Contacts of the helix formed by residues 258 - 272 (chain C) in PDB entry 3EZZ
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 TRP 258 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244C CYS 4.6 2.2 - - - -
245C ILE* 3.6 38.6 - - + -
246C PRO* 3.3 41.2 + - + -
247C VAL* 4.1 8.7 - - + +
254C ASP 3.5 14.1 + - - -
255C ILE* 3.5 14.4 - - + +
256C SER 3.2 0.4 - - - -
257C SER* 1.3 87.2 + - - +
259C PHE* 1.3 67.0 + - - +
260C MET 3.1 2.9 - - - -
261C GLU* 3.0 42.1 + - - +
262C ALA* 2.8 24.7 + - - +
290C ILE* 5.8 0.9 - - + -
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Residues in contact with PHE 259 (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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255C ILE* 3.6 20.2 - - + -
256C SER* 2.9 44.4 + - - +
258C TRP* 1.3 76.8 - - - +
260C MET* 1.3 58.7 + - + +
262C ALA* 3.6 3.7 - - - +
263C ILE* 2.8 37.7 + - + +
289C THR* 3.8 30.3 - - + -
290C ILE* 4.6 11.4 - - + -
293C ALA* 3.6 27.1 - - + -
326C GLN 3.9 7.6 - - - -
327C LEU* 4.1 8.1 - - + -
330C PHE* 3.7 50.9 - + + -
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Residues in contact with MET 260 (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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257C SER 4.0 7.9 + - - +
258C TRP 3.1 0.8 - - - -
259C PHE* 1.3 72.8 - - + +
261C GLU* 1.3 62.0 + - - +
263C ILE* 3.3 21.4 + - + +
264C GLU* 2.8 48.2 + - + +
297C MET* 4.3 17.0 - - - +
330C PHE* 4.3 17.9 - - + -
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Residues in contact with GLU 261 (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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243C LYS* 2.8 40.9 + - - +
244C CYS 4.5 2.8 - - - +
245C ILE* 5.3 2.7 - - + -
257C SER 4.9 0.8 + - - +
258C TRP* 3.0 45.3 + - + +
260C MET* 1.3 78.3 - - - +
262C ALA* 1.3 58.3 + - - +
264C GLU* 3.2 16.2 + - - +
265C TYR* 3.0 27.4 + - - +
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Residues in contact with ALA 262 (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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226C LEU* 4.1 11.4 - - + -
243C LYS* 6.0 0.2 - - - -
245C ILE* 3.3 31.2 - - + +
258C TRP 2.8 13.3 + - - +
259C PHE* 3.6 5.4 - - - +
261C GLU* 1.3 76.2 - - - +
263C ILE* 1.3 67.3 - - + +
265C TYR* 3.1 8.7 + - - +
266C ILE* 2.8 28.4 + - - +
290C ILE* 4.2 16.4 - - + -
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C PHE* 2.8 34.9 + - + +
260C MET* 3.7 15.3 - - + +
262C ALA* 1.3 72.3 - - + +
264C GLU* 1.3 50.8 + - - +
266C ILE* 3.2 3.4 + - + +
267C ASP* 2.7 57.1 + - - +
290C ILE* 5.7 0.7 - - + +
293C ALA* 4.3 6.7 - - + +
294C TYR* 3.7 35.7 - - + +
297C MET* 3.8 41.3 - - + -
298C LYS* 4.5 4.7 - - + -
330C PHE* 4.0 17.5 - - + -
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Residues in contact with GLU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C MET* 2.8 39.5 + - + +
261C GLU* 3.2 15.3 + - - +
263C ILE* 1.3 76.4 - - + +
265C TYR* 1.3 54.0 + - - +
267C ASP* 2.9 11.1 + - - +
268C ALA* 2.7 36.4 + - - +
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Residues in contact with TYR 265 (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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224C ALA* 3.4 6.2 - - - +
225C LEU 3.4 11.8 + - - -
226C LEU* 3.9 15.9 - - + -
241C GLN* 3.2 51.5 + - + +
242C TYR 3.6 4.5 - - - -
243C LYS* 3.2 46.9 - - + -
261C GLU 3.0 10.4 + - - +
262C ALA* 3.1 9.6 + - - +
264C GLU* 1.3 78.1 - - - +
266C ILE* 1.3 65.3 + - - +
268C ALA* 2.9 24.7 - - + +
269C VAL* 3.0 25.2 + - + +
276C VAL* 4.1 18.4 - - + -
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Residues in contact with ILE 266 (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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202C PHE* 3.7 15.7 - - + -
203C LEU* 4.1 27.4 - - + -
226C LEU* 4.2 16.4 - - + -
262C ALA 2.8 23.7 + - - +
263C ILE 3.5 6.1 - - - +
265C TYR* 1.3 75.7 - - + +
267C ASP* 1.3 62.5 + - - +
268C ALA 3.2 0.2 + - - -
269C VAL* 3.3 4.2 + - - +
270C LYS* 2.9 20.4 + - - +
276C VAL* 4.4 13.7 - - + -
278C VAL* 4.2 11.4 - - + -
290C ILE* 4.5 9.4 - - + -
291C CYS* 5.7 0.2 - - - -
294C TYR* 3.3 47.3 - - + -
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Residues in contact with ASP 267 (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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263C ILE* 2.7 42.6 + - - +
264C GLU* 3.3 9.1 + - - +
266C ILE* 1.3 72.7 - - - +
268C ALA* 1.3 59.4 + - - +
270C LYS* 3.0 18.0 + - + +
271C ASP* 2.6 38.7 + - - +
294C TYR* 3.2 9.2 + - - -
298C LYS* 3.1 32.1 + - - +
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Residues in contact with ALA 268 (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 GLN* 5.9 1.6 - - - +
264C GLU 2.7 16.6 + - - +
265C TYR* 2.9 18.8 - - + +
267C ASP* 1.3 71.9 - - - +
269C VAL* 1.3 65.8 + - + +
271C ASP* 3.0 20.9 + - - +
272C CYS* 3.1 18.8 + - - -
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Residues in contact with VAL 269 (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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202C PHE* 5.5 0.4 - - - +
223C THR* 3.6 24.0 - - - +
224C ALA* 3.6 17.7 - - + -
241C GLN* 4.5 9.9 - - - +
265C TYR* 3.0 29.2 + - + +
266C ILE 3.8 0.9 - - - +
268C ALA* 1.3 74.9 - - + +
270C LYS* 1.3 58.7 + - - +
272C CYS* 3.3 14.2 + - + +
274C GLY* 2.8 29.4 + - - -
275C ARG 3.6 10.3 - - - +
276C VAL* 3.1 34.5 - - + -
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Residues in contact with LYS 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C PHE* 3.5 44.6 - - + +
266C ILE 2.9 14.3 + - - +
267C ASP* 3.0 26.6 + - + +
269C VAL* 1.3 79.3 - - - +
271C ASP* 1.3 63.5 + - - +
273C ARG* 3.0 21.5 + - - +
294C TYR* 3.7 19.5 + - - +
298C LYS* 4.8 8.1 - - - +
299C LYS* 5.3 8.7 - - - +
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Residues in contact with ASP 271 (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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267C ASP* 2.6 25.1 + - - +
268C ALA* 3.4 9.5 - - - +
270C LYS* 1.3 85.0 - - - +
272C CYS* 1.3 57.3 + - - +
273C ARG* 2.9 15.4 + - - +
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Residues in contact with CYS 272 (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 GLN* 5.3 10.3 - - - -
268C ALA* 3.1 22.0 + - - -
269C VAL* 3.3 11.9 + - + +
270C LYS 3.3 0.4 - - - -
271C ASP* 1.3 76.3 - - - +
273C ARG* 1.3 71.1 + - - +
274C GLY* 3.2 3.7 + - - +
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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