Contacts of the helix formed by residues 235 - 246 (chain A) in PDB entry 2XEZ
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLU* 3.5 24.2 + - - +
233A LYS 4.1 1.2 + - - -
234A ILE* 1.3 79.9 - - - +
236A SER* 1.3 78.7 + - - +
237A ALA* 3.3 16.3 + - - +
238A PRO* 3.2 10.8 - - + +
239A LEU* 3.1 19.1 + - - +
267A LYS* 4.3 11.5 + - - -
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Residues in contact with SER 236 (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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234A ILE 3.7 1.2 + - - -
235A ASP* 1.3 82.7 + - - +
237A ALA* 1.3 60.7 + - - +
239A LEU* 3.8 9.2 - - - +
240A ALA* 3.0 28.6 + - - +
263A ARG* 5.3 4.9 + - - -
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Residues in contact with ALA 237 (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* 3.4 7.7 + - - +
236A SER* 1.3 82.3 + - - +
238A PRO* 1.3 70.9 - - + +
240A ALA* 3.4 13.6 + - - +
241A LEU* 3.5 7.6 + - - +
262A ASP* 4.7 1.4 - - - +
263A ARG* 4.6 21.5 - - + +
264A TRP* 3.4 32.9 + - + +
267A LYS* 4.5 13.9 - - + +
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Residues in contact with PRO 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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104A GLU* 3.7 16.6 - - - +
198A LEU* 4.9 1.5 - - + +
202A LEU* 3.5 28.0 - - + -
234A ILE* 3.8 3.6 - - + -
235A ASP* 3.2 23.1 - - + +
237A ALA* 1.3 98.1 - - + +
239A LEU* 1.3 59.7 + - - +
241A LEU* 3.2 8.0 + - - +
242A LEU* 3.1 23.8 + - - +
264A TRP* 3.3 37.5 - - + +
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Residues in contact with LEU 239 (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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221A TRP* 4.1 12.8 - - + -
226A THR* 4.2 20.0 - - + +
231A TRP* 3.9 50.3 - - + +
234A ILE* 3.8 15.2 - - + +
235A ASP 3.1 14.6 + - - +
236A SER* 3.8 8.5 - - - +
237A ALA 3.3 0.2 - - - -
238A PRO* 1.3 78.1 - - - +
240A ALA* 1.3 59.2 + - - +
242A LEU* 3.2 9.8 + - + +
243A HIS* 2.9 41.8 + - + +
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Residues in contact with ALA 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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236A SER 3.0 17.9 + - - +
237A ALA* 3.6 8.7 - - - +
238A PRO 3.2 0.2 - - - -
239A LEU* 1.3 76.0 - - - +
241A LEU* 1.3 61.7 + - - +
243A HIS* 3.4 13.0 + - - +
244A LYS* 3.4 29.4 + - - +
262A ASP* 5.4 2.7 - - - +
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Residues in contact with LEU 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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111A PHE* 3.9 15.9 - - + -
198A LEU* 3.9 16.8 - - + -
237A ALA 3.5 3.6 + - - +
238A PRO* 3.2 12.7 + - + +
240A ALA* 1.3 76.7 - - - +
242A LEU* 1.3 60.7 + - - +
244A LYS* 3.0 12.0 + - - +
245A ILE* 2.9 43.0 + - + +
254A ILE* 4.6 3.6 - - + -
259A ILE* 4.2 16.4 - - + -
262A ASP* 3.5 44.3 + - + +
264A TRP* 3.7 22.0 - - + -
265A TYR* 4.9 1.6 - - + -
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Residues in contact with LEU 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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195A GLY* 3.4 34.8 - - - +
198A LEU* 3.9 24.9 - - + -
199A THR* 3.6 19.7 - - - +
202A LEU* 4.9 1.8 - - + -
221A TRP* 3.7 12.3 - - + -
231A TRP* 4.2 5.6 - - + -
234A ILE* 3.8 28.9 - - + -
238A PRO 3.1 17.7 + - - +
239A LEU* 3.2 13.0 + - - +
241A LEU* 1.3 72.5 - - - +
243A HIS* 1.3 60.3 + - - +
245A ILE* 4.3 4.7 - - + +
246A LEU* 2.8 41.0 + - + +
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Residues in contact with HIS 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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221A TRP* 3.3 35.3 - + - -
224A LYS* 4.8 23.6 - - + +
226A THR* 3.7 23.0 + - + +
239A LEU* 2.9 36.1 + - + +
240A ALA* 3.5 12.6 - - - +
241A LEU 3.2 0.2 - - - -
242A LEU* 1.3 77.9 - - - +
244A LYS* 1.3 61.6 - - + +
246A LEU 4.1 4.7 + - - +
247A VAL* 3.3 17.5 - - - +
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Residues in contact with LYS 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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240A ALA* 3.4 18.1 + - - +
241A LEU* 3.0 10.1 + - - +
243A HIS* 1.3 79.8 - - + +
245A ILE* 1.3 60.2 + - - +
247A VAL* 3.3 14.0 - - - +
254A ILE* 3.3 53.7 + - + +
258A ASP 5.3 0.6 + - - -
262A ASP* 3.0 38.0 + - - +
263A ARG 5.2 0.2 - - - +
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Residues in contact with ILE 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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111A PHE* 4.1 21.3 - - + -
191A VAL* 3.4 30.1 - - + +
192A TRP* 3.9 2.0 - - - -
194A CYS* 5.9 0.4 - - + -
195A GLY* 3.7 25.6 - - - +
198A LEU* 4.7 0.7 - - + -
241A LEU* 2.9 40.8 + - + +
242A LEU* 3.3 9.4 + - + +
244A LYS* 1.3 75.2 - - - +
246A LEU* 1.3 65.7 + - + +
247A VAL 3.0 8.6 + - - -
253A ARG* 3.2 22.7 + - - +
254A ILE* 3.8 20.0 - - + -
259A ILE* 4.4 9.4 - - + -
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Residues in contact with LEU 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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192A TRP* 3.6 54.8 - - + +
195A GLY 4.3 0.2 - - - -
196A ILE* 3.9 15.7 - - + +
199A THR* 4.2 9.2 - - - +
208A TRP* 4.1 10.1 - - + -
218A TYR* 5.6 0.2 + - - -
221A TRP* 3.1 33.6 + - + +
231A TRP* 3.7 34.1 - - + -
242A LEU* 2.8 26.1 + - + +
243A HIS 4.2 2.4 - - - +
245A ILE* 1.3 78.2 - - + +
247A VAL* 1.3 61.9 + - - +
248A GLU 4.1 0.9 + - - -
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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