Contacts of the helix formed by residues 224 - 242 (chain A) in PDB entry 2QU7
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 GLY 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASP* 4.6 0.9 - - - -
102A GLU* 3.6 26.0 + - - -
103A GLU* 2.8 22.4 + - - +
223A LEU* 1.3 75.1 - - - +
225A THR* 1.3 63.8 + - - -
226A ASN 3.6 2.0 - - - -
227A ALA* 3.6 0.6 - - - +
228A GLN* 3.2 31.0 + - - -
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Residues in contact with THR 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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73A ASP* 3.6 1.6 - - - +
74A GLN* 3.0 56.8 + - + +
102A GLU* 3.1 15.0 + - - -
224A GLY* 1.3 70.5 - - - -
226A ASN* 1.3 72.0 + - - +
228A GLN* 3.3 5.2 + - - +
229A ILE* 3.2 31.6 + - + +
253A LEU* 4.0 28.9 - - + +
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Residues in contact with ASN 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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223A LEU 5.4 0.2 + - - -
225A THR* 1.3 82.6 - - - +
227A ALA* 1.3 59.8 + - - +
229A ILE* 3.3 12.1 + - - +
230A TYR* 2.9 33.0 + - - +
282B TYR* 3.6 37.1 + - - -
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Residues in contact with ALA 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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103A GLU* 5.1 0.2 - - - +
219A SER* 3.8 3.5 + - - +
222A GLN* 3.5 45.9 + - + +
223A LEU 3.4 31.8 + - - +
224A GLY 3.6 2.0 - - - +
226A ASN* 1.3 79.3 - - - +
228A GLN* 1.3 56.5 + - - +
230A TYR* 3.8 2.1 - - - +
231A SER* 2.9 29.3 + - - -
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Residues in contact with GLN 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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73A ASP* 3.0 31.8 + - - +
103A GLU* 3.0 32.6 + - - +
186A ALA* 4.7 5.5 - - + +
219A SER* 3.3 25.8 - - - +
224A GLY 3.2 14.5 + - - +
225A THR 3.7 5.8 - - - +
226A ASN 3.3 0.6 - - - -
227A ALA* 1.3 73.9 - - - +
229A ILE* 1.3 65.6 + - - +
232A GLY* 3.1 17.7 + - - -
251A ASN* 3.2 25.9 + - - +
253A LEU* 3.7 18.6 - - + +
254A LEU* 3.1 19.3 - - + +
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Residues in contact with ILE 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 THR* 3.2 26.5 + - + +
226A ASN* 3.3 18.6 + - - +
228A GLN* 1.3 74.2 - - - +
230A TYR* 1.3 58.4 + - - +
232A GLY 3.2 1.9 + - - -
233A TYR* 2.9 23.7 + - - +
253A LEU* 3.5 26.5 - - + +
256A LEU* 3.5 23.6 - - + -
257A GLY* 3.1 22.2 - - - +
260A GLN* 3.6 30.1 - - - +
282B TYR* 4.0 17.9 - - + -
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Residues in contact with TYR 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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222A GLN* 4.1 20.6 - - - +
226A ASN 2.9 17.7 + - - +
227A ALA* 3.8 4.7 - - - +
229A ILE* 1.3 75.7 - - - +
231A SER* 1.3 58.9 + - - +
233A TYR* 3.1 28.5 + + - +
234A GLU* 2.8 58.5 + - + +
260A GLN* 5.6 0.4 - - - -
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Residues in contact with SER 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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185A LEU 4.7 0.2 + - - -
217A HIS* 5.5 1.6 - - - +
218A TYR 3.5 7.6 + - - -
219A SER* 3.3 40.6 + - - -
227A ALA 2.9 18.6 + - - -
228A GLN 3.8 2.7 - - - -
230A TYR* 1.3 79.2 - - - +
232A GLY* 1.3 56.4 + - - +
234A GLU* 3.4 3.7 + - - +
235A ALA* 3.0 33.7 + - - +
254A LEU* 4.1 3.9 - - - +
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Residues in contact with GLY 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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184A LEU* 3.9 9.0 - - - +
228A GLN 3.1 13.8 + - - -
229A ILE 3.5 4.0 - - - -
231A SER* 1.3 77.2 + - - +
233A TYR* 1.3 59.5 + - - +
235A ALA* 4.7 1.6 - - - -
236A THR* 2.9 31.2 + - - -
254A LEU* 3.7 25.3 - - - +
257A GLY 3.6 6.1 - - - -
258A ALA 3.7 1.2 + - - -
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Residues in contact with TYR 233 (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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229A ILE 2.9 12.7 + - - +
230A TYR* 3.1 36.3 + + - +
232A GLY* 1.3 73.7 - - - +
234A GLU* 1.3 80.1 + - - +
236A THR 3.3 1.6 + - - -
237A LYS* 2.9 66.0 + - - +
257A GLY 3.1 16.0 - - - +
260A GLN* 4.0 20.4 - - + +
261A ALA* 3.4 33.3 - - + +
264A GLU* 2.9 28.7 + - - -
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Residues in contact with GLU 234 (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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230A TYR* 2.8 47.2 + - + +
231A SER* 4.2 3.6 - - - +
233A TYR* 1.3 76.2 - - + +
235A ALA* 1.3 57.3 + - - +
237A LYS* 3.3 33.4 + - - +
238A THR* 3.0 41.5 + - - +
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Residues in contact with ALA 235 (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 LEU* 3.8 14.4 - - + -
217A HIS* 3.4 45.2 + - + +
231A SER* 3.0 19.1 + - - +
232A GLY* 4.1 1.1 - - - +
234A GLU* 1.3 74.1 - - - +
236A THR* 1.3 61.1 + - - +
238A THR* 3.2 3.0 + - - -
239A LEU* 2.8 33.6 + - - +
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Residues in contact with THR 236 (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 LEU* 3.4 11.6 - - - +
232A GLY 2.9 19.2 + - - -
233A TYR 3.3 0.2 + - - -
235A ALA* 1.3 78.1 - - - +
237A LYS* 1.3 52.7 + - - +
239A LEU* 3.1 8.1 + - - +
240A LEU* 2.6 52.8 + - + +
247A ILE* 3.9 18.4 - - + +
258A ALA* 3.2 35.7 - - + +
261A ALA* 3.6 13.2 - - + -
262A ILE* 4.0 5.6 - - + -
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Residues in contact with LYS 237 (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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230A TYR* 5.7 0.2 + - - -
233A TYR* 2.9 57.4 + - + +
234A GLU* 3.3 31.8 + - - +
236A THR* 1.3 75.6 - - - +
238A THR* 1.3 58.0 + - - +
240A LEU* 3.9 5.9 - - - +
241A SER* 2.8 38.7 + - - +
261A ALA* 3.7 14.8 - - + +
264A GLU* 3.9 13.6 + - - +
265A SER* 6.6 0.2 - - - -
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Residues in contact with THR 238 (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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217A HIS* 4.2 19.4 - - + -
234A GLU* 3.0 24.7 + - - +
235A ALA 3.5 7.9 - - - -
236A THR 3.2 0.2 - - - -
237A LYS* 1.3 79.2 - - - +
239A LEU* 1.3 62.1 + - - +
241A SER* 3.2 13.8 + - - -
242A LYS* 3.2 38.3 - - + +
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Residues in contact with LEU 239 (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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182A GLY* 3.9 32.3 - - - -
184A LEU* 3.7 27.6 - - + -
215A LEU* 4.0 16.2 - - + +
217A HIS* 3.8 21.8 - - + +
235A ALA 2.8 23.7 + - - +
236A THR* 3.5 4.0 - - - +
238A THR* 1.3 71.8 - - - +
240A LEU* 1.3 61.8 + - - +
242A LYS* 3.2 17.3 + - - +
244A ILE* 3.2 45.2 + - + +
247A ILE* 4.1 18.2 - - + -
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Residues in contact with LEU 240 (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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236A THR* 2.6 35.9 + - + +
237A LYS* 4.0 4.9 - - - +
239A LEU* 1.3 68.3 - - - +
241A SER* 1.3 57.9 + - - +
242A LYS 3.0 4.7 - - - -
243A GLY 3.0 11.9 + - - +
244A ILE 4.1 9.6 - - - +
247A ILE* 4.6 7.2 - - + -
261A ALA* 4.1 6.7 - - + +
262A ILE* 3.8 20.6 - - + -
265A SER* 3.7 27.1 - - - +
267A LYS* 2.7 45.6 + - + +
273A VAL* 4.1 32.5 - - + -
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Residues in contact with SER 241 (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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237A LYS* 2.8 28.6 + - - +
238A THR* 3.2 10.6 + - - -
240A LEU* 1.3 74.5 - - - +
242A LYS* 1.3 59.5 + - - +
243A GLY 3.4 0.6 + - - -
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Residues in contact with LYS 242 (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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214A SER* 3.7 31.1 + - - -
215A LEU* 4.3 11.9 - - - +
217A HIS* 5.5 0.6 + - - -
238A THR* 3.2 31.1 - - + +
239A LEU* 3.2 21.5 + - - +
240A LEU 3.0 1.4 + - - -
241A SER* 1.3 79.6 - - - +
243A GLY* 1.3 60.8 + - - +
244A ILE* 3.4 10.1 + - + +
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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
------------------------------------------------------------
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