Contacts of the helix formed by residues 266 - 279 (chain J) in PDB entry 2QC8
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 266 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260J ALA 3.4 25.1 - - - -
261J MET* 3.6 14.8 - - - -
263J GLU 2.9 11.1 + - - -
264J GLU 3.2 0.6 - - - -
265J ASN* 1.3 73.9 - - - +
267J LEU* 1.3 58.0 + - - +
268J LYS 3.2 0.4 - - - -
269J TYR* 2.9 27.2 + - - +
270J ILE* 3.0 14.2 + - - +
333J LYS 3.1 3.2 + - - -
334J LYS* 4.1 0.2 - - - +
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Residues in contact with LEU 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265J ASN 3.0 1.1 - - - +
266J GLY* 1.3 73.6 - - - +
268J LYS* 1.3 59.8 + - - +
270J ILE* 3.2 13.4 + - + +
271J GLU* 2.8 48.7 + - - +
325J ILE* 4.1 28.5 - - + -
329J VAL* 4.4 22.9 - - + +
330J GLY* 4.4 9.0 - - - +
333J LYS* 2.9 46.7 + - + +
334J LYS* 4.1 1.0 - - - +
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Residues in contact with LYS 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265J ASN* 3.3 16.1 + - + +
267J LEU* 1.3 77.8 - - - +
269J TYR* 1.3 85.5 + - + +
271J GLU* 3.2 10.6 + - - +
272J GLU* 3.0 44.9 + - + +
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Residues in contact with TYR 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258J THR* 5.3 0.2 - - - +
260J ALA* 3.6 39.3 - - + -
261J MET* 3.5 27.4 - - + +
264J GLU 6.0 1.1 - - - -
265J ASN 5.1 2.0 - - - -
266J GLY* 2.9 17.7 + - - +
268J LYS* 1.3 100.8 + - + +
270J ILE* 1.3 60.2 + - - +
272J GLU* 3.4 27.2 + - - +
273J ALA 3.0 20.8 + - - -
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Residues in contact with ILE 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261J MET* 3.7 24.5 - - + +
266J GLY 3.0 11.7 + - - +
267J LEU* 3.2 21.7 + - + +
269J TYR* 1.3 76.5 - - - +
271J GLU* 1.3 57.3 + - - +
273J ALA* 2.8 21.8 + - - +
274J ILE* 2.9 22.9 + - + +
325J ILE* 4.6 11.9 - - + -
329J VAL* 3.7 20.2 - - + -
335J GLY 4.0 7.4 - - - +
336J TYR* 3.6 28.7 - - - +
337J PHE* 3.7 29.8 - - + -
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Residues in contact with GLU 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267J LEU* 2.8 47.9 + - + +
268J LYS* 3.6 10.1 - - - +
270J ILE* 1.3 72.3 - - - +
272J GLU* 1.3 60.7 + - - +
274J ILE* 4.0 10.1 - - + +
275J GLU* 3.3 22.2 + - - +
325J ILE* 4.7 14.1 - - + +
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Residues in contact with GLU 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268J LYS* 3.0 32.5 + - + +
269J TYR* 3.5 33.0 - - - +
270J ILE 3.1 0.4 + - - -
271J GLU* 1.3 73.3 - - - +
273J ALA* 1.3 66.5 + - - +
275J GLU* 3.3 6.6 + - - +
276J LYS* 3.2 42.1 + - - +
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Residues in contact with ALA 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261J MET* 3.5 29.4 - - + -
269J TYR 3.0 4.4 + - - -
270J ILE 2.8 14.7 + - - +
272J GLU* 1.3 71.9 - - - +
274J ILE* 1.3 60.3 + - - +
276J LYS* 3.3 9.4 + - - +
277J LEU* 3.0 28.8 + - - +
337J PHE* 3.7 16.2 - - + -
359J CYS* 3.9 21.5 - - + +
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Residues in contact with ILE 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270J ILE* 2.9 25.3 + - + +
271J GLU* 4.0 9.6 - - + +
273J ALA* 1.3 75.7 - - - +
275J GLU* 1.3 58.8 + - - +
277J LEU* 3.0 10.5 + - - +
278J SER* 2.9 26.0 + - - -
312J PHE* 3.8 12.9 - - + -
314J ALA* 3.9 25.6 - - + -
323J ILE* 4.0 28.5 - - + -
325J ILE* 4.0 30.3 - - + -
337J PHE* 4.4 10.1 - - + -
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Residues in contact with GLU 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271J GLU 3.3 16.9 + - - +
272J GLU* 3.6 8.5 - - - +
273J ALA 3.3 0.2 - - - -
274J ILE* 1.3 78.6 - - - +
276J LYS* 1.3 64.7 + - + +
278J SER* 2.5 33.6 + - - -
279J LYS* 3.7 29.6 + - - +
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Residues in contact with LYS 276 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272J GLU* 3.2 31.0 + - - +
273J ALA* 3.6 6.7 - - - +
275J GLU* 1.3 79.1 - - + +
277J LEU* 1.3 61.9 + - - +
279J LYS* 3.3 22.5 + - - +
280J ARG* 3.8 4.3 + - - +
358J THR* 3.7 28.3 - - + +
359J CYS* 3.5 23.6 + - - +
362J ASN* 2.4 39.3 + - - +
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Residues in contact with LEU 277 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273J ALA 3.0 22.7 + - - +
274J ILE* 3.0 9.2 + - - +
276J LYS* 1.3 75.9 - - - +
278J SER* 1.3 64.7 + - - +
280J ARG* 3.1 20.5 + - - +
281J HIS* 3.7 0.7 + - - -
284J HIS* 3.2 40.6 - - + +
312J PHE* 3.6 19.9 - - + -
323J ILE* 4.7 7.4 - - + -
337J PHE* 3.6 34.8 - - + -
341J ARG* 4.1 9.9 + - - +
355J LEU* 4.1 6.7 - - + -
358J THR* 3.7 7.0 - - + -
359J CYS* 3.7 18.6 - - - -
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Residues in contact with SER 278 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J ILE* 2.9 9.9 + - - -
275J GLU* 2.5 35.1 + - - -
277J LEU* 1.3 76.8 - - - +
279J LYS* 1.3 64.6 + - - +
280J ARG 3.5 0.7 + - - -
281J HIS* 4.3 10.0 + - - +
312J PHE* 3.6 36.9 - - - +
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Residues in contact with LYS 279 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275J GLU* 3.7 39.0 + - - +
276J LYS* 3.7 12.6 - - - +
277J LEU 3.1 1.0 - - - -
278J SER* 1.3 81.7 - - - +
280J ARG* 1.3 64.3 + - + +
281J HIS 3.8 1.3 - - - -
364J THR* 6.6 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