Contacts of the helix formed by residues 211 - 224 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209C GLY 3.8 1.0 - - - -
210C SER* 1.3 79.6 - - - +
212C TYR* 1.3 84.5 + - - -
213C SER 3.3 2.2 - - - -
214C ALA* 3.1 3.9 + - - +
215C GLU* 3.1 30.7 + - - +
276C CYS 5.2 0.8 + - - -
501C NAP 2.9 52.9 + - - -
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Residues in contact with TYR 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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78C ASP* 4.4 11.2 - - + -
211C SER* 1.3 91.9 + - - +
213C SER* 1.3 57.1 + - - +
215C GLU* 3.3 12.6 + - - +
216C ASP* 2.8 32.8 + - - +
324C TRP* 5.0 7.8 - + - -
374C TYR* 5.0 0.2 + - - -
405C TRP* 4.2 7.6 - + - -
406C LYS* 3.4 19.7 + - - -
409C LYS* 3.9 24.9 - - - -
501C NAP 3.3 90.1 + + - +
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Residues in contact with SER 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C TYR* 5.8 0.7 - - - -
191C ALA* 4.0 12.0 - - - +
212C TYR* 1.3 74.8 - - - +
214C ALA* 1.3 62.6 + - - +
216C ASP* 4.6 1.8 - - - +
217C ILE* 2.8 48.2 + - - +
276C CYS* 3.6 18.4 - - - -
279C TYR* 5.1 2.6 + - - -
500C FAD 5.9 2.6 - - - +
501C NAP 2.7 34.3 + - - -
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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
----------------------------------------------------------
207C LEU* 4.3 13.1 - - + +
209C GLY 3.4 31.9 - - - +
211C SER 3.1 10.4 + - - +
213C SER* 1.3 78.8 - - - +
215C GLU* 1.3 65.7 + - - +
218C GLY* 2.9 22.5 + - - -
238C MET* 4.0 13.2 - - + -
246C TRP* 4.2 2.9 - - - -
276C CYS* 3.8 19.2 - - + +
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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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210C SER 4.7 1.7 - - - +
211C SER* 3.1 20.5 + - - +
212C TYR* 3.5 17.3 + - - +
214C ALA* 1.3 79.0 - - - +
216C ASP* 1.3 58.5 + - + +
219C SER* 2.8 32.1 + - - -
238C MET* 3.7 17.9 - - - +
240C TYR* 3.6 30.2 + - + -
242C TRP* 4.5 15.6 - - + -
246C TRP* 3.8 2.9 - - - -
409C LYS* 2.9 29.5 + - - -
413C ILE* 4.6 6.4 - - + +
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Residues in contact with ASP 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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72C TYR* 2.6 29.6 + - - +
75C LEU* 4.9 5.4 - - - +
78C ASP* 6.2 0.4 - - - -
212C TYR* 2.8 20.4 + - + +
213C SER* 4.5 0.9 - - - +
215C GLU* 1.3 74.1 - - + +
217C ILE* 1.3 63.7 + - - +
219C SER* 3.3 5.7 + - - -
220C GLN* 3.0 46.7 + - - +
416C PHE* 5.2 2.3 - - - -
417C ARG* 2.9 38.6 + - - -
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Residues in contact with ILE 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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72C TYR* 4.0 25.4 - - + +
191C ALA* 3.3 41.7 - - + +
194C PHE* 3.7 37.0 - - + -
207C LEU* 4.1 9.4 - - + -
213C SER* 2.8 31.1 + - - +
216C ASP* 1.3 71.9 - - - +
218C GLY* 1.3 62.4 + - - +
220C GLN* 3.3 7.8 + - - +
221C CYS* 3.1 22.5 + - - -
274C ILE* 3.9 17.3 - - + -
276C CYS* 3.9 6.3 - - - -
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Residues in contact with GLY 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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207C LEU* 3.6 18.6 - - - +
214C ALA 2.9 12.7 + - - -
217C ILE* 1.3 77.6 - - - +
219C SER* 1.3 56.2 + - - +
221C CYS* 3.0 9.1 + - - +
222C TYR* 2.9 27.7 + - - +
229C LEU* 3.9 2.8 - - - +
246C TRP* 3.4 24.6 - - - -
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Residues in contact with SER 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 19.6 + - - -
216C ASP* 3.3 12.8 + - - -
218C GLY* 1.3 73.5 - - - +
220C GLN* 1.3 57.3 + - - +
222C TYR* 3.4 5.3 + - - +
223C LYS* 2.9 30.3 + - - +
242C TRP* 4.9 0.9 - - - -
246C TRP* 3.5 8.6 - - - -
413C ILE* 5.1 4.9 + - - +
414C MET* 3.6 23.7 - - - +
417C ARG* 5.7 0.4 - - - -
437C TRP* 3.8 23.6 - - - -
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Residues in contact with GLN 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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72C TYR* 3.9 21.9 - - + -
73C ARG 4.8 1.1 - - - +
74C TYR* 3.4 38.0 + - + +
75C LEU* 5.0 0.8 - - - +
76C TRP 5.4 0.4 - - - +
194C PHE* 4.5 6.1 - - + -
197C ALA* 3.8 15.7 - - + -
216C ASP* 3.0 38.6 + - - +
217C ILE* 3.8 5.8 - - - +
219C SER* 1.3 74.4 - - - +
221C CYS* 1.3 58.5 + - - +
223C LYS* 4.4 2.6 + - - +
224C TYR* 2.9 44.9 + - + +
417C ARG* 4.5 3.6 - - - +
437C TRP* 3.8 24.5 - - - +
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Residues in contact with CYS 221 (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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194C PHE* 4.0 25.1 - - - -
197C ALA* 4.2 8.9 - - - +
200C PHE* 4.2 21.1 - - + -
205C VAL* 4.6 14.8 - - + -
207C LEU* 5.5 0.4 - - - -
217C ILE* 3.1 19.6 + - - -
218C GLY* 3.0 10.1 + - - +
220C GLN* 1.3 76.0 - - - +
222C TYR* 1.3 61.6 + - - +
224C TYR 3.4 1.4 + - - -
225C GLY 3.2 5.9 + - - -
226C ALA* 2.9 33.8 + - + +
229C LEU* 3.7 17.5 - - + -
274C ILE* 4.7 0.2 - - - -
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Residues in contact with TYR 222 (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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218C GLY 2.9 12.9 + - - +
219C SER* 3.5 9.9 - - - +
221C CYS* 1.3 77.5 - - - +
223C LYS* 1.3 65.5 + - + +
224C TYR 3.2 0.5 + - - -
225C GLY* 3.3 9.4 + - - -
226C ALA* 4.4 5.0 + - - +
229C LEU* 3.7 17.3 - - + +
243C PRO* 3.6 35.0 - - + +
245C ASN* 3.7 27.4 - - - -
246C TRP* 4.5 3.4 - - + -
414C MET* 3.9 26.7 - - + -
437C TRP* 5.3 0.4 - + - -
438C ILE* 3.9 25.0 - - + +
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Residues in contact with LYS 223 (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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74C TYR* 5.6 1.2 + - - +
76C TRP* 4.4 6.5 - - - +
219C SER 2.9 18.3 + - - +
220C GLN* 3.8 5.4 + - - +
222C TYR* 1.3 81.2 - - - +
224C TYR* 1.3 94.0 + - + +
225C GLY 3.7 0.3 + - - -
437C TRP* 2.8 70.1 + - + +
438C ILE* 3.9 24.2 - - + +
440C ALA 3.0 21.7 + - - -
441C LEU* 4.1 14.1 - - + +
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Residues in contact with TYR 224 (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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74C TYR* 3.1 63.2 - + + +
197C ALA* 3.8 16.2 - - + -
198C LEU* 3.8 34.4 - - + +
201C LYS* 3.8 13.7 - - - +
220C GLN* 2.9 26.8 + - - +
221C CYS 3.8 2.5 - - - +
222C TYR 3.2 0.2 - - - -
223C LYS* 1.3 112.0 + - + +
225C GLY* 1.3 55.9 + - - +
226C ALA 3.9 0.2 - - - -
440C ALA 4.0 0.7 + - - -
441C LEU* 2.7 45.4 + - + -
443C ASP* 5.4 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