Contacts of the helix formed by residues 233 - 244 (chain A) in PDB entry 4WMB
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 ASN 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A LEU 3.5 15.1 + - - +
128A ALA* 3.2 4.7 - - - +
129A LYS* 2.8 59.2 + - + +
130A PHE* 4.4 0.2 - - - -
232A THR* 1.3 78.9 + - - +
234A ILE* 1.3 56.9 + - - +
235A ARG* 3.1 22.5 + - - +
236A GLU* 2.8 50.7 + - - +
237A LEU 4.2 0.3 + - - -
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Residues in contact with ILE 234 (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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100A LEU* 4.1 24.9 - - + -
124A LEU* 3.6 28.0 + - + -
128A ALA* 4.0 15.5 - - + +
130A PHE* 4.0 18.6 - - + -
136A LEU* 4.8 2.9 - - + -
222A ILE* 5.2 0.4 - - + -
224A LEU* 4.3 9.6 - - + -
230A TYR* 3.9 27.4 - - + -
232A THR* 3.3 8.7 + - - +
233A ASN* 1.3 71.8 + - - +
235A ARG* 1.3 64.6 + - - +
237A LEU* 2.9 45.7 + - + +
238A PHE* 3.8 7.7 - - + -
351A TRP* 5.2 2.2 - - + -
380A ILE* 4.6 2.9 - - + -
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Residues in contact with ARG 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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98A TYR* 3.9 15.2 + - + -
129A LYS 3.4 14.6 - - - +
130A PHE* 3.6 27.6 - - + -
131A GLU* 3.5 31.6 + - - +
134A GLU* 2.3 45.7 + - - -
233A ASN* 2.9 22.7 + - - +
234A ILE* 1.3 80.7 - - - +
236A GLU* 1.3 60.7 + - + +
238A PHE* 3.3 21.6 + - - +
239A GLU* 4.1 2.9 + - - +
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Residues in contact with GLU 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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232A THR* 2.7 31.6 + - - +
233A ASN* 2.8 32.9 + - + +
235A ARG* 1.3 70.5 - - + +
237A LEU* 1.3 64.4 + - - +
239A GLU* 3.1 45.3 + - - +
240A GLU* 4.2 1.2 + - - +
351A TRP* 4.1 14.5 - - + -
379A LYS* 5.2 5.7 - - - -
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Residues in contact with LEU 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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222A ILE* 3.9 15.0 - - + -
224A LEU* 4.9 0.2 - - + -
234A ILE* 2.9 32.3 + - + +
236A GLU* 1.3 79.4 - - - +
238A PHE* 1.3 61.7 + - - +
240A GLU* 3.0 25.2 + - + +
291A VAL* 3.9 24.2 - - + -
293A LEU* 3.7 27.3 - - + +
347A LEU* 4.3 12.1 - - + -
351A TRP* 3.6 52.2 - - + +
380A ILE* 4.4 2.2 - - + -
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Residues in contact with PHE 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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98A TYR* 3.6 42.0 - + + -
99A HIS 3.7 33.2 - - - -
100A LEU* 3.7 15.3 - - + -
130A PHE* 5.0 4.0 - + - -
136A LEU* 5.2 0.4 - - + -
220A ARG* 5.5 8.1 - - + -
221A ILE* 5.3 2.0 - - - -
222A ILE* 3.6 26.7 - - + -
234A ILE* 3.8 19.3 - - + -
235A ARG* 3.3 15.1 + - - +
236A GLU 3.2 0.8 - - - -
237A LEU* 1.3 77.2 - - - +
239A GLU* 1.3 62.0 + - - +
241A PHE* 3.1 47.6 + + - +
242A ASP* 4.9 1.4 - - - +
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Residues in contact with GLU 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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235A ARG 4.1 2.1 + - - +
236A GLU* 3.1 39.9 + - - +
237A LEU 3.1 1.4 + - - -
238A PHE* 1.3 77.9 - - - +
240A GLU* 1.3 66.0 + - - +
241A PHE 3.1 0.4 - - - -
242A ASP* 2.9 42.2 + - - +
243A ASN* 3.9 6.4 + - - +
351A TRP* 5.4 2.1 - - - -
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Residues in contact with GLU 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 GLU 5.0 2.2 - - - +
237A LEU* 3.0 18.1 + - + +
239A GLU* 1.3 82.2 - - + +
241A PHE* 1.3 62.9 + - - +
242A ASP 3.2 0.2 - - - -
243A ASN* 3.1 36.3 + - - +
244A PHE* 3.3 13.2 - - - -
293A LEU* 3.6 15.7 - - + -
345A HIS* 2.7 33.1 + - - -
347A LEU* 3.9 19.5 - - + +
348A ASP 5.8 0.8 + - - -
351A TRP* 4.2 22.2 + - + +
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Residues in contact with PHE 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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220A ARG* 3.8 47.3 - - + -
221A ILE 4.0 6.3 - - - -
222A ILE* 3.9 5.2 - - + -
238A PHE* 3.1 50.9 + + + +
239A GLU 3.1 0.6 - - - -
240A GLU* 1.3 76.5 - - - +
242A ASP* 1.3 65.7 + - - +
243A ASN 3.2 1.0 + - - -
244A PHE* 3.2 36.8 + + - +
293A LEU* 3.6 49.1 - - + -
294A LEU 4.0 2.7 - - - -
295A ASN* 3.9 20.2 + - + +
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Residues in contact with ASP 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 PHE 5.1 1.3 - - - -
239A GLU* 2.9 28.5 + - - +
241A PHE* 1.3 79.5 - - - +
243A ASN* 1.3 63.1 + - - +
244A PHE 3.4 5.0 + - - +
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Residues in contact with ASN 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 GLU* 4.4 6.1 + - - +
240A GLU* 3.1 44.4 + - - +
242A ASP* 1.3 84.6 - - - +
244A PHE* 1.3 64.2 + - - +
245A LEU* 3.3 10.9 + - - +
345A HIS* 3.5 26.8 + - + -
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Residues in contact with PHE 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 GLU 3.3 20.0 - - - -
241A PHE* 3.2 30.3 + + - +
242A ASP 3.4 4.7 - - - +
243A ASN* 1.3 75.9 - - - +
245A LEU* 1.3 67.4 + - - +
246A PRO* 4.6 0.9 - - - +
248A ALA* 3.7 24.7 - - + +
249A VAL 3.6 26.2 - - - -
250A ILE 3.7 2.9 - - - -
251A GLY* 3.3 24.5 - - - -
293A LEU* 3.8 10.5 - - + -
295A ASN* 3.9 22.0 - - + +
345A HIS* 3.8 26.9 - + + -
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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