Contacts of the helix formed by residues 220 - 232 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ASN* 5.6 0.9 - - - +
184A GLY* 3.3 15.4 + - - +
185A ALA* 3.6 18.5 + - - +
219A PHE* 1.3 76.5 - - - +
221A ILE* 1.3 65.9 + - - +
222A PRO* 3.2 13.1 - - + +
223A SER* 2.7 33.8 + - - -
224A SER* 2.9 23.0 + - - -
243A THR* 4.3 2.0 - - - -
244A PRO* 5.6 0.2 - - - -
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Residues in contact with ILE 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ASP* 1.3 75.5 - - - +
222A PRO* 1.3 75.0 - - + +
224A SER* 3.6 3.2 - - - -
225A ILE* 3.0 46.2 + - + +
243A THR* 4.5 4.6 - - + +
250A ALA* 3.8 39.9 - - + +
253A GLU* 5.0 10.5 - - + -
254A VAL* 4.5 8.3 - - + -
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Residues in contact with PRO 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ASP* 3.2 16.8 - - + +
221A ILE* 1.3 101.2 - - + +
223A SER* 1.3 55.7 - - - +
225A ILE* 3.7 6.5 - - + +
226A ARG* 2.9 31.5 + - - +
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A GLY 3.5 10.0 + - - -
185A ALA* 3.6 1.4 - - - +
186A ILE* 3.2 44.1 + - - +
191A HIS* 5.6 0.2 + - - -
219A PHE* 4.1 2.5 - - - -
220A ASP* 2.7 33.4 + - - -
222A PRO* 1.3 70.2 - - - +
224A SER* 1.3 58.2 + - - +
226A ARG* 3.1 8.0 + - - +
227A PHE* 2.8 37.6 + - - +
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Residues in contact with SER 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A MSE 4.0 14.3 - - - +
219A PHE 3.9 2.3 + - - -
220A ASP 2.9 20.7 + - - -
221A ILE 3.6 3.8 - - - -
223A SER* 1.3 75.9 - - - +
225A ILE* 1.3 58.3 + - - +
227A PHE* 3.7 1.4 - - - +
228A ALA* 2.8 33.4 + - - +
239A LEU* 5.3 0.5 - - - +
242A PRO* 3.4 28.5 + - - +
243A THR* 3.2 23.7 - - - +
254A VAL* 4.0 11.2 - - - -
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ILE* 3.0 36.3 + - + +
222A PRO* 3.7 5.8 - - + +
224A SER* 1.3 79.6 - - - +
226A ARG* 1.3 67.3 + - - +
228A ALA* 3.2 5.5 + - - +
229A ARG* 3.1 22.3 + - + +
253A GLU* 5.0 10.3 - - + +
254A VAL* 4.5 13.9 - - + -
257A SER* 3.7 34.1 - - - +
258A THR* 4.4 2.0 - - + +
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Residues in contact with ARG 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ILE* 6.1 1.6 - - - -
188A PRO* 5.6 8.0 + - - +
191A HIS* 3.0 52.1 + - + +
222A PRO 2.9 19.9 + - - +
223A SER* 3.5 7.0 - - - +
225A ILE* 1.3 80.6 - - - +
227A PHE* 1.3 63.8 + - - +
228A ALA 3.2 0.2 + - - -
229A ARG* 3.3 12.0 + - - +
230A ALA* 3.4 11.3 + - - +
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Residues in contact with PHE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL* 4.3 18.8 - - + -
186A ILE* 4.6 7.0 - - + -
191A HIS* 3.7 26.9 - + + +
194A MSE 3.4 41.7 - - + -
195A VAL* 4.0 14.8 - - + -
198A VAL* 4.6 5.8 - - + -
213A ILE* 5.0 0.7 - - + -
215A MSE 3.8 34.3 - - + -
223A SER 2.8 20.2 + - - +
224A SER 3.8 2.5 - - - +
226A ARG* 1.3 74.2 - - - +
228A ALA* 1.3 62.1 + - - +
230A ALA* 3.1 16.6 - - - +
231A MSE 3.3 41.2 + - + +
239A LEU* 4.3 6.7 - - + -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A SER 2.8 21.9 + - - +
225A ILE* 3.2 3.7 + - - +
227A PHE* 1.3 72.2 - - - +
229A ARG* 1.3 65.2 + - - +
231A MSE 3.0 11.4 + - - +
239A LEU* 4.2 22.9 - - + +
254A VAL* 4.7 9.6 - - + -
258A THR* 3.5 26.5 - - + +
260A THR* 3.1 22.5 + - - -
262A ILE* 5.5 2.2 - - + -
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 3.1 11.7 + - + +
226A ARG* 3.3 9.8 + - - +
228A ALA* 1.3 75.0 - - - +
230A ALA* 1.3 63.4 + - - +
232A GLU* 3.1 40.4 + - - +
233A PRO* 3.6 3.8 - - - +
258A THR* 3.9 7.0 - - + +
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Residues in contact with ALA 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A HIS* 4.0 21.5 - - + +
195A VAL* 4.2 14.6 - - + +
226A ARG 3.4 9.4 + - - +
227A PHE 3.1 15.0 + - - +
229A ARG* 1.3 80.0 - - - +
231A MSE 1.3 57.1 + - + +
233A PRO* 3.2 17.9 - - - +
234A PHE* 3.3 15.9 - - - -
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Residues in contact with MSE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A VAL* 4.2 12.8 - - + -
198A VAL* 3.8 33.7 - - + -
213A ILE* 4.0 3.1 - - - -
227A PHE* 3.4 50.0 - - + +
228A ALA* 3.0 11.6 + - - +
230A ALA* 1.3 82.8 - - + +
232A GLU* 1.3 66.0 + - - +
233A PRO* 3.4 0.4 - - - -
234A PHE* 2.9 35.0 + - + +
235A GLY 3.8 2.9 + - - -
236A LEU* 3.5 35.5 - - + +
239A LEU* 4.5 5.6 - - + -
260A THR* 3.7 9.2 + - + +
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Residues in contact with GLU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ALA 3.6 3.4 - - - +
229A ARG* 3.1 30.5 + - - +
231A MSE 1.3 75.4 - - - +
233A PRO* 1.3 63.1 - - + +
234A PHE 2.8 6.9 + - - -
235A GLY* 3.3 11.3 + - - +
258A THR* 3.1 9.2 - - - -
259A SER* 2.6 43.6 + - - +
260A THR* 3.1 20.4 + - - +
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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