Contacts of the helix formed by residues 210 - 220 (chain C) in PDB entry 3Q29
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 210 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C SO4 2.9 21.4 + - - +
151C ASN* 3.4 11.9 - - - -
153C GLN* 3.7 14.1 - - + -
208C ASP 3.3 3.4 + - - +
209C THR* 1.3 75.5 - - - +
211C TYR* 1.3 62.2 + - - +
212C SER* 3.3 8.4 + - - -
213C ILE* 2.9 39.8 + - - +
214C ALA* 3.0 24.8 + - - +
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Residues in contact with TYR 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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1C SO4 2.8 24.1 + - - +
15C ASP* 4.4 15.5 - - + +
151C ASN* 3.3 19.0 + - + +
157C PHE* 3.9 22.0 - + - -
210C ASP* 1.3 72.2 - - - +
212C SER* 1.3 61.2 + - - +
214C ALA* 3.9 1.9 - - - +
215C GLU* 2.9 57.9 + - - +
228C ASN* 3.3 36.1 + - - -
231C TRP* 3.0 32.9 + + - -
232C ALA* 3.9 6.1 - - - +
1D GLC 6.0 0.4 - - - -
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Residues in contact with SER 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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1C SO4 4.4 1.1 + - - -
210C ASP* 3.3 10.6 + - - -
211C TYR* 1.3 83.7 - - - +
213C ILE* 1.3 61.1 + - - +
215C GLU* 3.9 7.6 - - - +
216C ALA* 2.9 31.7 + - - +
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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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149C MET* 3.7 21.5 - - + -
208C ASP* 4.2 14.1 - - + +
209C THR* 4.2 8.3 - - + +
210C ASP* 2.9 32.5 + - - +
212C SER* 1.3 76.0 - - - +
214C ALA* 1.3 65.7 + - - +
216C ALA* 3.4 4.6 + - - +
217C ALA* 3.0 23.8 + - + +
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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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149C MET* 3.7 20.1 - - - +
150C PHE* 3.5 36.6 - - - +
151C ASN 4.1 1.3 - - - +
209C THR* 3.9 4.3 - - + -
210C ASP 3.0 16.9 + - - +
211C TYR* 4.0 2.9 - - - +
213C ILE* 1.3 76.5 - - - +
215C GLU* 1.3 58.3 + - - +
217C ALA* 3.3 2.4 + - - +
218C PHE* 2.9 30.0 + - - +
226C THR* 4.3 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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211C TYR* 2.9 46.5 + - + +
212C SER* 3.9 7.6 - - - +
214C ALA* 1.3 77.2 - - - +
216C ALA* 1.3 57.5 + - - +
218C PHE* 3.3 3.7 + - - -
219C ASN* 2.8 51.2 + - - +
226C THR* 5.5 2.7 - - - -
228C ASN* 5.3 7.2 - - - +
232C ALA* 5.0 7.1 - - + +
235C ASN* 2.9 35.6 + - - +
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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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212C SER 2.9 18.4 + - - +
213C ILE* 3.8 4.9 - - - +
215C GLU* 1.3 76.6 + - - +
217C ALA* 1.3 58.0 + - - +
219C ASN* 3.8 2.9 - - - -
220C LYS* 2.9 58.5 + - + +
222C GLU* 5.0 0.2 - - - -
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Residues in contact with ALA 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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149C MET* 3.4 34.3 - - + -
213C ILE* 3.0 16.3 + - + +
214C ALA 3.7 2.7 - - - +
216C ALA* 1.3 78.8 - - - +
218C PHE* 1.3 59.8 + - - +
221C GLY 3.3 2.6 + - - -
222C GLU* 2.8 54.5 + - + +
223C THR* 3.5 6.4 + - + -
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Residues in contact with PHE 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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117C ILE* 3.8 22.9 - - + -
118C TYR* 3.6 23.6 - - - -
119C ASN* 3.6 10.2 + - + -
214C ALA 2.9 17.5 + - - +
215C GLU* 3.9 3.8 - - - +
217C ALA* 1.3 76.5 - - - +
219C ASN* 1.3 72.9 + - - +
220C LYS 3.2 0.7 - - - -
221C GLY* 3.2 16.8 + - - -
223C THR* 3.6 24.0 - - + +
224C ALA 3.5 22.2 - - - -
225C MET 3.9 14.8 - - - -
226C THR* 3.9 17.5 - - + -
236C ILE* 3.8 27.4 - - + -
241C VAL* 3.9 13.5 - - + +
243C TYR* 4.1 5.4 - - + -
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Residues in contact with ASN 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* 2.8 42.2 + - + +
216C ALA* 4.2 3.1 - - - +
218C PHE* 1.3 94.4 - - - +
220C LYS* 1.3 61.7 + - + +
221C GLY 3.4 1.6 - - - -
235C ASN* 3.7 27.3 - - - +
236C ILE* 3.5 21.1 + - - +
239C SER* 3.2 32.1 - - - +
241C VAL* 3.6 7.9 - - - +
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Residues in contact with LYS 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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145C LYS* 5.2 1.6 + - - -
216C ALA* 2.9 38.2 + - + +
219C ASN* 1.3 80.1 - - + +
221C GLY* 1.3 61.6 + - - +
222C GLU* 3.4 26.5 + - - +
241C VAL* 5.0 1.3 - - - -
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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