Contacts of the helix formed by residues 237 - 255 (chain A) in PDB entry 1EZW
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 ASP 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A ASP* 2.7 17.3 + - - +
236A LYS* 1.3 80.2 - - + +
238A GLU* 1.3 65.4 + - - +
239A ASP* 2.9 25.1 + - - +
240A LYS* 3.0 40.5 + - + +
241A ALA 3.1 9.9 + - - -
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASP 4.1 0.6 + - - -
236A LYS 3.6 5.5 + - - -
237A ASP* 1.3 72.0 + - - +
239A ASP* 1.3 66.8 + - - +
241A ALA* 3.2 2.5 + - - +
242A ILE* 3.0 41.5 + - + +
301A ALA 5.0 0.2 - - - -
302A GLY* 3.7 10.3 - - - -
303A ASP* 3.0 37.6 + - - +
306A THR* 2.5 34.5 + - - +
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 2.9 11.5 + - - +
238A GLU* 1.3 79.2 - - - +
240A LYS* 1.3 58.0 + - + +
242A ILE* 3.4 12.7 + - - +
243A GLU* 3.0 29.6 + - - +
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ASP* 3.9 20.4 - - - +
236A LYS* 6.2 1.1 - - - +
237A ASP* 3.0 38.8 + - + +
239A ASP* 1.3 75.2 - - + +
241A ALA* 1.3 66.7 + - - +
243A GLU* 3.3 7.3 + - - +
244A ALA 3.2 16.8 + - - -
330A PRO* 3.6 27.5 - - - +
334A LYS* 5.8 3.1 - - - +
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A SER* 2.7 51.7 + - - +
235A ASP* 3.7 20.7 - - + +
237A ASP 3.1 6.5 + - - +
238A GLU 3.2 7.8 + - - +
240A LYS* 1.3 75.6 - - - +
242A ILE* 1.3 63.8 + - - +
244A ALA 3.2 7.8 + - - -
245A THR 3.6 0.7 + - - -
301A ALA* 4.6 0.7 - - - -
302A GLY 3.5 21.1 - - - +
330A PRO* 4.1 2.7 - - - -
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLU* 3.0 45.2 + - + +
239A ASP* 3.7 12.1 - - - +
240A LYS 3.3 0.2 - - - -
241A ALA* 1.3 75.7 - - - +
243A GLU* 1.3 62.7 + - - +
245A THR* 2.7 24.3 + - - -
246A LYS* 3.8 8.3 + - - +
292A GLU* 6.6 0.2 - - + -
295A ILE* 3.5 34.3 - - + -
301A ALA* 4.2 26.0 - - + +
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASP 3.0 16.8 + - - +
240A LYS* 3.7 8.5 - - - +
242A ILE* 1.3 77.0 - - - +
244A ALA* 1.3 62.3 - - - +
245A THR 3.2 0.9 + - - -
246A LYS* 3.0 60.6 + - - +
247A ILE 4.9 0.5 + - - -
287A ILE* 3.9 12.0 - - - +
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Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A SER* 3.5 18.8 - - - +
240A LYS 3.2 10.6 + - - +
241A ALA 3.2 2.4 + - - +
243A GLU* 1.3 78.5 - - - +
245A THR* 1.3 60.7 + - - +
246A LYS 3.3 0.2 - - - -
247A ILE* 4.3 13.0 - - - +
327A PRO* 3.6 23.4 - - + +
330A PRO* 3.9 22.0 - - + -
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Residues in contact with THR 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A CYS* 4.3 6.7 - - - -
233A SER* 3.3 28.7 - - - +
241A ALA 3.7 2.9 - - - +
242A ILE 2.7 15.8 + - - +
244A ALA* 1.3 78.3 - - - +
246A LYS* 1.3 66.3 + - - +
247A ILE 3.5 0.2 - - - -
248A VAL* 3.0 7.3 + - - +
249A VAL* 2.8 31.5 + - - +
295A ILE* 3.9 19.4 - - - +
299A SER* 3.9 9.9 - - - +
301A ALA* 3.5 22.4 - - + -
327A PRO* 4.2 7.9 - - + -
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ILE* 4.1 8.5 - - - +
243A GLU* 3.0 52.2 + - - +
245A THR* 1.3 76.0 + - - +
247A ILE* 1.3 57.9 + - - +
249A VAL* 3.2 3.4 + - - +
250A ALA* 2.8 33.5 + - - +
287A ILE* 3.5 37.8 + - + +
288A GLY* 6.2 0.2 - - - -
290A VAL* 3.7 29.5 + - + +
295A ILE* 4.1 18.8 - - + -
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU 4.9 0.2 + - - -
244A ALA 4.3 9.6 + - - +
246A LYS* 1.3 78.3 - - - +
248A VAL* 1.3 86.6 + - + +
250A ALA* 3.4 5.9 + - + +
251A PHE* 3.3 43.2 + - + -
283A PHE* 3.8 28.3 - - + +
286A ALA* 5.6 1.1 - - + -
287A ILE* 4.0 23.9 - - + +
327A PRO* 6.2 0.2 - - + -
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Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A CYS* 3.7 23.6 - - + -
244A ALA 4.9 0.2 - - - +
245A THR 3.0 7.4 + - - +
247A ILE* 1.3 95.8 - - + +
249A VAL* 1.3 63.9 + - - +
251A PHE* 3.2 9.3 + - + +
252A ILE* 3.0 34.4 + - + +
326A SER* 3.6 31.0 - - - +
327A PRO* 4.1 15.3 - - + -
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A CYS* 4.2 2.9 - - - -
245A THR* 2.8 30.8 + - - +
246A LYS 3.8 2.9 - - - +
248A VAL* 1.3 69.2 - - - +
250A ALA* 1.3 58.3 + - - +
252A ILE* 2.9 7.8 + - - +
253A VAL* 2.7 47.6 + - + +
290A VAL* 3.8 23.8 - - + -
294A MET* 3.8 18.8 - - + +
295A ILE* 4.5 5.6 - - + -
298A PHE* 4.2 14.8 - - + +
299A SER* 4.0 27.4 - - - +
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LYS 2.8 20.8 + - - +
247A ILE* 3.5 10.8 - - + +
249A VAL* 1.3 73.3 - - - +
251A PHE* 1.3 56.4 + - + +
253A VAL* 3.4 3.1 + - - +
254A MET* 3.0 23.7 + - - +
274A ILE* 3.5 26.6 - - + +
278A ILE* 3.9 9.9 - - + -
286A ALA* 4.3 15.3 - - + +
290A VAL* 3.8 17.9 - - + +
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Residues in contact with PHE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ILE* 3.3 31.1 + - + +
248A VAL* 3.2 10.4 + - + +
249A VAL 3.2 0.6 - - - -
250A ALA* 1.3 75.6 - - - +
252A ILE* 1.3 67.1 + - + +
254A MET* 3.4 23.9 + - + +
255A GLY* 3.1 18.5 + - - -
278A ILE* 3.6 28.5 - - + -
283A PHE* 3.5 35.2 - + - -
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A CYS* 3.8 17.5 - - + -
248A VAL* 3.2 23.3 - - + +
249A VAL* 2.9 13.1 + - - +
251A PHE* 1.3 76.0 - - + +
253A VAL* 1.3 60.6 + - - +
255A GLY* 3.2 3.7 + - - -
256A SER* 2.6 35.1 + - - +
298A PHE* 3.6 52.5 - - + +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A VAL* 2.7 35.7 + - + +
250A ALA* 3.6 7.4 - - - +
252A ILE* 1.3 72.8 - - - +
254A MET* 1.3 66.0 + - - +
256A SER* 3.3 18.2 + - - +
261A LEU* 4.1 13.9 - - + +
266A ILE* 4.8 2.0 - - + -
271A ALA* 4.0 32.6 - - + +
272A GLU 5.0 1.2 + - - +
274A ILE* 4.3 12.6 - - + -
294A MET* 3.8 28.5 - - + -
298A PHE* 3.9 17.0 - - + -
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Residues in contact with MET 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ALA 3.0 13.8 + - - +
251A PHE* 3.5 40.6 - - + +
252A ILE 3.2 0.2 - - - -
253A VAL* 1.3 80.4 - - - +
255A GLY* 1.3 63.5 + - - +
256A SER 3.5 2.9 + - - +
272A GLU 5.4 2.5 - - - +
274A ILE* 4.8 1.1 - - - +
275A ALA* 3.5 35.2 - - + +
278A ILE* 4.0 30.3 - - + -
279A GLY* 6.1 0.4 - - - -
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Residues in contact with GLY 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A PHE 3.1 11.7 + - - -
252A ILE* 3.2 4.0 + - - -
254A MET* 1.3 83.4 - - - +
256A SER* 1.3 60.0 + - - +
257A PRO* 3.6 7.4 - - - +
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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