Contacts of the helix formed by residues 209 - 224 (chain C) in PDB entry 2QLR
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 THR 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C SER* 3.8 18.6 + - - +
207C SER 3.7 2.4 + - - +
208C LEU* 1.3 76.0 - - - +
210C SER* 1.3 65.6 - - - +
211C GLU* 2.9 21.8 + - - +
212C ARG* 3.0 39.8 + - - +
213C LYS* 3.2 11.3 + - - +
243C VAL* 3.9 3.4 - - - -
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Residues in contact with SER 210 (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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209C THR* 1.3 71.6 - - - +
211C GLU* 1.3 69.0 + - - +
213C LYS* 3.3 14.2 + - - +
214C LYS* 3.1 40.4 + - - +
243C VAL* 3.4 23.6 - - - +
244C PRO* 4.4 17.6 - - - +
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Residues in contact with GLU 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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209C THR* 3.1 24.4 - - - +
210C SER* 1.3 79.2 + - - +
212C ARG* 1.3 65.2 + - + +
214C LYS* 3.5 18.7 + - - +
215C GLU* 3.5 25.9 + - - +
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Residues in contact with ARG 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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162C ASP* 2.4 43.6 + - - -
164C SER* 3.5 26.3 + - - -
165C GLY 3.1 17.0 + - - -
166C ILE 3.3 17.3 + - - -
167C VAL* 3.8 13.9 - - - +
168C PRO* 3.7 17.7 - - + +
208C LEU* 3.5 15.0 - - + -
209C THR* 3.0 20.9 + - - +
211C GLU* 1.3 82.0 - - + +
213C LYS* 1.3 56.7 + - - +
215C GLU* 3.4 10.9 + - - +
216C ILE* 2.9 36.0 + - - +
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Residues in contact with LYS 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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198C PRO* 3.7 31.8 - - - +
199C ASN* 4.4 12.3 + - - +
208C LEU* 3.8 18.8 - - + -
209C THR 3.2 11.6 + - - +
210C SER* 3.5 8.5 - - - +
212C ARG* 1.3 73.4 - - - +
214C LYS* 1.3 60.3 + - - +
216C ILE* 3.7 1.2 - - - +
217C TYR* 2.8 33.6 + - - +
229C GLU* 4.4 2.0 + - - -
243C VAL* 4.0 16.0 + - + +
244C PRO 3.2 28.9 + - - +
245C THR* 3.9 10.5 - - - +
246C PHE* 3.5 38.2 - - + +
249C MET* 3.9 11.9 - - - -
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Residues in contact with LYS 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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210C SER* 3.1 38.2 + - - +
211C GLU* 3.5 15.1 + - - +
212C ARG 3.5 0.4 - - - -
213C LYS* 1.3 76.4 - - - +
215C GLU* 1.3 56.6 + - - +
217C TYR* 3.8 2.4 - - - +
218C GLU* 3.0 36.3 + - - +
249C MET* 3.2 26.5 - - + +
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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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168C PRO* 3.1 40.1 - - + +
169C ASP* 4.4 3.5 - - - +
172C ARG* 3.5 23.5 + - - +
211C GLU* 3.5 15.0 + - - +
212C ARG* 3.4 12.0 + - - +
214C LYS* 1.3 74.8 - - - +
216C ILE* 1.3 65.4 + - - +
218C GLU* 3.3 9.4 + - - +
219C LEU* 3.0 28.5 + - - +
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Residues in contact with ILE 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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166C ILE* 2.7 46.7 - - + -
168C PRO* 4.3 12.6 - - + -
171C LEU* 3.3 18.5 - - + +
194C LEU* 3.5 26.9 - - + -
208C LEU* 4.6 5.4 - - + -
212C ARG 2.9 33.0 + - - +
213C LYS* 3.7 4.7 - - - +
215C GLU* 1.3 73.6 - - - +
217C TYR* 1.3 58.6 - - - +
219C LEU* 3.3 6.6 - - - +
220C ALA* 3.0 24.5 + - + +
225C PHE* 4.9 0.6 - - + -
227C ILE* 4.1 5.4 - - + -
246C PHE* 4.0 18.6 - - + -
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Residues in contact with TYR 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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213C LYS 2.8 17.9 + - - +
214C LYS 3.8 0.7 - - - +
216C ILE* 1.3 78.4 - - - +
218C GLU* 1.3 55.8 + - + +
220C ALA* 3.3 2.6 + - - +
221C ARG* 2.9 43.5 + - + +
227C ILE* 3.9 22.7 - - + -
246C PHE* 4.6 2.5 - + + -
249C MET* 3.5 44.0 - - + -
250C ASP* 2.9 34.9 + - - -
251C VAL* 3.5 5.6 + - + -
252C ASP* 2.9 40.1 + - - +
254C ARG* 3.4 18.7 - - + +
255C VAL* 4.0 9.0 - - + -
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Residues in contact with GLU 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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214C LYS* 3.0 23.6 + - - +
215C GLU* 3.3 9.2 + - - +
217C TYR* 1.3 75.3 - - + +
219C LEU* 1.3 57.7 + - - +
221C ARG* 3.0 21.5 - - - +
222C LYS* 2.9 26.7 + - - +
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Residues in contact with LEU 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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168C PRO* 4.5 6.5 - - + +
171C LEU* 4.6 11.4 - - + -
172C ARG* 3.5 59.2 - - + +
175C LEU* 3.7 18.2 - - + -
215C GLU 3.0 19.5 + - - +
216C ILE* 3.3 9.0 - - - +
218C GLU* 1.3 72.6 - - - +
220C ALA* 1.3 61.6 + - - +
222C LYS* 3.3 14.6 + - + +
223C TYR* 2.9 61.3 + - + +
225C PHE* 3.7 2.5 - - + -
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Residues in contact with ALA 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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216C ILE 3.0 8.3 + - - +
217C TYR 3.4 8.7 - - - +
219C LEU* 1.3 70.3 - - - +
221C ARG* 1.3 67.3 + - - +
224C ASP* 2.7 25.6 + - - -
225C PHE* 3.1 45.1 + - + +
227C ILE* 3.7 19.5 - - + -
254C ARG* 3.7 12.6 + - - -
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Residues in contact with ARG 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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217C TYR* 2.9 22.5 + - + +
218C GLU* 3.0 28.1 - - - +
220C ALA* 1.3 72.3 - - - +
222C LYS* 1.3 57.4 + - - +
224C ASP* 2.7 30.1 + - - +
251C VAL* 2.7 39.8 - - - +
252C ASP* 3.1 35.0 + - - +
254C ARG* 3.9 13.7 + - - +
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Residues in contact with LYS 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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172C ARG* 6.2 1.8 - - - +
179C LYS* 5.0 5.1 - - - +
180C PRO* 3.6 41.5 - - + +
218C GLU 2.9 10.8 + - - +
219C LEU* 3.3 19.3 + - + +
221C ARG* 1.3 80.1 - - - +
223C TYR* 1.3 93.1 + - + +
224C ASP* 3.5 2.1 + - - +
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Residues in contact with TYR 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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5C ARG* 5.0 0.3 + - - -
172C ARG* 4.9 1.7 + - + -
175C LEU* 3.2 55.9 + - + +
176C SER* 4.0 2.9 + - - -
178C TRP* 3.8 17.0 - + + -
179C LYS* 2.9 25.6 + - - -
180C PRO* 3.9 25.1 - - + -
183C ALA* 3.4 16.8 - - - +
190C THR* 4.8 12.2 + - + -
191C PRO* 5.0 1.6 - - + +
219C LEU* 2.9 29.8 + - + +
222C LYS* 1.3 107.7 + - + +
224C ASP* 1.3 69.6 + - - +
225C PHE* 3.4 20.9 + - + +
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Residues in contact with ASP 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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1C MET 4.2 12.7 + - - -
2C ASN* 5.4 2.3 + - - +
5C ARG* 2.6 56.9 + - - +
6C PHE* 3.7 13.1 - - - -
183C ALA* 4.1 9.7 - - + +
184C LYS* 6.0 2.3 - - + +
220C ALA 2.7 8.7 + - - -
221C ARG 2.7 13.2 + - - +
222C LYS 3.2 2.0 - - - +
223C TYR* 1.3 79.8 - - - +
225C PHE* 1.3 56.9 + - - +
254C ARG* 3.1 23.3 + - - +
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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