Contacts of the helix formed by residues 251 - 265 (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 ASN 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ASN* 4.1 9.8 - - - +
186A ALA* 4.1 13.5 - - - +
196A ARG* 4.4 6.5 - - - +
228A GLN* 3.2 22.5 + - - -
249A ALA 3.3 2.2 + - - +
250A THR* 1.3 79.0 + - - +
252A HIS* 1.3 57.0 + - - +
253A LEU* 2.9 19.9 + - - +
254A LEU* 2.9 30.1 + - - +
255A LEU* 2.9 28.1 + - - +
278A PHE* 3.6 9.9 - - - -
279A ASP* 3.6 12.3 - - - +
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Residues in contact with HIS 252 (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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75A ASN* 3.6 10.1 - - - +
76A PRO* 3.6 31.5 - - + +
251A ASN* 1.3 72.8 - - - +
253A LEU* 1.3 67.8 + - + +
255A LEU* 3.4 10.6 + - - +
256A LEU* 2.9 27.7 + - + +
278A PHE 3.4 7.3 + - - -
279A ASP* 2.9 33.0 + - + +
281A SER* 3.4 37.3 - - - -
283A TRP* 4.6 2.1 - + - -
284A ASN* 5.1 0.4 + - - -
283B TRP* 3.5 38.7 + + - -
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Residues in contact with LEU 253 (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* 4.0 18.8 - - - -
74A GLN 4.8 2.2 - - - +
75A ASN* 4.2 23.1 - - + +
76A PRO* 4.9 1.1 - - + -
225A THR* 4.0 35.0 - - + +
228A GLN* 3.7 38.8 - - + +
229A ILE* 3.5 24.7 - - + -
251A ASN* 2.9 8.1 + - - +
252A HIS* 1.3 89.2 - - + +
254A LEU* 1.3 65.3 + - - +
256A LEU* 3.4 7.6 + - + +
257A GLY 3.1 17.8 + - - -
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Residues in contact with LEU 254 (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* 3.6 35.1 - - + +
185A LEU* 3.5 33.4 - - - +
186A ALA* 3.8 3.8 - - - +
219A SER* 4.2 7.6 - - - -
228A GLN* 3.1 31.4 - - + +
231A SER* 4.1 10.3 - - - +
232A GLY* 3.7 14.9 - - - +
249A ALA* 4.1 4.7 - - + -
250A THR* 3.9 6.5 - - - +
251A ASN* 2.9 33.1 + - - +
253A LEU* 1.3 75.0 - - - +
255A LEU* 1.3 52.0 + - - +
257A GLY* 3.3 2.1 + - - -
258A ALA* 2.8 33.4 + - - +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA* 3.7 12.2 - - + +
251A ASN 2.9 17.9 + - - +
252A HIS* 3.5 12.6 - - - +
254A LEU* 1.3 73.5 - - - +
256A LEU* 1.3 60.4 + - - +
258A ALA* 3.0 4.3 + - - +
259A LEU* 2.8 51.9 + - + +
275A ILE* 4.0 24.2 - - + -
277A GLY* 4.1 25.4 - - - +
278A PHE 4.4 7.4 - - - +
279A ASP 5.2 0.2 - - - +
284A ASN* 4.2 21.5 - - - +
291A LEU* 4.4 13.2 - - + -
292A THR 5.8 0.2 - - - +
293A VAL* 4.4 9.6 - - + -
283B TRP* 4.6 5.2 - - + -
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Residues in contact with LEU 256 (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* 3.5 35.9 - - + -
252A HIS* 2.9 19.8 + - - +
253A LEU* 3.6 9.6 - - + +
255A LEU* 1.3 75.4 - - - +
257A GLY* 1.3 62.9 - - - +
259A LEU* 3.3 4.2 + - - +
260A GLN* 3.0 30.6 + - + +
282B TYR* 4.0 28.5 - - + -
283B TRP* 3.6 46.8 - - + +
286B ILE* 3.8 15.9 - - + -
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Residues in contact with GLY 257 (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* 3.1 28.2 - - - +
233A TYR* 3.1 20.8 - - - +
253A LEU 3.1 12.1 + - - -
254A LEU 3.6 2.5 - - - -
256A LEU* 1.3 76.0 - - - +
258A ALA* 1.3 62.1 + - - +
260A GLN* 3.4 12.3 + - - +
261A ALA 3.1 17.2 + - - -
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Residues in contact with ALA 258 (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* 3.7 9.2 - - + -
232A GLY 3.7 1.0 + - - -
236A THR* 3.2 28.8 - - + +
247A ILE* 5.1 0.4 - - + -
254A LEU 2.8 17.2 + - - +
255A LEU* 3.0 9.8 + - - +
257A GLY* 1.3 72.7 - - - +
259A LEU* 1.3 58.0 + - - +
261A ALA* 3.1 3.6 + - - +
262A ILE* 2.9 34.1 + - - +
275A ILE* 3.8 23.3 - - + -
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Residues in contact with LEU 259 (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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255A LEU* 2.8 31.8 + - + +
256A LEU 3.7 1.1 - - - +
258A ALA* 1.3 73.0 - - - +
260A GLN* 1.3 59.1 + - - +
262A ILE* 3.4 11.6 + - + +
263A LYS* 2.9 30.5 + - - +
269A ILE* 4.0 23.1 - - + -
275A ILE* 4.6 4.0 - - + -
287A TYR* 3.9 12.7 + - + +
291A LEU* 3.7 31.9 - - + -
283B TRP* 3.3 39.0 - - + -
286B ILE* 3.6 18.1 - - + +
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Residues in contact with GLN 260 (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* 3.6 25.1 - - - +
230A TYR* 5.6 0.3 - - - -
233A TYR* 4.0 19.9 - - + +
256A LEU* 3.0 23.5 + - + +
257A GLY* 3.5 8.9 - - - +
259A LEU* 1.3 75.5 - - - +
261A ALA* 1.3 61.7 + - - +
263A LYS* 3.3 2.3 + - - +
264A GLU* 3.0 24.1 + - - +
282B TYR* 3.8 38.2 + - - +
285B GLU* 5.0 5.2 + - - +
286B ILE* 3.8 22.6 - - + +
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Residues in contact with ALA 261 (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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233A TYR* 3.4 40.6 - - + +
236A THR* 3.6 16.4 - - + -
237A LYS* 3.7 15.9 - - + +
240A LEU* 4.1 2.9 - - - +
257A GLY 3.1 10.1 + - - +
258A ALA 3.5 7.6 - - - +
260A GLN* 1.3 76.3 - - - +
262A ILE* 1.3 62.3 + - - +
264A GLU* 3.5 3.8 + - - +
265A SER* 3.1 23.4 + - - -
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Residues in contact with ILE 262 (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* 4.0 6.7 - - + -
240A LEU* 3.8 16.4 - - + -
247A ILE* 5.4 1.3 - - + -
258A ALA 2.9 26.4 + - - +
259A LEU* 3.7 9.2 - - + +
261A ALA* 1.3 74.3 - - - +
263A LYS* 1.3 65.2 + - - +
265A SER* 2.7 28.5 + - - +
267A LYS* 3.5 20.4 - - + +
269A ILE* 3.8 37.9 - - + +
273A VAL* 4.5 19.1 - - + -
275A ILE* 4.1 23.8 - - + -
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Residues in contact with LYS 263 (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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259A LEU 2.9 17.6 + - - +
260A GLN 3.3 3.8 + - - +
262A ILE* 1.3 77.6 - - - +
264A GLU* 1.3 57.9 + - - +
265A SER 2.9 14.6 - - - +
267A LYS 5.4 0.7 - - - -
287A TYR* 4.4 6.5 - - - +
288A THR 6.0 0.7 - - - -
285B GLU 3.9 7.4 + - - +
286B ILE* 3.3 48.2 + - + +
287B TYR 3.3 15.0 + - - -
288B THR* 3.3 17.6 + - - +
290B LYS* 4.7 15.5 - - - +
331B GLU* 5.9 0.4 + - - -
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Residues in contact with GLU 264 (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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233A TYR* 2.9 36.2 + - + -
237A LYS* 3.9 16.0 + - - +
260A GLN 3.0 17.1 + - - +
261A ALA* 3.7 6.1 - - - +
263A LYS* 1.3 75.8 - - - +
265A SER* 1.3 63.3 + - - +
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Residues in contact with SER 265 (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* 6.6 0.2 - - - -
240A LEU* 3.7 13.4 - - - +
261A ALA 3.1 12.6 + - - -
262A ILE* 2.7 27.2 + - - +
263A LYS 2.9 16.8 - - - +
264A GLU* 1.3 78.6 - - - +
266A GLU* 1.3 63.0 + - - +
267A LYS* 3.1 25.5 + - - +
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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