Contacts of the helix formed by residues 261 - 277 (chain N) in PDB entry 3Q84
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 261 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97N LEU* 3.1 31.5 - - - +
100N GLU* 5.2 1.2 - - - +
257N ASN 4.7 1.3 - - - +
258N LEU* 2.5 30.4 - - - +
260N GLU* 1.3 77.6 + - - +
262N SER* 1.3 78.3 + - - +
263N SER* 3.9 10.5 - - - +
264N TYR* 2.8 21.9 + - + +
265N ILE* 3.4 11.4 + - - +
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Residues in contact with SER 262 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260N GLU 4.2 0.2 - - - -
261N ASN* 1.3 79.4 + - - +
263N SER* 1.3 65.0 + - - +
264N TYR 3.1 0.2 + - - -
265N ILE* 3.5 6.7 + - - +
266N HIS* 3.0 25.1 + - - +
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Residues in contact with SER 263 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97N LEU* 4.0 23.6 - - - -
261N ASN* 3.0 7.3 - - - +
262N SER* 1.3 82.8 + - - +
264N TYR* 1.3 63.8 + - - +
266N HIS* 3.2 7.9 + - - +
267N VAL* 3.0 25.6 + - - +
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Residues in contact with TYR 264 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M LEU 4.7 0.9 + - - -
258M LEU* 3.8 23.3 + - + +
259M ALA* 4.3 28.9 - - + -
264M TYR* 4.5 15.9 + + - -
94N VAL* 4.4 20.0 - - + +
97N LEU* 4.0 19.7 - - + +
98N HIS* 5.7 0.8 + - - -
258N LEU* 3.9 41.7 - - + +
259N ALA* 4.6 4.7 - - - -
261N ASN* 2.8 15.0 + - + +
263N SER* 1.3 76.1 - - - +
265N ILE* 1.3 70.9 + - + +
267N VAL* 2.9 22.1 + - + +
268N TYR* 3.5 36.3 + + - -
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Residues in contact with ILE 265 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257M ASN* 5.7 0.2 - - - +
259M ALA* 4.1 26.0 - - + -
265M ILE* 6.1 1.6 - - + -
259N ALA* 5.2 3.4 - - + -
260N GLU* 4.7 13.5 - - - +
261N ASN 3.4 13.9 + - - +
262N SER* 4.0 7.2 - - - +
264N TYR* 1.3 87.4 - - + +
266N HIS* 1.3 67.2 + - + +
268N TYR* 3.2 6.9 + - - +
269N ARG* 3.0 52.1 + - + +
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Residues in contact with HIS 266 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93N LYS* 5.2 3.7 + - - +
262N SER 3.0 17.8 + - - +
263N SER* 3.3 9.3 + - - +
264N TYR 2.9 0.2 - - - -
265N ILE* 1.3 86.8 - - + +
267N VAL* 1.3 64.9 + - - +
269N ARG* 3.1 11.0 + - + +
270N GLU* 2.9 48.6 + - + +
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Residues in contact with VAL 267 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90N GLU* 4.1 16.2 - - + +
93N LYS* 4.1 31.6 - - + -
94N VAL* 4.3 7.6 - - + -
97N LEU* 4.6 9.9 - - + -
263N SER* 3.0 19.9 + - - +
264N TYR* 2.9 14.3 + - + +
266N HIS* 1.3 78.0 + - - +
268N TYR* 1.3 87.7 + - + +
270N GLU* 3.2 10.3 + - - +
271N LEU* 2.9 25.6 + - - +
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Residues in contact with TYR 268 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M ARG* 4.5 1.9 + - - -
253M LYS* 3.9 12.5 - - + -
256M LEU* 3.4 32.2 + - + +
257M ASN* 3.5 46.9 - - + +
90N GLU* 2.6 34.8 + - + -
94N VAL* 3.7 10.0 - - + +
264N TYR* 3.8 34.3 + + - -
265N ILE* 3.2 6.5 + - - +
266N HIS 3.2 0.2 - - - -
267N VAL* 1.3 94.2 - - + +
269N ARG* 1.3 65.6 + - - +
271N LEU* 3.4 17.0 - - + +
272N GLU* 2.8 24.6 + - - +
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Residues in contact with ARG 269 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265N ILE* 3.0 37.2 + - + +
266N HIS* 3.1 16.1 + - + +
268N TYR* 1.3 77.3 - - - +
270N GLU* 1.3 62.4 + - - +
272N GLU* 3.4 5.9 + - - +
273N GLN* 3.1 34.0 + - - +
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Residues in contact with GLU 270 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89N THR* 4.7 10.4 - - - +
93N LYS* 2.3 38.5 + - - +
266N HIS* 2.9 33.7 + - + +
267N VAL* 3.2 10.7 - - - +
269N ARG* 1.3 77.8 - - - +
271N LEU* 1.3 57.4 + - - +
273N GLN* 3.2 15.0 + - - +
274N ALA* 3.0 27.0 + - - +
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Residues in contact with LEU 271 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253M LYS* 3.6 32.8 - - + -
256M LEU* 4.9 1.8 - - + -
86N ALA* 3.7 34.5 - - + +
87N ILE* 4.0 13.0 - - + +
90N GLU* 4.0 29.6 - - + +
267N VAL 2.9 13.7 + - - +
268N TYR* 3.4 18.6 - - + +
270N GLU* 1.3 74.9 - - - +
272N GLU* 1.3 69.4 + - - +
273N GLN 3.1 0.2 + - - -
274N ALA* 3.2 9.0 + - - +
275N ILE* 3.2 21.7 + - + +
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Residues in contact with GLU 272 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250M LEU* 4.9 6.7 - - + -
253M LYS* 2.7 44.6 + - - +
254M ARG* 5.9 1.2 + - - -
268N TYR 2.8 16.2 + - - +
269N ARG* 3.8 6.5 - - - +
271N LEU* 1.3 79.1 - - - +
273N GLN* 1.3 65.1 - - + +
275N ILE* 3.6 4.4 + - - +
276N ARG* 3.0 59.1 + - + +
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Residues in contact with GLN 273 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269N ARG* 3.1 24.3 + - - +
270N GLU* 3.5 14.5 - - - +
271N LEU 3.0 0.6 - - - -
272N GLU* 1.3 77.8 - - + +
274N ALA* 1.3 66.1 + - - +
276N ARG* 3.3 7.4 + - - +
277N GLY* 3.0 20.4 + - - -
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Residues in contact with ALA 274 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N SER 5.5 0.3 - - - +
82N ARG* 5.2 2.2 - - - +
83N ALA* 4.1 10.9 + - - +
86N ALA* 3.5 30.3 - - + -
270N GLU 3.0 17.0 + - - +
271N LEU* 3.2 2.8 + - - +
273N GLN* 1.3 76.0 - - - +
275N ILE* 1.3 63.6 + - - +
277N GLY* 3.2 13.6 + - - -
278N ALA 3.9 1.9 + - - -
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Residues in contact with ILE 275 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246M LYS* 4.4 11.8 - - + +
249M LEU* 3.7 38.8 - - + +
250M LEU* 2.9 45.3 - - + +
253M LYS* 4.3 9.4 - - + -
83N ALA* 3.7 25.4 - - + +
87N ILE* 4.6 7.4 - - + -
271N LEU* 3.2 31.2 + - + +
272N GLU 3.8 0.4 - - - +
274N ALA* 1.3 78.6 - - - +
276N ARG* 1.3 55.8 - - - +
278N ALA* 2.9 30.5 + - - +
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Residues in contact with ARG 276 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246M LYS* 3.6 17.6 + - - +
250M LEU* 3.5 33.5 - - + +
254M ARG* 4.4 12.3 - - - +
272N GLU* 3.0 47.5 + - + +
273N GLN* 3.9 6.1 - - - +
275N ILE* 1.3 73.9 - - - +
277N GLY* 1.3 60.6 + - - +
278N ALA 3.0 13.8 + - - +
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Residues in contact with GLY 277 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N SER* 4.6 4.7 + - - -
273N GLN 3.0 13.9 + - - -
274N ALA* 3.2 8.5 + - - -
275N ILE 3.0 1.2 - - - -
276N ARG* 1.3 77.7 - - - +
278N ALA* 1.3 61.2 + - - +
279N ASP* 3.8 4.5 + - - +
282N GLU* 5.7 0.2 - - - +
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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