Contacts of the helix formed by residues 215 - 229 (chain B) in PDB entry 3QN3
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 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B ASN* 3.1 18.4 + - - -
214B ASN* 1.3 82.7 - - + +
216B GLU* 1.3 66.3 + - - +
217B PRO* 3.3 0.7 - - - -
218B ILE* 3.0 8.7 + - - +
219B ASP* 2.9 28.5 + - - +
266B ARG* 3.7 20.6 - - - +
270B LEU* 3.7 30.1 - - + -
273B LYS* 5.9 0.2 - - - +
274B TYR* 3.7 19.1 - - + +
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.6 25.7 - - + +
212B ALA* 3.1 38.7 + - - +
213B ASN* 2.8 20.6 + - - +
215B THR* 1.3 77.2 + - - +
217B PRO* 1.3 69.5 - - + +
219B ASP* 3.0 14.5 + - + +
220B LEU* 2.9 22.9 + - - +
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Residues in contact with PRO 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ILE* 3.7 23.1 - - + +
159B VAL* 4.0 12.6 - - + -
164B PHE* 3.7 31.9 - - + -
211B LEU* 3.8 21.7 - - + -
213B ASN 3.0 28.0 - - - +
214B ASN 3.6 4.7 - - - -
215B THR 3.5 3.8 - - - -
216B GLU* 1.3 86.5 - - + +
218B ILE* 1.3 56.3 + - - +
220B LEU* 3.3 2.9 + - + +
221B LEU* 2.9 33.3 + - - +
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Residues in contact with ILE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 5.5 0.4 - - + -
164B PHE* 3.8 17.9 - - + -
214B ASN 3.4 21.8 - - - +
215B THR* 3.0 9.8 + - - +
217B PRO* 1.3 76.7 - - - +
219B ASP* 1.3 57.0 + - - +
221B LEU* 3.2 9.7 + - - +
222B MET* 2.9 29.5 + - + +
236B ILE* 4.5 18.6 - - + -
238B LEU* 4.4 17.3 - - + -
270B LEU* 4.7 9.2 - - + -
274B TYR* 3.4 50.3 - - + -
276B ILE* 4.5 11.4 - - + -
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Residues in contact with ASP 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B THR* 2.9 24.2 + - - +
216B GLU* 3.5 14.1 - - - +
218B ILE* 1.3 75.4 - - - +
220B LEU* 1.3 53.9 + - - +
222B MET* 3.3 7.5 + - - +
223B THR* 2.6 42.8 + - + +
273B LYS* 4.4 3.3 + - - -
274B TYR* 2.8 33.4 + - - -
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Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ILE* 4.3 9.2 - - + -
188B LEU* 3.5 30.5 - - + -
191B GLU* 4.5 15.0 - - + +
192B LEU* 3.7 21.8 - - + -
209B PRO* 5.3 0.2 - - + -
211B LEU* 4.4 16.4 - - + -
216B GLU 2.9 12.0 + - - +
217B PRO* 3.5 10.5 - - + +
219B ASP* 1.3 73.8 - - - +
221B LEU* 1.3 65.8 + - - +
223B THR* 3.2 12.4 + - + +
224B CYS* 3.0 34.8 + - - -
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ILE* 3.5 36.8 - - + -
149B ILE* 3.8 14.4 - - + -
164B PHE* 3.9 33.9 - - + -
165B MET 4.2 1.3 - - - +
166B ILE* 4.0 13.9 - - + -
184B ILE* 5.0 2.2 - - + +
188B LEU* 4.5 4.3 - - + -
217B PRO 2.9 18.5 + - - +
218B ILE* 3.6 9.2 - - - +
220B LEU* 1.3 75.0 - - - +
222B MET* 1.3 57.0 + - - +
224B CYS* 3.2 4.5 + - + +
225B ILE* 2.8 35.7 + - - +
236B ILE* 3.8 31.0 - - + -
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Residues in contact with MET 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ILE* 2.9 20.7 + - + +
219B ASP* 3.6 10.3 - - - +
220B LEU 3.3 0.2 - - - -
221B LEU* 1.3 73.0 - - - +
223B THR* 1.3 60.1 + - + +
225B ILE* 3.4 16.0 + - + +
226B LYS* 3.0 28.4 + - - +
231B GLU* 6.0 7.0 - - + +
232B ASN 6.3 1.3 - - - +
234B VAL 5.7 1.3 - - - +
236B ILE* 4.2 17.9 - - - -
274B TYR* 4.3 18.8 - - + -
275B PRO* 3.4 41.1 - - + -
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B GLU* 4.6 5.4 + - - -
219B ASP* 2.6 31.1 + - + +
220B LEU* 4.0 14.2 + - + +
222B MET* 1.3 77.1 - - + +
224B CYS* 1.3 60.4 + - - +
226B LYS* 3.3 5.3 + - - +
227B LYS* 2.8 45.7 + - - +
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Residues in contact with CYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ILE* 3.9 24.1 - - + +
187B ILE* 4.2 11.0 - - + +
188B LEU* 3.6 41.7 - - + -
191B GLU* 3.9 17.9 - - - -
220B LEU* 3.0 24.6 + - - +
221B LEU* 3.8 5.8 - - + +
223B THR* 1.3 75.2 - - - +
225B ILE* 1.3 59.6 + - - +
227B LYS* 3.9 1.1 - - - +
228B ALA* 3.0 32.1 + - - +
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Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 4.4 4.7 - - + -
184B ILE* 4.0 27.8 - - + -
221B LEU 2.8 26.4 + - - +
222B MET* 3.5 17.9 - - + +
224B CYS* 1.3 76.7 - - - +
226B LYS* 1.3 63.6 + - - +
228B ALA* 3.4 2.3 + - - +
229B GLY 3.3 4.0 + - - -
230B TYR* 3.0 49.1 + - + +
231B GLU* 4.0 7.2 - - + +
232B ASN 4.9 0.7 - - - +
234B VAL* 3.8 37.2 - - + +
236B ILE* 4.1 18.8 - - + -
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Residues in contact with LYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B MET 3.0 17.1 + - - +
223B THR* 3.9 5.8 - - - +
225B ILE* 1.3 79.2 - - - +
227B LYS* 1.3 61.9 + - + +
229B GLY* 2.9 16.1 + - - -
231B GLU* 3.3 42.9 + - + +
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ILE* 4.0 21.2 - - + +
190B LYS* 5.9 1.7 - - - +
191B GLU* 3.2 38.0 + - + +
223B THR* 2.8 31.7 + - - +
224B CYS 4.0 3.4 - - - +
226B LYS* 1.3 72.8 - - - +
228B ALA* 1.3 61.4 + - - +
229B GLY* 3.1 1.6 + - - -
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B GLU* 4.5 5.6 - - + +
184B ILE* 3.5 28.0 - - + +
187B ILE* 3.4 22.4 - - + +
224B CYS 3.0 19.8 + - - +
225B ILE 3.8 1.3 - - - +
227B LYS* 1.3 75.9 - - - +
229B GLY* 1.3 60.1 + - - +
230B TYR* 3.5 24.1 - - + -
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Residues in contact with GLY 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LYS 2.9 14.5 + - - -
227B LYS 3.1 2.1 - - - -
228B ALA* 1.3 79.4 - - - +
230B TYR* 1.3 67.1 + - - +
231B GLU* 3.6 4.0 + - - -
233B ARG* 4.9 6.2 + - - -
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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