8 48.7 + - - +
209C GLU* 1.3 74.6 - - + +
211C ILE* 1.3 59.6 + - - +
213C GLU* 3.3 16.7 - - - +
214C ILE* 2.9 38.8 + - + +
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Residues in contact with ILE 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* 3.8 30.1 - - + -
170C ASN* 4.5 7.2 - - - +
206C CYS* 3.8 19.7 - - + +
207C THR 2.8 25.6 + - - +
208C VAL* 3.0 12.1 + - - +
210C GLN* 1.3 69.6 - - - +
212C TYR* 1.3 68.4 + - + +
214C ILE* 3.0 11.3 + - - +
215C LEU* 2.9 40.3 + - + +
234C ILE* 5.2 6.1 - - + -
236C SER* 6.2 0.2 - - - -
243C ILE* 4.4 20.9 - - + -
245C GLY* 4.7 2.9 - - - -
256C ALA* 5.5 3.1 - - + -
261C LEU* 4.4 17.7 - - + -
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Residues in contact with TYR 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 VAL* 3.0 42.8 + - + -
209C GLU* 3.6 12.8 - - - +
211C ILE* 1.3 76.3 - - + +
213C GLU* 1.3 53.1 + - + +
215C LEU* 3.1 7.0 + - + +
216C LYS* 2.8 36.1 + - - +
255C GLU 4.5 1.6 + - - -
256C ALA* 3.9 7.0 - - + -
257C PRO* 3.6 18.4 - - - +
260C GLU* 3.6 32.8 + - + +
261C LEU* 3.6 27.1 - - + -
264C GLN* 4.8 12.2 + - + +
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Residues in contact with GLU 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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209C GLU* 3.1 38.2 + - + +
210C GLN* 3.3 19.3 - - - +
212C TYR* 1.3 76.4 - - - +
214C ILE* 1.3 63.8 + - + +
216C LYS* 3.1 17.2 + - - +
217C ILE* 3.1 20.5 + - + +
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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
----------------------------------------------------------
166C LEU* 4.0 18.8 - - + -
168C ILE* 4.1 9.4 - - + -
203C HIS* 3.1 61.9 - - + +
206C CYS* 3.8 16.4 - - + -
210C GLN* 2.9 18.8 + - + +
211C ILE* 3.0 6.5 + - - +
213C GLU* 1.3 75.9 - - + +
215C LEU* 1.3 63.6 + - + +
217C ILE* 3.3 16.9 + - + +
218C TYR* 3.1 30.5 - - + -
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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
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166C LEU* 3.7 25.8 - - + -
168C ILE* 5.7 3.4 - - + -
211C ILE* 2.9 27.5 + - + +
212C TYR* 3.6 8.5 - - + +
214C ILE* 1.3 73.9 - - + +
216C LYS* 1.3 56.0 + - - +
218C TYR* 3.2 2.7 + - - +
219C GLN* 2.7 37.7 + - - +
232C CYS* 4.1 17.7 - - - -
234C ILE* 5.6 0.9 - - + -
261C LEU* 3.7 48.0 - - + +
264C GLN* 4.6 10.3 - - + -
265C PHE* 3.7 26.0 - - + -
280C PHE* 5.2 0.9 - - + -
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Residues in contact with LYS 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 TYR 2.8 14.2 + - - +
213C GLU* 3.1 14.1 + - - +
215C LEU* 1.3 77.1 - - - +
217C ILE* 1.3 63.3 + - + +
219C GLN* 3.0 35.8 + - - +
220C LEU* 2.9 53.2 + - + +
264C GLN* 4.5 8.2 - - - +
269C LYS* 4.8 9.1 - - - +
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Residues in contact with ILE 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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203C HIS* 6.4 1.6 - - + -
213C GLU* 3.1 15.0 + - + +
214C ILE* 3.4 16.6 - - + +
215C LEU 3.1 0.2 - - - -
216C LYS* 1.3 76.8 - - + +
218C TYR* 1.3 81.7 + - + +
220C LEU* 3.0 9.4 + - - +
221C MET* 3.0 34.5 + - + +
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Residues in contact with TYR 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 TYR* 3.7 35.4 - + + -
166C LEU* 3.4 36.3 - - + -
201C LYS* 3.3 30.2 - - + +
203C HIS* 4.4 6.6 + + - -
214C ILE* 3.1 33.0 - - + +
215C LEU 3.2 4.9 + - - +
217C ILE* 1.3 91.3 - - + +
219C GLN* 1.3 65.6 + - - +
221C MET* 3.3 25.8 + - - -
224C HIS* 2.9 27.1 + + - +
230C PHE* 4.2 17.9 - + + -
265C PHE* 3.9 9.3 - - + -
270C CYS* 4.5 0.3 - - - -
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Residues in contact with GLN 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 2.7 23.0 + - - +
216C LYS* 3.0 39.9 + - - +
217C ILE 3.1 0.2 - - - -
218C TYR* 1.3 75.1 - - - +
220C LEU* 1.3 78.2 + - - +
221C MET 4.0 1.2 - - - +
264C GLN* 3.2 39.9 + - + +
265C PHE* 3.7 14.1 - - + -
269C LYS* 3.2 35.8 + - - +
270C CYS* 3.5 22.1 - - + +
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Residues in contact with LEU 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 LYS* 2.9 45.0 + - + +
217C ILE* 3.5 5.8 - - - +
219C GLN* 1.3 100.2 - - - +
221C MET* 1.3 65.4 + - - +
269C LYS 5.3 0.7 - - - +
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Residues in contact with MET 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 TYR* 3.3 44.6 - - + +
217C ILE* 3.0 26.8 + - + +
218C TYR* 3.3 30.7 + - - +
219C GLN 4.0 3.3 - - - +
220C LEU* 1.3 83.7 - - - +
222C ASP* 1.3 73.9 + - - +
224C HIS* 3.6 14.4 - - - +
272C SER* 3.3 13.3 + - - -
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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