Contacts of the helix formed by residues 220 - 232 (chain B) in PDB entry 2QQ6
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 ASP 220 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B ASN* 5.4 1.7 - - - +
184B GLY* 3.2 15.8 + - - +
185B ALA* 3.5 23.4 + - - +
219B PHE* 1.3 74.2 - - - +
221B ILE* 1.3 60.3 + - - +
222B PRO* 3.6 14.4 - - + +
223B SER* 2.8 27.0 + - - -
224B SER* 2.7 24.3 + - - -
243B THR* 4.5 1.1 - - - -
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Residues in contact with ILE 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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220B ASP* 1.3 74.9 - - - +
222B PRO* 1.4 74.4 - - + +
224B SER* 3.3 2.9 + - - -
225B ILE* 3.0 43.5 + - + +
243B THR* 4.6 4.1 - - + +
250B ALA* 4.0 35.4 - - + +
253B GLU* 3.5 31.4 - - + +
254B VAL* 4.2 12.3 - - + -
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Residues in contact with PRO 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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220B ASP* 3.4 18.4 - - + +
221B ILE* 1.4 98.2 - - + +
223B SER* 1.3 58.0 + - - +
225B ILE* 3.4 4.8 + - + +
226B ARG* 2.9 31.8 + - - +
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Residues in contact with SER 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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184B GLY 3.7 6.3 - - - -
185B ALA* 3.2 4.7 - - - +
186B ILE* 2.7 55.3 + - - +
191B HIS* 5.5 0.3 + - - -
219B PHE* 4.0 2.5 - - - -
220B ASP* 2.8 25.2 + - - -
222B PRO* 1.3 73.2 - - - +
224B SER* 1.3 63.9 + - - +
226B ARG* 3.8 5.0 - - - +
227B PHE* 2.8 27.7 + - - +
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Residues in contact with SER 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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186B ILE* 5.7 0.2 - - - -
215B MSE 5.1 5.2 - - - +
219B PHE* 3.5 4.9 + - - +
220B ASP 2.7 22.6 + - - -
221B ILE 3.5 3.6 - - - -
223B SER* 1.3 75.9 - - - +
225B ILE* 1.3 54.4 + - - +
227B PHE* 3.7 4.0 - - - +
228B ALA* 2.8 37.7 + - - +
242B PRO* 3.4 31.6 + - - -
243B THR* 3.3 16.7 - - - +
254B VAL* 3.9 17.7 - - - +
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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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221B ILE* 3.0 35.7 + - + +
222B PRO* 3.8 4.7 - - + +
224B SER* 1.3 73.0 - - - +
226B ARG* 1.3 67.8 + - - +
228B ALA* 3.7 5.3 - - - +
229B ARG* 3.0 26.2 + - + +
253B GLU* 4.6 9.9 - - + +
254B VAL* 4.5 13.9 - - + -
257B SER* 3.5 35.1 - - - +
258B THR* 5.6 0.5 - - - -
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Residues in contact with ARG 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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186B ILE 4.9 5.9 + - - -
187B SER 4.8 0.4 + - - -
188B PRO* 4.1 27.3 + - - +
191B HIS* 3.7 34.6 + - + +
192B GLU* 3.8 20.2 + - - -
222B PRO 2.9 21.9 + - - +
223B SER* 3.9 4.7 - - - +
225B ILE* 1.3 75.4 - - - +
227B PHE* 1.3 62.2 + - - +
229B ARG* 3.7 7.0 + - - +
230B ALA* 3.5 14.4 + - - +
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Residues in contact with PHE 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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170B VAL* 4.2 14.1 - - + -
186B ILE* 4.2 9.0 - - + -
191B HIS* 3.8 22.1 - + + -
194B MSE 3.6 43.7 - - + -
195B VAL* 4.0 9.2 - - + -
198B VAL* 4.4 5.4 - - + -
213B ILE* 5.0 0.2 - - + -
215B MSE 3.6 29.6 - - + -
223B SER 2.8 18.5 + - - +
224B SER* 3.8 3.4 - - - +
226B ARG* 1.3 75.3 - - - +
228B ALA* 1.3 67.7 + - - +
230B ALA* 3.1 13.0 + - - +
231B MSE 3.1 54.3 + - + +
239B LEU* 4.3 7.4 - - + -
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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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215B MSE 5.4 0.4 - - + -
224B SER 2.8 22.8 + - - +
225B ILE* 3.3 6.7 + - - +
227B PHE* 1.3 69.9 - - - +
229B ARG* 1.3 56.8 + - - +
230B ALA 2.9 4.3 - - - -
231B MSE 2.7 20.4 + - - +
232B GLU 3.4 0.2 + - - -
239B LEU* 4.0 22.2 - - + -
254B VAL* 4.6 10.8 - - + -
257B SER* 5.9 0.4 - - - -
258B THR* 3.4 28.4 + - + -
260B THR* 3.1 16.5 + - - -
262B ILE* 5.4 0.2 - - + -
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Residues in contact with ARG 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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225B ILE* 3.0 20.0 + - + +
226B ARG* 3.9 7.2 - - - +
228B ALA* 1.3 75.8 - - - +
230B ALA* 1.3 57.6 + - - +
232B GLU* 3.1 28.5 - - - +
233B PRO* 4.2 2.8 - - - +
258B THR* 3.8 12.7 + - - -
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Residues in contact with ALA 230 (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 HIS* 4.2 17.0 - - - +
195B VAL* 4.4 15.9 - - + +
226B ARG 3.5 10.1 + - - +
227B PHE 3.1 10.7 + - - +
228B ALA 2.9 0.8 - - - -
229B ARG* 1.3 77.6 - - - +
231B MSE 1.3 60.8 + - + +
232B GLU 3.1 6.6 + - - -
233B PRO* 3.3 13.6 - - - +
234B PHE* 3.5 15.1 - - - -
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Residues in contact with MSE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B VAL* 4.2 11.2 - - + -
198B VAL* 3.7 32.8 - - + -
213B ILE* 4.0 2.2 - - - -
227B PHE* 3.1 51.4 + - + +
228B ALA 2.7 10.3 + - - +
230B ALA* 1.3 86.9 - - - +
232B GLU* 1.3 64.4 + - - +
233B PRO 3.5 0.7 - - - -
234B PHE* 3.5 27.8 + - + -
235B GLY 4.2 1.4 + - - -
236B LEU* 3.5 45.5 + - + +
239B LEU* 3.9 8.3 - - + -
260B THR* 3.5 15.3 + - + +
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Residues in contact with GLU 232 (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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228B ALA 3.6 0.7 - - - +
229B ARG* 3.1 23.7 - - - +
230B ALA 3.1 1.4 - - - -
231B MSE 1.3 79.6 - - - +
233B PRO* 1.3 70.4 - - + +
234B PHE 3.2 0.9 + - - -
235B GLY* 3.5 9.7 + - - -
257B SER 4.6 1.0 - - - +
258B THR* 2.4 37.7 + - - +
259B SER* 2.9 32.0 + - - +
260B THR* 3.4 8.7 - - - +
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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