Contacts of the helix formed by residues 270 - 282 (chain N) in PDB entry 3EXG
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 270 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134N ALA* 3.6 13.7 - - - -
263N GLU* 4.0 5.8 - - - -
266N TRP 4.2 0.7 - - - -
267N PRO 3.3 12.6 + - - -
268N GLN 3.0 5.2 - - - -
269N PHE* 1.3 81.1 - - - +
271N VAL* 1.3 66.6 + - - -
272N GLY 3.2 3.1 - - - -
273N ALA* 3.2 16.7 + - - +
274N GLU 3.4 4.7 + - - -
138P HIS* 4.1 6.5 - - - -
269P PHE* 3.6 6.3 - - - -
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Residues in contact with VAL 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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131N CYS* 6.0 1.3 - - - -
133N ALA* 4.0 27.6 - - + -
134N ALA* 4.1 10.5 - - + +
212N HIS* 4.1 11.0 - - + +
238N MET* 4.1 32.5 - - + -
241N ILE* 4.6 7.4 - - + -
244N MET* 4.5 5.2 - - + -
263N GLU* 3.0 22.3 + - + +
270N GLY* 1.3 72.8 - - - -
272N GLY* 1.3 63.4 + - - +
274N GLU* 3.3 3.6 + - - +
275N ILE* 3.2 24.3 + - + +
269P PHE* 3.6 18.8 - - + -
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Residues in contact with GLY 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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261N THR* 3.7 26.0 - - - -
263N GLU* 2.8 22.0 + - - -
271N VAL* 1.3 71.3 - - - +
273N ALA* 1.3 67.9 + - - +
275N ILE* 3.0 6.6 + - - +
276N CYS* 3.0 26.0 + - - -
294N ARG* 3.5 10.8 - - - -
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Residues in contact with ALA 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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263N GLU* 4.5 0.4 + - - -
269N PHE* 4.2 4.0 - - - -
270N GLY 3.2 18.7 + - - +
272N GLY* 1.3 76.4 - - - +
274N GLU* 1.3 56.8 + - - +
276N CYS* 3.3 2.6 + - - +
277N ALA* 2.9 28.9 + - - +
294N ARG* 3.5 18.3 - - - +
269P PHE* 6.0 0.2 - - - -
273P ALA* 3.7 22.3 - - + +
274P GLU* 3.4 24.9 - - - +
277P ALA* 4.1 4.3 - - - -
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Residues in contact with GLU 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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244N MET* 4.1 21.3 - - - -
270N GLY 3.4 1.8 + - - -
271N VAL 3.3 2.3 + - - +
272N GLY 3.1 0.6 - - - -
273N ALA* 1.3 79.9 - - - +
275N ILE* 1.3 69.4 + - - +
277N ALA 3.0 1.2 + - - -
278N ARG* 2.8 54.2 + - - +
268P GLN* 3.3 19.2 - - + +
269P PHE* 3.1 50.8 + - + +
273P ALA* 4.0 4.8 - - - +
294P ARG* 3.2 25.9 + - - -
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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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210N VAL* 4.1 20.0 - - + -
238N MET* 4.1 18.4 - - + -
244N MET* 4.0 17.0 - - + -
246N MET* 3.9 9.7 - - + +
249N ILE* 4.2 18.2 - - + -
259N LEU* 4.3 13.9 - - + -
261N THR* 3.7 31.6 - - + -
271N VAL* 3.2 18.4 - - + +
272N GLY* 3.0 6.8 + - - +
274N GLU* 1.3 79.1 - - - +
276N CYS* 1.3 57.0 + - - +
278N ARG* 3.5 5.3 + - - +
279N ILE* 2.9 27.4 + - - +
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Residues in contact with CYS 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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259N LEU* 5.3 2.2 - - - -
261N THR* 5.2 6.5 - - - -
272N GLY 3.0 12.1 + - - +
273N ALA 3.6 7.0 - - - +
275N ILE* 1.3 78.7 - - - +
277N ALA* 1.3 69.5 + - - +
279N ILE* 3.6 3.3 - - - +
280N MET* 3.0 24.5 + - - +
292N ALA* 4.1 21.5 - - - -
293N VAL 5.3 0.7 - - - -
294N ARG* 4.5 17.3 - - - -
277P ALA* 4.3 15.0 - - + -
280P MET* 3.5 26.3 - - + +
281P GLU* 5.9 1.6 - - - -
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Residues in contact with ALA 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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273N ALA 2.9 17.1 + - - +
274N GLU 3.0 4.0 + - - +
276N CYS* 1.3 78.3 - - - +
278N ARG* 1.3 62.5 + - - +
280N MET* 3.4 4.3 + - - +
281N GLU* 3.1 27.7 + - - +
273P ALA* 3.7 18.4 - - + -
276P CYS* 4.0 17.6 - - + +
294P ARG* 3.5 29.6 - - - +
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Residues in contact with ARG 278 (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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349M ARG* 5.1 4.4 - - - +
244N MET* 4.6 13.3 + - - +
246N MET* 3.7 45.3 - - + +
250N GLU* 4.6 2.1 - - - +
274N GLU* 2.8 43.8 + - + +
275N ILE* 3.6 4.3 - - - +
277N ALA* 1.3 73.9 - - - +
279N ILE* 1.3 72.9 + - - +
281N GLU* 3.0 25.6 + - - +
282N GLY* 3.0 9.9 + - - -
268P GLN* 4.6 14.1 + - - +
294P ARG* 4.2 2.2 - - - +
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Residues in contact with ILE 279 (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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246N MET* 3.3 23.9 - - + +
249N ILE* 4.9 0.9 - - + -
250N GLU* 4.1 13.9 - - + +
253N VAL* 4.7 9.2 - - + -
259N LEU* 3.6 30.1 - - + -
275N ILE 2.9 17.8 + - - +
276N CYS* 3.2 7.2 + - - +
278N ARG* 1.3 75.3 - - - +
280N MET* 1.3 79.6 + - + +
281N GLU 2.7 12.5 + - - -
282N GLY* 2.7 18.7 + - - +
284N ALA* 3.9 25.8 - - + -
285N PHE* 4.1 10.5 + - + +
288N LEU* 4.3 25.6 - - + -
292N ALA* 5.6 0.7 - - + -
280P MET* 4.6 6.1 - - + -
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Residues in contact with MET 280 (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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276N CYS 3.0 13.6 + - - +
277N ALA 3.7 2.7 - - - +
279N ILE* 1.3 87.4 - - + +
281N GLU* 1.3 59.4 + - - +
282N GLY 4.3 0.2 - - - +
285N PHE* 3.6 37.6 - - + +
276P CYS* 3.6 44.2 - - + +
279P ILE* 5.2 1.3 - - + -
280P MET* 4.4 14.1 - - + +
285P PHE* 4.8 2.5 - - - -
288P LEU* 4.7 13.0 - - - -
291P PRO* 3.2 21.8 - - + +
292P ALA* 3.4 40.6 - - + +
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Residues in contact with GLU 281 (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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349M ARG* 2.8 45.6 + - - -
353M GLN* 3.0 36.3 + - + +
277N ALA 3.1 12.6 + - - +
278N ARG* 3.0 15.9 + - - +
279N ILE 2.7 5.9 + - - -
280N MET* 1.3 76.7 - - - +
282N GLY* 1.3 57.8 + - - +
276P CYS* 5.8 0.7 - - - -
291P PRO* 5.1 2.0 - - - -
292P ALA 3.9 17.3 - - - +
293P VAL* 4.6 1.6 - - + -
294P ARG* 3.1 42.3 + - + +
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Residues in contact with GLY 282 (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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250N GLU* 3.9 5.4 - - - -
278N ARG* 3.0 6.1 + - - -
279N ILE 2.7 9.6 + - - +
280N MET 4.3 0.2 - - - +
281N GLU* 1.3 80.3 - - - +
283N PRO* 1.3 76.8 - - - +
284N ALA 3.1 4.4 + - - -
285N PHE* 3.3 15.8 + - - +
286N ASN* 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