Contacts of the helix formed by residues 270 - 282 (chain F) in PDB entry 3EXE
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134F ALA* 3.8 11.7 - - - -
263F GLU* 4.0 2.7 - - - -
266F TRP 3.8 15.3 - - - -
267F PRO 3.1 13.1 + - - -
268F GLN 3.1 4.0 - - - -
269F PHE* 1.3 82.2 - - - +
271F VAL* 1.3 66.6 + - - +
272F GLY 3.5 2.2 - - - -
273F ALA* 3.3 15.1 + - - +
274F GLU 3.6 0.3 + - - -
138H HIS* 4.2 1.8 - - - -
269H PHE* 3.5 9.4 - - - +
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Residues in contact with VAL 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F CYS* 5.8 0.9 - - - -
133F ALA* 3.8 29.6 - - + -
134F ALA* 3.9 11.0 - - + +
212F HIS* 4.0 14.6 - - + +
238F MET* 3.9 36.3 - - + -
241F ILE* 4.5 4.7 - - + -
244F MET* 4.7 0.4 - - + -
263F GLU* 2.9 20.0 + - + +
270F GLY* 1.3 71.8 - - - -
272F GLY* 1.3 64.5 + - - +
274F GLU* 3.1 15.1 + - - +
275F ILE* 3.2 14.9 + - + +
269H PHE* 3.6 19.3 - - + -
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Residues in contact with GLY 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F THR* 3.4 28.9 - - - -
263F GLU* 2.9 21.3 + - - -
271F VAL* 1.3 72.9 - - - +
273F ALA* 1.3 55.4 + - - +
275F ILE* 3.3 4.1 + - - +
276F CYS* 2.8 35.5 + - - -
294F ARG* 3.6 11.2 - - - -
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Residues in contact with ALA 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263F GLU* 4.7 0.2 + - - -
269F PHE* 4.3 2.2 - - - -
270F GLY* 3.3 19.5 + - - +
271F VAL 3.2 0.8 - - - -
272F GLY* 1.3 76.7 - - - +
274F GLU* 1.3 57.1 + - - +
276F CYS* 3.8 1.6 - - - +
277F ALA* 2.9 29.5 + - - +
294F ARG* 3.6 10.1 - - - +
269H PHE* 5.7 0.2 - - - -
273H ALA* 3.5 24.6 - - + +
274H GLU* 3.4 26.0 - - - +
277H ALA* 3.8 11.2 - - - -
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Residues in contact with GLU 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F MET* 4.0 13.0 - - + -
270F GLY 3.6 1.4 + - - -
271F VAL 3.1 2.4 + - - +
273F ALA* 1.3 75.6 - - - +
275F ILE* 1.3 63.0 + - - +
277F ALA 3.7 0.4 - - - +
278F ARG* 2.8 65.7 + - - +
267H PRO* 4.8 0.5 - - - +
268H GLN* 3.6 15.0 - - + +
269H PHE* 2.9 52.6 + - + +
273H ALA* 3.5 4.1 - - - +
294H ARG* 2.9 40.0 + - - -
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Residues in contact with ILE 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F VAL* 4.2 12.8 - - + +
238F MET* 3.9 29.4 - - + -
244F MET* 3.9 21.3 - - + -
246F MET* 4.0 8.0 - - + +
249F ILE* 4.3 17.9 - - + -
259F LEU* 4.1 15.3 - - + -
261F THR* 3.6 33.0 - - + -
271F VAL* 3.2 17.6 + - + +
272F GLY* 3.3 5.8 + - - +
274F GLU* 1.3 76.3 - - - +
276F CYS* 1.3 58.5 + - - +
278F ARG* 3.4 5.7 + - - +
279F ILE* 2.9 28.1 + - - +
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Residues in contact with CYS 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F THR* 4.4 11.4 - - - -
272F GLY 2.8 21.1 + - - +
273F ALA 3.9 3.6 - - - +
275F ILE* 1.3 74.7 - - - +
277F ALA* 1.3 65.9 + - - +
279F ILE* 3.4 4.7 + - - +
280F MET* 3.1 19.5 + - - +
292F ALA* 3.9 31.0 - - - -
293F VAL 4.7 0.7 - - - -
294F ARG* 3.8 22.4 - - - -
277H ALA* 3.9 16.2 - - + -
280H MET* 3.5 24.0 - - + +
281H GLU* 5.8 0.4 - - - -
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Residues in contact with ALA 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273F ALA 2.9 19.2 + - - +
274F GLU 3.8 2.0 - - - +
276F CYS* 1.3 74.5 - - - +
278F ARG* 1.3 63.5 + - - +
280F MET* 3.2 5.0 + - - +
281F GLU* 3.0 26.7 + - - +
273H ALA* 3.8 14.6 + - + -
276H CYS* 4.0 21.2 - - + +
294H ARG* 3.5 32.1 - - - +
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Residues in contact with ARG 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349E ARG* 4.8 6.1 - - - +
244F MET* 4.0 21.9 + - - +
246F MET* 3.8 43.5 - - + +
250F GLU* 3.9 4.4 - - - +
274F GLU* 2.8 50.0 + - - +
275F ILE* 3.7 4.0 - - - +
277F ALA* 1.3 78.2 - - - +
279F ILE* 1.3 61.9 + - - +
281F GLU* 3.8 10.1 - - - +
282F GLY* 3.0 22.7 + - - -
268H GLN* 3.6 22.1 + - - +
294H ARG* 3.9 8.1 - - - +
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Residues in contact with ILE 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F MET* 3.4 26.2 - - + -
249F ILE* 4.4 2.0 - - + -
250F GLU* 4.0 8.3 - - + -
253F VAL* 4.0 20.9 - - + -
259F LEU* 3.5 28.0 - - + -
275F ILE 2.9 13.2 + - - +
276F CYS* 3.8 5.4 - - - +
277F ALA 3.2 0.2 - - - -
278F ARG* 1.3 77.6 - - - +
280F MET* 1.3 64.6 + - - +
282F GLY* 3.4 6.9 + - - +
284F ALA* 4.0 26.0 + - + -
285F PHE* 3.4 20.9 + - - +
288F LEU* 3.9 30.3 - - + -
292F ALA* 4.7 0.7 - - + -
280H MET* 4.7 6.3 - - + -
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Residues in contact with MET 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F CYS 3.1 14.3 + - - +
277F ALA 3.7 2.9 - - - +
279F ILE* 1.3 79.5 - - - +
281F GLU* 1.3 58.3 + - - +
285F PHE* 3.5 46.8 - - + +
276H CYS* 3.4 43.1 - - + +
279H ILE* 5.4 0.7 - - + -
280H MET* 4.1 17.7 - - + +
285H PHE* 4.1 4.7 - - - -
288H LEU* 4.1 12.6 - - + -
291H PRO* 3.2 27.8 - - + +
292H ALA* 3.6 30.3 - - + +
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Residues in contact with GLU 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349E ARG* 3.0 30.4 + - - -
353E GLN* 2.8 41.8 + - + +
277F ALA* 3.0 16.5 + - + +
278F ARG* 3.4 10.4 + - - +
280F MET* 1.3 74.2 - - - +
282F GLY* 1.3 58.8 + - - +
276H CYS* 5.8 0.7 - - - -
291H PRO* 5.0 2.4 - - - +
292H ALA 4.0 15.9 - - - +
293H VAL* 4.4 3.8 - - - +
294H ARG* 2.7 60.9 + - + -
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Residues in contact with GLY 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250F GLU* 4.1 3.8 - - - -
278F ARG 3.0 16.1 + - - -
279F ILE 3.4 2.4 + - - -
280F MET 3.3 1.6 - - - +
281F GLU* 1.3 80.4 - - - +
283F PRO* 1.3 76.1 - - - +
284F ALA 3.2 4.9 + - - -
285F PHE* 3.4 15.2 + - - +
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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