Contacts of the helix formed by residues 209 - 219 (chain A) in PDB entry 3RIE
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 ASN 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A GLU 4.1 4.2 + - - -
206A THR* 3.2 32.3 + - - +
207A LEU 3.7 1.4 + - - -
208A PHE* 1.3 77.9 - - - +
210A GLN* 1.3 67.4 + - - +
211A ASN* 3.3 17.5 + - - +
212A PHE* 2.9 41.1 + - - +
213A TYR* 3.4 15.6 + - - -
243A MET* 4.8 0.6 - - - -
246A TYR* 3.9 13.6 - - + +
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Residues in contact with GLN 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ASN* 1.3 75.0 - - - +
211A ASN* 1.3 66.9 + - - +
213A TYR* 3.1 11.3 + - - -
214A GLU* 3.1 15.3 + - + +
245A GLY 4.4 0.4 + - - -
246A TYR* 3.0 64.4 - - + +
249A LYS* 3.9 34.3 - - + +
250A LEU* 3.9 11.1 - - - +
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Residues in contact with ASN 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ASN* 3.3 14.2 + - - +
210A GLN* 1.3 80.7 - - - +
212A PHE* 1.3 62.9 + - - +
214A GLU* 3.4 17.1 + - - +
215A LYS* 3.2 38.2 + - - +
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Residues in contact with PHE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 4.5 5.2 - - + -
179A ALA* 4.9 1.3 - - + -
180A SER* 5.0 7.0 - - - -
183A LEU* 3.4 24.2 - - + -
195A VAL* 4.0 28.9 - - + -
206A THR 3.9 9.4 - - - +
207A LEU* 3.2 57.2 - - + -
209A ASN* 2.9 22.9 + - - +
210A GLN 3.2 0.2 - - - -
211A ASN* 1.3 76.0 - - - +
213A TYR* 1.3 74.6 + + - +
215A LYS* 3.3 13.5 + - + +
216A ILE* 3.1 53.6 + - + +
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Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A LEU 4.3 8.5 + - - -
209A ASN 3.5 13.9 - - - -
210A GLN* 3.1 10.2 + - - +
212A PHE* 1.3 96.6 - + - +
214A GLU* 1.3 60.1 + - - +
216A ILE* 3.3 8.8 + - + +
217A TYR* 2.9 28.1 + - - +
226A CYS* 4.8 12.6 - - - -
228A ALA* 3.3 26.3 - - + +
243A MET* 4.4 19.7 - - - -
246A TYR* 4.2 23.3 - - + +
247A ALA* 4.6 7.9 - - + -
250A LEU* 3.5 14.7 - - + +
251A PHE* 4.0 17.2 - + + -
272A LEU* 3.5 24.5 - - + +
274A CYS* 4.3 10.8 - - - -
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Residues in contact with GLU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLN* 3.1 12.6 + - + +
211A ASN* 3.6 19.5 - - - +
213A TYR* 1.3 73.6 - - - +
215A LYS* 1.3 65.2 + - + +
217A TYR* 3.3 1.9 + - - +
218A ASN* 3.0 44.2 + - - +
250A LEU* 3.3 27.2 - - + +
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Residues in contact with LYS 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A SER* 2.9 44.0 + - - +
183A LEU* 3.9 29.9 - - + +
184A GLU* 2.7 41.7 + - + +
211A ASN* 3.2 28.8 + - - +
212A PHE* 3.3 13.5 + - + +
214A GLU* 1.3 79.7 - - + +
216A ILE* 1.3 62.1 + - - +
218A ASN* 3.5 7.0 + - - +
219A ALA* 3.1 24.6 + - - +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 4.9 0.7 - - + -
183A LEU* 3.6 22.0 - - + -
193A ILE* 3.7 32.7 - - + +
195A VAL* 4.0 6.1 - - + -
212A PHE* 3.1 40.2 + - + +
213A TYR* 3.5 12.8 - - + +
215A LYS* 1.3 71.3 - - - +
217A TYR* 1.4 69.7 + - - +
219A ALA* 3.2 3.5 + - - -
220A LEU* 3.2 22.8 + - + +
226A CYS* 3.6 33.0 - - + -
251A PHE* 4.1 9.6 - - + -
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Residues in contact with TYR 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A TYR 2.9 14.0 + - - +
214A GLU 3.3 8.3 + - - +
216A ILE* 1.4 77.6 - - - +
218A ASN* 1.3 71.5 + - - +
220A LEU 3.1 10.6 + - - -
250A LEU* 3.4 49.7 + - + -
251A PHE* 3.7 24.2 - + + -
276A LYS* 2.8 67.1 + - + +
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Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A THR* 3.7 15.1 - - - +
214A GLU* 3.0 36.9 + - - +
215A LYS* 3.8 7.4 - - - +
217A TYR* 1.3 90.4 - - - +
219A ALA* 1.3 60.7 + - - +
220A LEU 3.2 3.5 + - - +
276A LYS* 5.1 0.2 - - - +
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Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 4.0 18.6 - - + +
186A VAL* 4.4 17.3 - - + -
188A ASN 4.8 1.1 - - - +
189A THR* 3.3 10.5 - - - +
190A TYR* 2.8 30.7 + - + +
193A ILE* 3.9 16.6 - - + +
215A LYS 3.1 17.2 + - - +
216A ILE 3.2 1.3 + - - -
218A ASN* 1.3 74.9 - - - +
220A LEU* 1.4 59.0 + - - +
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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