Contacts of the helix formed by residues 284 - 295 (chain C) in PDB entry 3ENM
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 SER 284 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLU* 2.3 36.1 + - - -
283C PHE* 1.3 70.8 - - - +
285C ALA* 1.3 54.9 + - - +
286C GLU* 3.8 14.9 + - - +
287C PHE* 3.6 13.7 - - - -
288C VAL* 2.8 39.5 + - - +
313C PHE* 5.6 0.6 - - - -
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C PHE 3.7 1.0 + - - -
284C SER* 1.3 71.2 - - - +
286C GLU* 1.3 66.2 + - - +
288C VAL* 3.4 7.9 + - - +
289C ASP* 2.8 35.0 + - - +
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Residues in contact with GLU 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C SER* 3.2 15.3 + - - -
285C ALA* 1.3 88.5 + - - +
287C PHE* 1.3 59.2 + - - +
289C ASP* 4.4 1.8 - - - -
290C PHE* 2.9 23.9 + - - +
311C HIS* 3.1 16.2 - - + -
312C PRO* 4.1 24.9 - - + -
313C PHE* 3.7 21.9 - - + +
316C LEU* 5.0 12.8 - - + +
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Residues in contact with PHE 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C GLU* 3.3 34.8 - - + +
155C LEU* 3.9 21.1 - - + -
247C MSE 4.0 33.9 - - + -
251C ALA* 3.8 17.0 - - + -
278C LEU* 3.5 24.8 - - + +
283C PHE* 3.9 11.0 - + + -
284C SER* 3.2 5.9 + - - +
286C GLU* 1.3 77.0 - - - +
288C VAL* 1.3 64.1 + - - +
290C PHE* 4.2 4.3 - + - -
291C THR* 3.1 30.8 + - - -
313C PHE* 3.4 42.8 - + + -
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLN* 6.3 1.6 - - + -
278C LEU* 4.0 32.1 - - + +
280C ALA* 4.5 14.6 - - + -
283C PHE* 3.6 24.0 - - + +
284C SER 2.8 27.0 + - - +
285C ALA* 3.5 7.4 - - - +
287C PHE* 1.3 77.3 - - - +
289C ASP* 1.3 62.6 + - - +
291C THR* 3.4 4.2 + - - +
292C SER* 2.8 34.0 + - - +
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Residues in contact with ASP 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ALA 2.8 18.4 + - - +
286C GLU* 3.8 3.8 - - - +
288C VAL* 1.3 78.1 - - - +
290C PHE* 1.3 67.1 + - - +
292C SER* 3.0 8.2 + - - -
293C GLN* 2.8 45.8 + - - +
311C HIS* 3.0 25.7 + - + +
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Residues in contact with PHE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ALA* 4.2 15.5 - - + -
163C VAL* 4.5 6.7 - - + -
243C LEU* 4.4 13.0 - - + -
244C GLY* 6.1 0.7 - - - -
247C MSE 4.2 22.7 - - + -
286C GLU 2.9 19.5 + - - +
287C PHE* 3.7 6.7 - + - +
288C VAL 3.4 0.2 - - - -
289C ASP* 1.3 74.9 - - - +
291C THR* 1.3 70.7 + - - +
293C GLN* 3.5 4.9 + - - +
294C CYS* 3.3 40.5 + - - -
308C LEU* 4.2 28.2 - - + +
311C HIS* 3.5 31.3 + + + -
313C PHE* 3.6 30.3 - + + -
314C PHE* 4.8 7.9 - + + -
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Residues in contact with THR 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C GLY* 4.6 2.2 + - - -
247C MSE 4.3 8.5 - - - +
248C ILE* 3.3 39.7 - - + +
276C PRO 4.9 2.0 - - - +
277C GLN* 5.1 1.1 - - - -
278C LEU* 3.8 23.2 - - + +
287C PHE* 3.1 26.9 + - - -
288C VAL* 3.6 5.4 - - + +
289C ASP 3.1 0.2 - - - -
290C PHE* 1.3 80.7 - - - +
292C SER* 1.3 69.0 + - - +
294C CYS* 3.1 6.5 + - - +
295C LEU* 2.9 30.1 + - + +
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Residues in contact with SER 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C GLN* 5.6 5.9 - - - +
288C VAL* 2.8 22.9 + - - +
289C ASP* 3.0 14.0 + - - -
291C THR* 1.3 78.2 - - - +
293C GLN* 1.3 66.9 + - - +
295C LEU* 3.2 14.2 + - - +
296C LYS* 3.2 30.7 + - - +
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Residues in contact with GLN 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ASP* 2.8 45.8 + - - +
290C PHE* 3.8 5.8 - - - +
292C SER* 1.3 81.3 - - - +
294C CYS* 1.3 61.3 + - - +
296C LYS* 3.7 17.0 - - - +
301C GLU 4.3 12.6 - - - +
302C ARG* 3.4 12.6 - - - +
303C PRO* 3.0 37.3 - - + +
308C LEU* 5.4 1.6 - - + -
311C HIS* 4.6 11.2 - - + -
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Residues in contact with CYS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240C ILE* 3.4 35.9 - - - +
241C TRP* 3.4 11.1 + - - -
243C LEU* 4.2 13.0 - - - -
244C GLY* 3.7 15.3 - - - -
290C PHE* 3.3 35.2 + - - -
291C THR 3.1 9.2 + - - +
293C GLN* 1.3 77.0 - - - +
295C LEU* 1.3 55.7 + - - +
296C LYS 3.4 0.7 - - - -
302C ARG* 2.8 27.0 - - - -
308C LEU* 4.4 9.9 - - - -
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C TRP* 3.2 49.4 - - + +
244C GLY* 3.4 25.4 - - - +
245C ILE* 3.8 21.8 - - + +
248C ILE* 3.7 23.3 - - + -
275C SER* 2.5 41.6 + - - +
276C PRO* 4.0 9.6 - - + +
291C THR* 2.9 18.2 + - + +
292C SER* 3.2 7.6 + - - +
294C CYS* 1.3 75.2 - - - +
296C LYS* 1.3 59.6 + - - +
297C LYS 3.4 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