Contacts of the helix formed by residues 277 - 291 (chain C) in PDB entry 2E52
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 MET 277 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272C LEU* 3.2 44.0 + - + -
275C ILE* 3.7 20.2 - - + -
276C ASN* 1.3 73.8 - - - +
278C SER* 1.3 64.8 + - - +
280C LYS* 3.2 12.2 + - - +
281C ILE* 3.1 25.8 + - - +
252D TRP* 3.5 24.9 - - + +
255D GLN* 3.7 30.5 - - - -
256D ILE* 3.6 26.7 - - + -
259D ILE* 3.3 20.6 - - + -
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Residues in contact with SER 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ASN* 3.2 6.8 - - - +
277C MET* 1.3 78.8 - - - +
279C SER* 1.3 63.1 + - - +
281C ILE* 3.3 8.5 + - - +
282C GLU* 3.0 38.5 + - - +
256D ILE* 4.2 15.4 - - - +
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Residues in contact with SER 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C ASN* 3.1 38.8 + - - -
278C SER* 1.3 78.1 - - - +
280C LYS* 1.3 59.2 + - - +
282C GLU* 3.6 16.0 + - - +
283C THR* 2.8 39.1 + - - -
117D THR* 5.8 1.4 - - - +
9H T 4.1 11.6 + - - -
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Residues in contact with LYS 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ILE* 3.6 29.0 + - - -
276C ASN 3.2 7.1 + - - +
277C MET* 3.2 10.9 + - - +
279C SER* 1.3 77.1 - - - +
281C ILE* 1.3 57.3 + - - +
283C THR* 3.2 5.8 + - - -
284C ILE* 3.0 34.8 + - - +
115D SER* 3.8 23.6 + - - +
252D TRP* 3.3 52.3 - - + +
7H C 4.8 1.0 + - - -
8H T 3.3 32.9 + - - +
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Residues in contact with ILE 281 (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 MET 3.1 8.7 + - - +
278C SER* 3.3 8.7 + - - +
280C LYS* 1.3 77.6 - - - +
282C GLU* 1.3 59.5 + - + +
284C ILE* 3.2 9.2 + - - +
285C ASP* 2.9 41.6 + - - +
249D LYS* 4.0 24.2 - - + +
252D TRP* 3.7 28.5 - - + -
253D LYS* 3.9 24.0 - - + +
256D ILE* 4.1 18.8 - - + -
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C SER* 3.0 25.6 + - - +
279C SER* 3.6 19.6 + - - +
280C LYS 3.3 0.2 - - - -
281C ILE* 1.3 76.8 - - + +
283C THR* 1.3 58.9 + - - +
285C ASP* 3.5 8.1 + - - +
286C SER* 2.8 31.9 + - - -
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Residues in contact with THR 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C SER* 2.8 28.8 + - - -
280C LYS* 3.2 6.8 + - - -
282C GLU* 1.3 74.3 - - - +
284C ILE* 1.3 59.2 + - - +
286C SER* 3.3 6.6 + - - +
287C PHE* 2.9 29.8 + - + +
114D LEU 3.9 3.6 - - - +
115D SER 3.3 31.2 - - - +
116D ARG 3.7 12.8 - - - +
117D THR* 4.1 16.7 - - + +
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Residues in contact with ILE 284 (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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280C LYS 3.0 23.3 + - - +
281C ILE* 3.2 5.8 + - - +
283C THR* 1.3 76.4 - - - +
285C ASP* 1.4 61.8 + - - +
287C PHE* 3.3 3.1 + - - +
288C ILE* 3.0 23.9 + - + +
51D GLU* 3.7 30.1 - - + +
114D LEU* 3.6 17.0 - - + -
115D SER* 3.5 19.7 - - - +
245D SER* 3.8 26.5 - - - +
248D GLU* 4.4 2.7 - - + -
249D LYS* 3.7 38.6 - - + +
252D TRP* 4.4 6.5 - - + -
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Residues in contact with ASP 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C ILE* 2.9 32.0 + - - +
282C GLU* 3.8 7.3 - - - +
284C ILE* 1.4 76.0 - - - +
286C SER* 1.3 57.7 + - - +
288C ILE* 3.4 7.0 + - - +
289C LYS* 2.9 28.6 + - - +
249D LYS* 2.9 33.4 + - - +
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Residues in contact with SER 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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282C GLU 2.8 21.8 + - - -
283C THR* 3.7 6.8 + - - +
285C ASP* 1.3 70.6 - - - +
287C PHE* 1.3 60.7 + - - +
289C LYS* 3.5 8.2 + - - +
290C GLY* 3.0 24.1 + - - -
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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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283C THR* 2.9 18.4 + - + +
284C ILE 3.3 3.3 + - - +
286C SER* 1.3 75.0 + - - +
288C ILE* 1.3 76.2 + - + +
290C GLY* 3.2 2.9 + - - -
291C ILE* 3.0 43.8 + - + +
296C ARG* 4.7 3.3 + - - -
114D LEU* 3.5 41.5 - - + +
119D LYS* 5.6 1.1 - - - -
144D PRO* 6.1 1.1 - - + -
146D PHE* 3.5 34.5 - + + -
147D GLN* 3.6 32.1 - - + -
241D ILE* 3.9 19.1 - - + -
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Residues in contact with ILE 288 (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 ILE* 3.0 19.0 + - + +
285C ASP* 3.8 6.7 - - - +
287C PHE* 1.3 80.9 - - + +
289C LYS* 1.3 65.8 + - - +
291C ILE* 3.3 25.8 + - + +
292C LYS* 3.5 19.2 - - + +
114D LEU* 5.0 0.7 - - + -
241D ILE* 3.7 29.2 - - + -
242D GLU* 3.8 35.9 - - + +
245D SER* 3.6 31.4 - - - +
249D LYS* 6.2 0.7 - - - +
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Residues in contact with LYS 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 ASP 2.9 18.3 + - - +
286C SER* 3.8 8.3 - - - +
288C ILE* 1.3 78.1 - - - +
290C GLY* 1.3 63.5 + - - +
292C LYS* 3.4 21.4 + - - +
293C SER* 3.9 5.4 + - - -
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C SER 3.0 15.7 + - - -
287C PHE* 3.2 4.0 + - - -
289C LYS* 1.3 77.7 - - - +
291C ILE* 1.3 60.4 + - - +
292C LYS 3.1 0.2 - - - -
293C SER* 3.2 23.4 + - - -
296C ARG* 3.3 26.0 - - - +
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C PHE* 3.0 31.2 + - + +
288C ILE* 3.3 27.6 - - + +
290C GLY* 1.3 75.2 - - - +
292C LYS* 1.3 59.6 + - + +
293C SER 3.2 7.8 + - - +
296C ARG* 4.0 17.1 - - - +
146D PHE* 3.4 38.9 - - + -
238D ILE* 3.4 44.2 - - + +
241D ILE* 3.7 38.4 - - + -
242D GLU* 5.7 0.4 - - + -
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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