Contacts of the helix formed by residues 209 - 219 (chain C) in PDB entry 3IOT
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 ASP 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C ASN* 3.4 17.3 - - - +
152C GLN* 3.8 16.4 - - + -
207C ASP 3.2 5.0 + - - +
208C THR* 1.3 74.4 - - - +
210C TYR* 1.3 64.0 + - - +
211C SER* 3.1 9.9 + - - -
212C ILE* 2.8 40.9 + - - +
213C ALA* 3.3 22.9 + - - +
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Residues in contact with TYR 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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150C ASN* 3.6 24.6 - - + +
156C PHE* 4.7 16.8 - + - -
209C ASP* 1.3 77.6 - - - +
211C SER* 1.3 62.2 + - - +
213C ALA* 3.3 3.9 + - + +
214C GLU* 2.9 50.9 + - + +
227C ASN* 2.7 37.1 + - - -
230C TRP* 3.2 29.7 + + - -
231C ALA* 3.7 7.6 - - - +
234C ASN* 5.8 0.2 + - - -
417C LEU* 3.5 42.6 - - + -
418C PRO* 4.9 7.9 - - + -
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Residues in contact with SER 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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209C ASP* 3.1 10.1 + - - -
210C TYR* 1.3 80.3 - - - +
212C ILE* 1.3 64.9 + - - +
214C GLU* 3.9 9.7 - - - +
215C ALA* 3.0 26.9 + - - +
417C LEU* 6.1 2.1 - - - +
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Residues in contact with ILE 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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148C MET* 3.7 20.6 - - + -
207C ASP* 3.6 24.7 - - + +
208C THR* 4.4 7.0 - - + +
209C ASP* 2.8 33.3 + - - +
211C SER* 1.3 74.6 - - - +
213C ALA* 1.3 57.4 - - - +
215C ALA* 3.7 4.7 - - - +
216C ALA* 2.9 29.4 + - + +
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Residues in contact with ALA 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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148C MET* 3.7 31.2 - - - +
149C PHE* 3.7 17.5 - - - -
150C ASN 4.0 1.6 - - - +
208C THR* 4.0 5.8 - - + -
209C ASP 3.3 19.0 + - - +
210C TYR* 3.3 6.4 + - + +
212C ILE* 1.3 78.6 - - - +
214C GLU* 1.3 62.8 + - - +
216C ALA* 3.3 3.8 + - - +
217C PHE* 3.1 22.5 + - - +
222C THR* 4.8 0.3 - - - +
225C THR* 4.5 5.6 + - - +
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Residues in contact with GLU 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 TYR* 2.9 51.1 + - + +
211C SER* 3.9 8.8 - - - +
213C ALA* 1.3 71.6 - - - +
215C ALA* 1.3 58.2 + - - +
217C PHE* 3.3 5.1 + - - +
218C ASN* 2.9 52.9 + - - +
225C THR* 5.1 3.6 + - - -
227C ASN* 5.2 5.2 - - - +
231C ALA* 4.4 6.6 - - + +
234C ASN* 3.4 32.5 + - + +
235C ILE* 6.3 0.9 - - + -
419C GLN 4.5 11.7 + - - +
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Residues in contact with ALA 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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211C SER 3.0 19.8 + - - +
212C ILE* 3.7 4.5 - - - +
214C GLU* 1.3 74.5 - - - +
216C ALA* 1.3 66.0 + - - +
218C ASN* 3.8 5.6 - - - +
219C LYS* 2.9 46.6 + - - +
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Residues in contact with ALA 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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148C MET* 3.7 31.0 - - + -
212C ILE* 2.9 19.3 + - + +
213C ALA 3.5 5.2 - - - +
215C ALA* 1.3 75.1 - - - +
217C PHE* 1.3 59.7 + - - +
219C LYS 3.8 0.2 + - - -
220C GLY 3.4 2.3 + - - -
221C GLU* 2.9 50.7 + - + +
222C THR* 3.3 9.5 + - + -
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Residues in contact with PHE 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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116C ILE* 3.7 29.2 - - + -
117C TYR* 3.5 27.1 - - - -
118C ASN* 3.4 28.8 + - + -
213C ALA 3.1 11.8 + - - +
214C GLU* 3.7 7.4 - - - +
216C ALA* 1.3 75.4 - - - +
218C ASN* 1.3 74.4 + - - +
220C GLY* 2.9 21.0 + - - -
222C THR* 3.4 27.5 - - + +
223C ALA 3.8 5.4 - - - -
224C MET 4.2 2.7 - - - -
225C THR* 3.6 24.2 - - + -
235C ILE* 3.9 21.3 - - + -
240C VAL* 4.8 10.2 - - + +
242C TYR* 4.2 4.7 - - + -
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Residues in contact with ASN 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 GLU* 2.9 40.3 + - - +
215C ALA* 4.0 5.3 - - - +
217C PHE* 1.3 94.0 - - - +
219C LYS* 1.3 61.9 + - + +
220C GLY 3.3 0.4 + - - -
234C ASN* 4.1 17.6 - - - +
235C ILE* 3.7 23.0 - - - +
238C SER* 3.4 33.4 + - - +
240C VAL* 4.3 7.6 - - - +
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Residues in contact with LYS 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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144C LYS* 5.3 1.0 + - - -
215C ALA* 2.9 33.7 + - + +
216C ALA 4.8 0.2 - - - +
218C ASN* 1.3 76.8 - - + +
220C GLY* 1.3 61.5 + - - +
221C GLU* 3.4 36.8 + - - +
240C VAL* 5.4 2.2 - - - -
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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