Contacts of the helix formed by residues 208 - 221 (chain A) in PDB entry 1XR2
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 GLU 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ARG* 5.2 6.2 - - - +
167A PRO* 3.6 22.8 - - - +
206A ASP 5.3 0.4 - - - +
207A LEU* 1.3 79.7 - - - +
209A LYS* 1.3 68.1 + - - +
210A ALA* 3.0 7.5 - - + +
211A HIS* 2.9 41.8 + - + +
212A TRP* 3.4 8.8 + - - -
206B ASP* 3.4 37.2 - - - +
207B LEU 3.4 10.8 - - - +
208B GLU* 3.9 19.3 - - + +
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Residues in contact with LYS 209 (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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208A GLU* 1.3 72.0 - - - +
210A ALA* 1.3 64.1 + - - +
212A TRP* 2.9 23.6 + - + +
213A ASP* 3.1 24.4 + - - +
238A ASP* 3.0 30.2 + - - +
240A GLU* 6.1 1.4 - - - +
241A ALA* 4.8 7.5 - - - +
207B LEU 3.4 11.0 + - - +
208B GLU* 4.9 0.6 - - - +
209B LYS* 4.0 12.7 - - - +
212B TRP* 6.2 0.4 - - + +
237B SER* 3.4 27.8 - - - +
238B ASP* 4.1 23.4 + - + +
240B GLU* 6.1 1.6 - - - +
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Residues in contact with ALA 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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167A PRO* 3.9 14.1 - - + -
208A GLU* 3.0 8.4 - - + +
209A LYS* 1.3 81.0 - - - +
211A HIS* 1.3 61.7 + - - +
213A ASP* 3.4 13.5 + - - +
214A LEU* 3.4 25.7 + - + +
206B ASP* 3.9 13.0 - - - +
590B SER* 3.6 31.4 - - - +
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Residues in contact with HIS 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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151A PHE* 3.7 26.2 - + + -
155A TYR* 4.9 1.9 - + - -
165A ARG 2.6 30.2 + - - -
166A ARG* 4.9 0.4 - - - -
167A PRO* 3.5 25.9 - - + +
170A MET* 4.3 5.2 - - - -
206A ASP 5.4 0.9 - - - -
207A LEU* 3.7 32.1 - - + +
208A GLU* 2.9 49.0 + - + +
210A ALA* 1.3 76.8 - - - +
212A TRP* 1.3 59.4 + - - +
214A LEU* 3.0 11.4 + - + +
215A ILE* 2.9 30.1 + - - +
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Residues in contact with TRP 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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203A PHE* 3.8 33.2 - + - -
207A LEU* 4.0 16.5 + - + +
208A GLU 3.4 18.3 + - - -
209A LYS* 2.9 13.0 + - + +
211A HIS* 1.3 75.5 - - - +
213A ASP* 1.3 65.4 + - - +
215A ILE* 3.7 24.1 - - + +
216A LEU* 3.0 23.9 + - - +
236A VAL* 3.7 28.3 - - + -
237A SER* 3.1 29.5 + - - -
238A ASP* 3.3 24.4 - - + +
241A ALA* 3.9 28.9 - - + +
242A CYS* 3.7 23.1 - - + -
245A LEU* 4.3 3.3 - - + +
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Residues in contact with ASP 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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209A LYS* 3.1 28.5 + - - +
210A ALA* 3.8 14.6 - - - +
211A HIS 3.2 0.4 - - - -
212A TRP* 1.3 77.5 - - - +
214A LEU* 1.3 64.5 + - + +
216A LEU* 3.5 9.3 + - - +
217A ASN* 3.2 29.2 + - - +
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Residues in contact with LEU 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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151A PHE* 5.4 2.2 - - + -
167A PRO* 3.6 39.7 - - + +
170A MET* 4.2 7.6 - - + -
171A GLU* 3.9 32.5 - - + +
174A LEU* 4.0 20.9 - - + -
210A ALA* 3.4 13.2 - - + +
211A HIS* 3.0 12.6 + - - +
213A ASP* 1.3 80.7 - - + +
215A ILE* 1.3 66.9 + - + +
217A ASN* 3.0 13.2 + - - +
218A VAL* 2.9 27.3 + - - +
590B SER* 6.1 2.7 - - - +
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Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A PHE* 3.6 34.3 - - + -
203A PHE* 3.3 48.2 - - + -
207A LEU* 4.1 9.4 - - + -
211A HIS 2.9 19.5 + - - +
212A TRP* 3.3 24.0 + - + +
214A LEU* 1.3 76.1 - - - +
216A LEU* 1.3 60.1 + - - +
218A VAL* 3.7 6.2 - - - +
219A TYR* 3.1 29.0 + - + +
245A LEU* 3.8 22.8 - - + +
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Residues in contact with LEU 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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212A TRP 3.0 16.9 + - - +
213A ASP* 3.7 9.4 - - - +
214A LEU 3.1 0.4 - - - -
215A ILE* 1.3 74.6 - - - +
217A ASN* 1.3 65.5 + - - +
219A TYR* 4.0 0.2 - - - -
220A ARG* 2.9 35.6 + - + +
244A SER* 4.5 9.0 - - - +
245A LEU* 4.0 15.9 - - + -
246A PRO* 3.6 26.9 - - + -
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Residues in contact with ASN 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 ASP* 3.2 20.8 + - - +
214A LEU* 3.0 13.1 + - - +
216A LEU* 1.3 80.6 - - - +
218A VAL* 1.3 69.3 + - + +
220A ARG* 3.3 7.3 + - - +
221A GLU* 3.3 19.8 + - - +
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Residues in contact with VAL 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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150A PRO* 3.6 29.2 - - + -
151A PHE* 5.5 4.0 - - + +
174A LEU* 3.8 32.8 - - + -
178A VAL* 3.6 24.5 - - + +
214A LEU 2.9 17.6 + - - +
215A ILE* 3.7 10.3 - - - +
216A LEU 3.3 0.2 - - - -
217A ASN* 1.3 79.3 - - + +
219A TYR* 1.3 74.8 + - + +
221A GLU* 3.3 15.7 + - - +
222A LEU* 3.5 13.5 + - + +
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Residues in contact with TYR 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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150A PRO* 3.6 7.6 - - + +
151A PHE* 5.4 2.0 - - + -
198A VAL* 3.4 15.3 - - + +
200A GLU* 2.7 39.6 + - + +
203A PHE* 4.1 15.9 - + - -
215A ILE* 3.1 28.5 + - + +
216A LEU 4.4 0.9 - - - +
218A VAL* 1.3 87.1 - - + +
220A ARG* 1.3 66.9 + - - +
221A GLU 3.0 1.8 - - - -
222A LEU* 2.8 31.2 + - + +
223A SER* 3.0 13.0 + - - -
227A LEU* 4.5 13.2 - - + -
229A VAL* 3.9 18.2 - - + -
245A LEU* 4.5 9.0 - - + -
246A PRO* 3.8 19.7 - - + +
247A VAL* 4.0 20.2 - - + -
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Residues in contact with ARG 220 (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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216A LEU* 2.9 25.6 + - + +
217A ASN* 3.3 8.0 + - - +
219A TYR* 1.3 76.0 - - - +
221A GLU* 1.3 57.8 + - - +
223A SER* 3.0 23.6 + - - -
246A PRO* 3.6 16.9 - - + +
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Residues in contact with GLU 221 (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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178A VAL* 4.2 15.9 - - + +
182A LYS* 5.7 1.7 - - - +
217A ASN 3.3 8.8 + - - +
218A VAL* 3.3 12.9 + - - +
219A TYR 3.0 0.6 - - - -
220A ARG* 1.3 79.8 - - - +
222A LEU* 1.3 63.4 + - - +
223A SER 3.4 0.4 - - - -
224A GLU* 5.1 1.7 + - - +
225A PHE* 4.5 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