Contacts of the helix formed by residues 211 - 224 (chain D) in PDB entry 2XLR
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 SER 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D GLY 3.8 1.6 - - - -
210D SER* 1.3 78.7 - - - +
212D TYR* 1.3 86.2 + - - +
213D SER 3.2 2.2 - - - -
214D ALA* 3.0 4.1 + - - +
215D GLU* 2.9 30.8 + - - +
276D CYS 5.2 0.6 + - - -
501D NAP 2.8 53.5 + - - -
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Residues in contact with TYR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ASP* 4.5 11.9 - - + -
211D SER* 1.3 93.5 + - - +
213D SER* 1.3 57.5 + - - +
215D GLU* 3.3 12.6 + - - +
216D ASP* 2.8 33.8 + - + +
324D TRP* 4.9 9.0 - + - -
405D TRP* 4.2 5.2 - + - -
406D LYS* 3.4 21.9 + - - -
409D LYS* 4.0 24.9 - - - -
501D NAP 3.4 87.7 + + - +
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Residues in contact with SER 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 5.7 0.9 - - - -
191D ALA* 4.1 7.6 - - - +
212D TYR* 1.3 78.1 - - - +
214D ALA* 1.3 56.9 + - - +
216D ASP* 5.1 1.8 - - - -
217D ILE* 2.7 59.3 + - - +
276D CYS* 3.9 11.9 - - - -
279D TYR* 5.0 2.3 + - - -
501D NAP 2.2 41.9 + - - -
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Residues in contact with ALA 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LEU* 4.2 13.5 - - + +
209D GLY 3.2 32.8 - - - +
211D SER 3.0 11.9 + - - +
213D SER* 1.3 77.0 - - - +
215D GLU* 1.3 66.5 + - - +
218D GLY* 3.0 21.8 + - - -
238D MET* 4.1 11.9 - - + -
246D TRP* 4.3 2.3 - - - -
276D CYS* 3.7 20.9 - - + +
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Residues in contact with GLU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D SER 4.9 1.7 - - - +
211D SER* 2.9 24.8 + - - +
212D TYR* 3.6 16.5 + - - +
214D ALA* 1.3 76.6 - - - +
216D ASP* 1.3 63.0 + - + +
219D SER* 2.8 29.4 + - - +
238D MET* 3.7 19.2 - - - +
240D TYR* 3.4 29.6 + - + -
242D TRP* 4.4 16.7 - - + -
246D TRP* 3.8 3.4 - - - -
406D LYS* 5.8 0.2 + - - -
409D LYS* 2.9 31.0 + - - -
413D ILE* 4.6 5.6 - - + +
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Residues in contact with ASP 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D TYR* 2.8 26.6 + - - +
75D LEU* 5.0 5.4 - - - +
76D TRP 5.2 0.5 + - - -
78D ASP* 6.2 0.4 - - - -
212D TYR* 2.8 20.7 + - + +
213D SER* 4.3 1.1 - - - +
215D GLU* 1.3 73.5 - - + +
217D ILE* 1.3 61.3 + - - +
219D SER* 3.3 6.7 + - - -
220D GLN* 2.9 54.4 + - - +
416D PHE* 4.9 4.0 - - - -
417D ARG* 2.8 39.0 + - - -
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Residues in contact with ILE 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D TYR* 4.0 25.1 - - + +
191D ALA* 3.4 39.9 - - + +
194D PHE* 3.5 36.3 - - + -
207D LEU* 4.3 9.0 - - + -
213D SER* 2.7 39.7 + - - +
216D ASP* 1.3 72.8 - - - +
218D GLY* 1.3 62.4 + - - +
220D GLN* 3.2 7.6 + - - +
221D CYS* 3.1 21.8 + - - -
274D ILE* 4.2 14.6 - - + -
276D CYS* 3.9 6.5 - - - -
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Residues in contact with GLY 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LEU* 3.5 22.3 - - - +
214D ALA 3.0 10.1 + - - -
217D ILE* 1.3 74.4 - - - +
219D SER* 1.3 53.0 + - - +
221D CYS* 2.7 27.2 + - - +
222D TYR* 2.8 17.2 + - - +
229D LEU* 3.9 3.0 - - - +
246D TRP* 3.4 24.6 - - - -
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Residues in contact with SER 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D GLU 2.8 18.8 + - - -
216D ASP* 3.5 12.1 + - - -
218D GLY* 1.3 73.0 - - - +
220D GLN* 1.3 60.9 + - - +
222D TYR* 3.2 4.8 + - - +
223D LYS* 2.8 31.2 + - - +
242D TRP* 4.7 1.0 - - - -
246D TRP* 3.4 9.6 - - - -
413D ILE* 5.2 4.7 + - - +
414D MET* 3.6 24.7 - - - +
416D PHE* 6.1 1.0 - - - -
417D ARG* 5.7 0.9 - - - -
437D TRP* 4.0 21.7 - - - -
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Residues in contact with GLN 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D TYR* 3.8 21.5 - - + -
73D ARG 5.0 0.2 - - - +
74D TYR* 3.6 37.6 + - + +
75D LEU* 4.9 0.6 - - - +
76D TRP* 5.3 0.6 - - - +
194D PHE* 4.5 6.7 - - + -
197D ALA* 3.5 17.5 - - + +
216D ASP* 2.9 46.7 + - - +
217D ILE* 3.8 5.2 - - - +
218D GLY 3.1 0.4 - - - -
219D SER* 1.3 78.2 - - - +
221D CYS* 1.3 64.2 + - - +
223D LYS* 4.5 1.9 - - - +
224D TYR* 3.0 36.8 + - + -
417D ARG* 4.3 3.6 - - - +
437D TRP* 3.8 24.1 - - - +
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Residues in contact with CYS 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D PHE* 4.1 23.8 - - - -
197D ALA* 4.2 8.8 - - - +
200D PHE* 4.4 18.8 - - + -
205D VAL* 4.7 12.1 - - - -
207D LEU* 5.3 0.7 - - - -
217D ILE* 3.1 21.0 + - - -
218D GLY* 2.7 13.1 + - - +
220D GLN* 1.3 74.4 - - - +
222D TYR* 1.3 65.0 + - - +
224D TYR 3.1 2.1 + - - -
225D GLY 3.0 7.8 + - - -
226D ALA* 2.9 30.0 + - + -
229D LEU* 3.6 20.4 - - + -
274D ILE* 4.8 0.9 - - - -
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Residues in contact with TYR 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D GLY 2.8 10.6 + - - +
219D SER* 3.4 10.1 - - - +
221D CYS* 1.3 79.0 - - - +
223D LYS* 1.3 67.0 + - + +
224D TYR 3.0 1.4 + - - -
225D GLY* 3.2 9.5 + - - -
226D ALA* 4.3 5.2 + - - +
229D LEU* 3.6 17.8 - - + +
243D PRO* 3.6 28.8 - - + +
245D ASN* 3.7 33.0 - - - -
246D TRP* 4.5 2.5 - - + -
414D MET* 3.8 28.5 - - + -
437D TRP* 5.3 0.7 - + - -
438D ILE* 4.1 23.6 - - + +
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Residues in contact with LYS 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D TYR* 5.7 1.2 + - - +
76D TRP* 4.4 5.9 - - - +
219D SER 2.8 20.5 + - - +
220D GLN* 4.4 1.5 + - - -
222D TYR* 1.3 78.1 - - - +
224D TYR* 1.3 94.0 + - + +
225D GLY 3.5 0.4 + - - -
437D TRP* 2.7 69.2 + - + +
438D ILE* 3.8 21.8 - - + +
440D ALA* 2.5 33.9 + - - +
441D LEU* 4.1 13.2 - - + +
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Residues in contact with TYR 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D TYR* 3.1 59.2 - + - +
76D TRP* 6.0 0.2 + - - -
197D ALA* 4.0 13.8 - - + +
198D LEU* 3.9 28.7 - - + +
201D LYS* 3.7 18.9 - - - +
220D GLN* 3.0 35.0 + - - +
221D CYS 3.5 3.1 - - - +
222D TYR 3.1 0.2 - - - -
223D LYS* 1.3 114.8 + - + +
225D GLY* 1.3 59.6 + - - +
226D ALA 3.8 0.2 - - - -
440D ALA 3.9 0.7 + - - -
441D LEU* 2.6 45.7 + - + -
443D ASP* 5.3 0.5 - - - +
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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