Contacts of the helix formed by residues 270 - 282 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134J ALA* 3.8 3.6 - - - -
263J GLU* 3.8 3.1 - - - -
266J TRP 4.0 11.4 - - - -
267J PRO 3.5 6.1 + - - -
268J GLN 3.0 5.5 - - - -
269J PHE* 1.3 80.2 - - - +
271J VAL* 1.3 68.1 + - - +
272J GLY 3.3 2.7 - - - -
273J ALA* 2.8 19.8 + - - +
274J GLU 3.5 2.4 + - - -
138L HIS* 3.8 15.5 - - - -
269L PHE* 4.1 5.1 - - - -
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Residues in contact with VAL 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J ALA* 3.8 28.9 - - + -
134J ALA* 4.1 7.0 - - + +
212J HIS* 4.2 9.2 - - + +
238J MET* 4.0 29.8 - - + -
241J ILE* 4.7 6.3 - - + -
244J MET* 4.7 3.6 - - + -
263J GLU* 3.1 20.7 + - + +
270J GLY* 1.3 68.9 - - - -
272J GLY* 1.3 67.0 + - - +
274J GLU* 2.9 13.5 + - - +
275J ILE* 3.2 18.7 + - + +
269L PHE* 3.5 25.8 - - + -
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Residues in contact with GLY 272 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261J THR* 3.4 29.8 - - - -
263J GLU* 2.4 30.6 + - - -
271J VAL* 1.3 68.5 - - - +
273J ALA* 1.3 63.5 + - - +
275J ILE* 3.0 4.1 + - - +
276J CYS* 2.8 24.3 + - - -
294J ARG* 3.6 11.2 - - - -
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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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269J PHE* 4.4 3.1 - - - -
270J GLY 2.8 22.3 + - - +
272J GLY* 1.3 69.8 - - - +
274J GLU* 1.3 56.9 + - - +
276J CYS* 3.1 2.1 + - - +
277J ALA* 2.9 30.0 + - - +
294J ARG* 3.4 26.4 - - - +
269L PHE* 5.8 0.7 - - - -
273L ALA* 3.8 24.4 - - + +
274L GLU* 3.7 12.3 - - - +
277L ALA* 3.8 9.9 - - + -
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Residues in contact with GLU 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244J MET* 3.6 21.5 - - + -
270J GLY 3.5 1.4 + - - -
271J VAL 2.9 4.9 + - - +
273J ALA* 1.3 76.4 - - - +
275J ILE* 1.3 64.2 - - - +
277J ALA 3.2 1.0 + - - -
278J ARG* 2.9 60.6 + - - +
268L GLN* 3.5 23.2 + - - +
269L PHE* 3.2 45.2 + - + +
273L ALA* 3.5 4.2 - - - +
294L ARG* 3.2 24.1 + - - -
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Residues in contact with ILE 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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210J VAL* 4.1 12.1 - - + +
238J MET* 4.0 26.7 - - + -
244J MET* 3.9 17.9 - - - -
246J MET* 3.9 9.8 - - + +
249J ILE* 4.2 21.1 - - + -
259J LEU* 4.2 16.2 - - + -
261J THR* 3.8 31.6 - - + -
271J VAL* 3.2 19.4 + - + +
272J GLY 3.0 6.1 + - - +
274J GLU* 1.3 76.5 - - - +
276J CYS* 1.3 57.5 + - - +
278J ARG* 3.7 5.0 - - - +
279J ILE* 2.9 26.7 + - - +
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Residues in contact with CYS 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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259J LEU* 5.5 0.9 - - - -
261J THR* 4.5 10.1 - - - -
272J GLY 2.8 15.1 + - - -
273J ALA 3.6 7.0 - - - +
275J ILE* 1.3 74.4 - - - +
277J ALA* 1.3 67.0 + - - +
279J ILE* 3.3 5.4 + - - +
280J MET* 3.1 23.0 + - - +
292J ALA* 4.0 18.8 - - - -
293J VAL 5.2 0.4 - - - -
294J ARG* 3.8 24.5 - - - -
276L CYS* 5.3 0.2 - - - -
277L ALA* 4.2 13.2 - - + -
280L MET* 3.3 31.0 - - + +
281L GLU* 6.0 0.7 - - - -
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Residues in contact with ALA 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 2.9 16.3 + - - +
274J GLU 3.8 2.5 - - - +
276J CYS* 1.3 76.8 - - - +
278J ARG* 1.3 62.3 + - - +
280J MET* 3.3 5.5 + - - +
281J GLU* 3.0 29.2 + - - +
273L ALA* 3.9 9.9 - - + -
276L CYS* 3.8 26.8 - - + +
294L ARG* 3.6 30.3 - - - +
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Residues in contact with ARG 278 (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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349I ARG* 4.7 4.7 - - - +
244J MET* 4.0 22.4 + - - +
246J MET* 3.2 50.4 - - + +
250J GLU* 4.2 1.8 - - - +
274J GLU* 2.9 45.5 + - - +
275J ILE 3.7 3.8 - - - +
277J ALA* 1.3 75.9 - - - +
279J ILE* 1.3 60.1 + - - +
281J GLU* 3.2 10.2 + - - +
282J GLY* 2.8 31.2 + - - -
268L GLN* 3.3 18.2 + - - +
294L ARG* 3.9 11.0 - - - +
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Residues in contact with ILE 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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246J MET* 3.7 22.2 - - + -
249J ILE* 4.7 2.0 - - + -
250J GLU* 3.9 15.5 - - + +
253J VAL* 4.8 8.5 - - + -
259J LEU* 3.6 29.2 - - + -
275J ILE 2.9 14.1 + - - +
276J CYS* 3.7 6.7 - - - +
277J ALA 3.3 0.2 - - - -
278J ARG* 1.3 78.4 - - - +
280J MET* 1.3 64.4 - - + +
282J GLY 3.5 6.4 + - - +
284J ALA* 3.7 28.3 - - + -
285J PHE* 3.5 23.4 + - + -
288J LEU* 4.1 28.5 - - + -
292J ALA* 5.2 0.2 - - + -
280L MET* 5.0 5.4 - - + -
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Residues in contact with MET 280 (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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276J CYS 3.1 7.3 + - - +
277J ALA 3.5 7.4 - - - +
279J ILE* 1.3 81.7 - - + +
281J GLU* 1.3 60.9 + - - +
282J GLY 3.6 0.9 - - - +
285J PHE* 3.3 44.8 - - + +
276L CYS* 3.6 41.5 - - + +
279L ILE* 4.8 7.0 - - + -
280L MET* 4.4 19.1 - - + -
285L PHE* 4.9 6.7 - - - -
288L LEU* 5.3 2.7 - - - -
291L PRO* 3.3 19.1 - - + +
292L ALA* 3.6 41.3 - - + +
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Residues in contact with GLU 281 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349I ARG* 2.7 36.3 + - - -
353I GLN* 3.2 39.4 + - + +
277J ALA 3.0 14.8 + - - +
278J ARG* 4.0 9.2 - - - +
280J MET* 1.3 72.7 - - + +
282J GLY* 1.3 65.3 + - - +
276L CYS* 6.1 0.9 - - - -
291L PRO* 4.9 4.2 - - - +
292L ALA 4.2 15.9 - - - +
293L VAL* 4.8 1.6 - - + -
294L ARG* 2.6 46.6 + - + +
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Residues in contact with GLY 282 (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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250J GLU* 3.6 6.1 - - - -
278J ARG 2.8 17.1 + - - -
279J ILE 3.5 6.1 + - - +
280J MET 3.3 5.5 - - - +
281J GLU* 1.3 82.4 - - - +
283J PRO* 1.3 75.9 - - - +
284J ALA 3.3 3.6 + - - -
285J PHE* 3.7 4.7 + - - +
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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