Contacts of the helix formed by residues 233 - 245 (chain A) in PDB entry 1EX0
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 GLY 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A GLU 4.9 1.6 + - - -
71A ASN* 6.1 1.2 - - - +
231A GLU 3.3 1.0 + - - -
232A ASP* 1.3 80.3 + - - +
234A ILE* 1.3 57.9 + - - +
235A LEU 3.5 2.0 - - - -
236A ASP* 3.7 16.4 + - - +
237A THR* 2.8 32.0 + - - -
300A LEU* 3.9 10.2 - - - +
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A GLY 3.4 17.5 - - - +
229A GLN* 3.8 16.2 - - - +
231A GLU* 3.3 20.6 + - + +
232A ASP 4.2 1.8 - - - +
233A GLY* 1.3 74.8 - - - +
235A LEU* 1.3 61.9 + - - +
237A THR* 3.1 3.0 + - - -
238A CYS* 2.9 31.8 + - - -
296A VAL* 4.1 17.5 - - + +
299A LEU* 4.1 22.9 - - + -
300A LEU* 4.0 24.7 - - + -
323A THR* 3.8 27.4 - - + -
327A CYS* 4.0 7.0 - - - -
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Residues in contact with LEU 235 (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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69A TYR* 4.0 26.5 - - + -
71A ASN* 4.7 8.7 - - - +
75A ILE* 4.2 11.2 - - + -
181A TYR* 3.6 37.2 - - + -
183A LEU* 4.0 26.7 - - + -
229A GLN 4.4 1.2 + - - -
231A GLU 4.7 1.2 + - - -
233A GLY 3.5 1.2 - - - +
234A ILE* 1.3 74.8 - - - +
236A ASP* 1.3 63.8 + - - +
238A CYS* 3.1 10.9 + - - +
239A LEU* 3.1 18.6 + - + +
327A CYS* 3.4 29.0 - - - +
328A LEU* 4.2 12.8 - - + -
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Residues in contact with ASP 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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71A ASN* 4.4 6.8 + - - -
156A LYS* 4.3 9.3 + - - +
181A TYR* 2.6 38.9 + - - -
233A GLY* 3.7 15.8 + - - +
234A ILE 3.3 0.4 - - - -
235A LEU* 1.3 74.5 - - - +
237A THR* 1.3 57.5 + - - +
239A LEU* 3.4 10.5 + - - +
240A TYR* 3.0 27.0 + - - +
303A ARG* 5.0 3.8 - - - -
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Residues in contact with THR 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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233A GLY 2.8 19.2 + - - -
234A ILE* 3.1 9.6 + - - -
236A ASP* 1.3 76.5 - - - +
238A CYS* 1.3 58.9 + - - +
240A TYR* 3.3 7.3 + - + +
241A VAL* 2.9 25.6 + - - +
299A LEU* 3.5 46.9 - - + +
300A LEU* 3.7 8.5 - - - +
302A TYR* 4.4 8.7 - - + -
303A ARG* 3.7 27.1 - - + +
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Residues in contact with CYS 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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234A ILE* 2.9 24.8 + - - -
235A LEU* 3.1 8.9 + - - +
237A THR* 1.3 74.1 - - - +
239A LEU* 1.3 67.1 + - - +
241A VAL* 3.2 14.8 + - - +
242A MET* 3.3 12.0 + - - +
299A LEU* 5.0 7.4 - - - -
324A PHE* 3.6 52.0 - - + -
327A CYS* 3.8 17.7 - - - -
328A LEU* 4.0 15.7 - - + -
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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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20A ASN* 3.7 26.2 - - + +
154A VAL* 4.8 0.7 - - + +
155A GLY* 4.0 17.9 - - - -
156A LYS* 3.8 24.2 - - + +
181A TYR* 4.0 17.9 - - + -
183A LEU* 6.0 1.1 - - + -
235A LEU* 3.1 18.1 + - + +
236A ASP* 3.6 11.7 - - - +
238A CYS* 1.3 76.6 - - - +
240A TYR* 1.3 55.6 + - - +
242A MET* 3.3 27.1 + - + +
243A ASP* 2.9 33.7 + - - +
252A ARG* 3.9 1.4 + - - +
328A LEU* 4.1 13.7 - - + -
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Residues in contact with TYR 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 ASP 3.0 14.5 + - - +
237A THR 3.4 8.3 - - - +
238A CYS 3.3 0.2 - - - -
239A LEU* 1.3 72.0 - - - +
241A VAL* 1.3 55.2 + - - +
243A ASP* 3.2 13.0 + - + +
244A ARG* 2.8 75.8 + - + +
302A TYR* 3.5 34.3 - + - -
303A ARG* 3.5 63.9 - - + +
306A GLU* 3.1 23.5 + - + +
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Residues in contact with VAL 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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237A THR 2.9 21.1 + - - +
238A CYS* 3.2 13.9 + - - +
240A TYR* 1.3 73.5 - - - +
242A MET* 1.3 59.2 + - - +
244A ARG* 3.1 5.1 + - - +
245A ALA* 2.9 26.5 + - - +
262A GLY* 4.8 5.8 - - - +
265A MET* 3.7 31.3 - - + +
266A VAL* 6.5 0.2 - - + -
274A VAL* 4.4 11.7 - - + -
299A LEU* 4.6 11.7 - - + -
302A TYR* 4.1 27.1 - - + -
324A PHE* 4.1 21.8 - - + -
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Residues in contact with MET 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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154A VAL* 4.7 7.2 - - + +
238A CYS 3.3 9.8 + - - +
239A LEU* 3.3 31.9 + - + +
241A VAL* 1.3 80.2 - - + +
243A ASP* 1.3 62.0 + - - +
245A ALA* 3.1 13.0 + - - +
247A MET* 3.0 45.1 + - + +
252A ARG* 3.6 42.4 - - + +
258A VAL* 4.4 11.0 - - - -
261A VAL* 5.7 0.9 - - + -
262A GLY* 5.7 2.7 - - - -
324A PHE* 4.0 22.7 - - + -
328A LEU* 4.0 20.0 - - + -
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Residues in contact with ASP 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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18A ASN 4.1 3.9 - - - +
19A SER* 3.7 10.8 - - - +
20A ASN* 2.7 27.0 + - - +
21A ALA* 3.1 30.8 + - + +
239A LEU* 2.9 19.7 + - - +
240A TYR* 3.2 15.3 + - + +
242A MET* 1.3 73.1 - - - +
244A ARG* 1.3 57.4 + - + +
246A GLN* 2.7 28.8 + - - +
252A ARG* 2.8 29.2 + - - +
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Residues in contact with ARG 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 TYR* 2.8 59.9 + - + +
241A VAL 3.1 3.6 + - - +
243A ASP* 1.3 73.8 - - - +
245A ALA* 1.3 59.7 + - - +
246A GLN* 3.4 9.4 + - - +
265A MET* 3.8 10.3 - - + +
271A ASP 4.3 7.9 + - - -
272A GLU* 3.4 36.9 + - - +
302A TYR* 3.3 31.5 + - - +
306A GLU* 2.8 32.7 + - - +
307A ASN* 5.2 0.6 + - - +
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Residues in contact with ALA 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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241A VAL 2.9 7.4 + - - +
242A MET* 3.1 13.0 + - - +
244A ARG* 1.3 76.4 - - - +
246A GLN* 1.3 69.8 + - - +
247A MET* 4.1 2.1 - - + +
261A VAL* 3.7 24.6 - - + +
265A MET* 3.7 32.9 - - + +
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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