Contacts of the helix formed by residues 224 - 235 (chain A) in PDB entry 4U2M
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 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A GLU* 3.9 25.8 + - - +
205A GLY* 6.2 0.7 - - - -
208A ILE* 3.3 29.8 - - + +
219A ASN 3.4 7.1 + - - -
220A LEU* 3.6 6.8 - - - +
221A ARG* 3.0 45.5 + - + +
223A GLY* 1.3 77.4 - - - +
225A ILE* 1.3 69.6 + - - +
226A MET 3.2 2.8 + - - -
227A ALA* 3.3 11.6 + - + +
228A VAL* 3.0 27.2 + - + +
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Residues in contact with ILE 225 (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 LEU* 4.6 11.7 - - + -
221A ARG 3.0 21.8 - - - +
222A GLU* 3.6 28.7 + - + +
223A GLY 3.7 1.2 - - - -
224A ASN* 1.3 82.9 - - - +
226A MET* 1.3 60.1 + - + +
228A VAL* 3.4 4.8 + - - +
229A MET* 2.9 28.1 + - - +
244A CYS* 3.9 24.2 - - + +
247A PHE* 4.9 17.5 - - + +
248A ILE* 3.9 33.2 - - + -
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Residues in contact with MET 226 (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 GLU 5.3 2.4 + - - +
223A GLY 5.5 0.2 - - - -
224A ASN 3.3 0.8 - - - -
225A ILE* 1.3 78.7 - - + +
227A ALA* 1.3 56.6 + - - +
229A MET* 3.7 11.6 - - - +
230A ALA* 3.0 29.7 + - - +
248A ILE* 3.6 32.3 - - - -
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Residues in contact with ALA 227 (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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202A ASN* 4.1 33.0 - - + +
205A GLY* 4.6 5.4 - - - -
223A GLY 5.7 0.7 - - - +
224A ASN* 3.3 14.3 + - + +
226A MET* 1.3 75.9 - - - +
228A VAL* 1.3 57.1 + - - +
230A ALA* 3.5 4.9 + - - +
231A THR* 2.6 38.5 + - - -
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Residues in contact with VAL 228 (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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205A GLY* 4.2 11.7 - - - -
208A ILE* 3.9 28.3 - - + -
209A LEU* 3.8 23.6 - - + +
218A LEU* 4.4 6.5 - - + -
220A LEU* 3.8 22.2 - - + -
224A ASN* 3.0 34.4 + - + +
225A ILE 3.8 3.6 - - - +
227A ALA* 1.3 75.5 - - - +
229A MET* 1.3 58.6 + - - +
231A THR* 3.2 6.1 + - - -
232A ALA* 2.9 28.6 + - - +
240A VAL* 4.7 0.2 - - + -
244A CYS* 3.8 8.7 - - - -
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Residues in contact with MET 229 (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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225A ILE 2.9 19.4 + - - +
226A MET* 3.7 13.9 - - - +
228A VAL* 1.3 77.6 - - - +
230A ALA* 1.3 60.7 + - - +
232A ALA* 3.3 4.4 + - - +
233A MET* 3.0 37.1 + - - +
241A VAL* 3.6 19.7 - - + +
244A CYS* 3.3 22.8 - - + -
245A ARG* 3.0 59.2 - - + +
248A ILE* 3.7 19.1 - - + -
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Residues in contact with ALA 230 (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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201A ILE* 5.6 1.1 - - - +
226A MET 3.0 18.4 + - - +
227A ALA* 3.8 6.1 - - - +
229A MET* 1.3 73.8 - - - +
231A THR* 1.3 67.1 + - - +
233A MET* 3.2 16.5 + - - +
234A TYR* 3.1 22.9 + - - +
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Residues in contact with THR 231 (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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201A ILE* 4.0 25.1 - - + +
202A ASN* 4.3 9.2 + - - +
205A GLY* 4.1 10.0 - - - -
206A PHE* 4.0 21.5 - - + -
209A LEU* 3.5 21.1 - - + -
227A ALA 2.6 23.6 + - - -
228A VAL 3.7 0.9 - - - -
230A ALA* 1.3 75.7 - - - +
232A ALA* 1.3 57.2 + - - +
234A TYR* 3.4 8.3 + - + +
235A LEU* 2.9 37.7 + - + +
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Residues in contact with ALA 232 (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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209A LEU* 3.4 12.1 - - + +
228A VAL 2.9 17.2 + - - +
229A MET* 3.7 5.8 - - - +
230A ALA 3.2 0.4 - - - -
231A THR* 1.3 74.0 - - - +
233A MET* 1.3 62.3 + - - +
235A LEU* 3.4 3.8 + - - +
236A GLN 3.0 7.3 + - - -
237A MET* 2.9 35.8 + - + +
240A VAL* 3.8 26.5 - - + -
241A VAL* 3.7 14.8 - - + +
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Residues in contact with MET 233 (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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229A MET* 3.0 36.3 + - - +
230A ALA* 3.4 16.6 - - - +
232A ALA* 1.3 77.8 - - - +
234A TYR* 1.3 63.0 + - - +
236A GLN* 3.1 18.1 + - - +
241A VAL* 3.6 24.9 - - + -
245A ARG* 5.7 6.1 - - - +
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Residues in contact with TYR 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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179A LEU* 3.6 37.1 - - + +
183A ILE* 5.9 0.3 - - - +
197A LEU* 3.8 20.5 - - + +
198A ASP* 3.6 26.1 + - + +
201A ILE* 3.6 41.3 - - + -
230A ALA 3.1 10.2 + - - +
231A THR* 3.5 7.6 - - + +
233A MET* 1.3 81.4 - - - +
235A LEU* 1.3 74.5 + - + +
236A GLN* 3.3 10.4 + - - +
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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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177A SER* 2.8 24.5 + - - +
178A GLY 3.5 2.4 + - - -
179A LEU* 3.4 18.0 + - + -
180A PHE* 3.9 23.3 - - + -
197A LEU* 4.7 2.2 - - + -
206A PHE* 4.0 28.9 - - + -
209A LEU* 4.0 13.5 - - + -
213A MET* 4.3 2.2 - - + -
231A THR* 2.9 22.2 + - + +
232A ALA 4.0 0.9 - - - +
233A MET 3.3 0.2 - - - -
234A TYR* 1.3 91.3 - - + +
236A GLN* 1.3 69.8 + - - +
237A MET* 2.7 38.5 + - + -
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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