Contacts of the helix formed by residues 291 - 303 (chain A) in PDB entry 1MU5
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 GLU 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A THR* 2.7 10.7 + - - +
290A GLU* 1.3 76.4 - - - +
292A GLU* 1.3 67.5 + - + +
293A ILE 3.2 0.9 - - - -
294A THR* 3.7 8.5 - - - +
295A ARG* 2.3 59.4 + - - +
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Residues in contact with GLU 292 (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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279A LEU* 3.5 32.2 - - + +
283A LYS* 2.4 39.6 + - - +
288A LEU* 2.9 23.4 - - + +
289A THR* 2.8 31.3 + - + +
291A GLU* 1.3 77.6 - - + +
293A ILE* 1.3 57.9 + - - +
295A ARG* 3.2 23.3 + - - +
296A LEU* 3.1 22.7 + - - +
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Residues in contact with ILE 293 (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 ARG* 3.8 41.1 - - + +
241A ILE* 4.8 10.1 - - + -
242A LYS* 4.8 20.2 - - + +
245A ILE* 4.8 7.6 - - + -
288A LEU* 3.9 30.3 - - + -
289A THR 2.8 19.9 + - - +
290A GLU* 3.7 19.3 - - - +
292A GLU* 1.3 71.6 - - - +
294A THR* 1.3 59.4 + - - +
295A ARG 2.8 1.1 - - - -
296A LEU* 2.4 33.0 + - + +
297A VAL* 2.9 14.1 + - + +
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Residues in contact with THR 294 (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 ARG* 2.7 33.6 + - - +
290A GLU 2.3 31.4 + - - -
291A GLU* 3.7 10.0 - - - -
293A ILE* 1.3 78.4 - - - +
295A ARG* 1.3 56.3 + - - +
297A VAL* 3.3 2.8 + - - +
298A GLU* 2.9 55.1 + - + +
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Residues in contact with ARG 295 (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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276A LEU 5.1 1.8 - - - +
277A ALA* 2.5 32.8 + - + +
278A GLY* 2.8 32.1 + - - -
279A LEU* 4.1 1.6 - - - +
291A GLU* 2.3 48.4 + - - +
292A GLU* 3.2 31.6 + - - +
293A ILE 2.7 4.0 + - - -
294A THR* 1.3 75.2 - - - +
296A LEU* 1.3 55.4 + - - +
298A GLU* 4.0 9.8 - - - +
299A THR* 2.6 40.0 + - - +
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Residues in contact with LEU 296 (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 ILE* 4.6 13.5 - - + -
254A ILE* 5.4 2.5 - - + -
257A PHE* 4.7 8.7 - - + -
258A LEU* 3.8 24.7 - - + -
273A ILE* 3.7 29.8 - - + -
277A ALA* 4.3 4.7 - - + +
279A LEU* 3.7 26.0 - - + -
288A LEU* 4.7 15.5 - - + -
292A GLU 3.1 9.0 + - - +
293A ILE* 2.4 20.3 + - - +
295A ARG* 1.3 71.1 - - - +
297A VAL* 1.3 51.8 + - - +
299A THR* 3.1 5.2 + - - -
300A PHE* 2.7 59.5 + - + -
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Residues in contact with VAL 297 (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 VAL 4.0 16.2 - - - +
237A ASP* 4.2 2.0 - - - -
238A ARG* 3.6 44.9 - - + +
241A ILE* 3.9 20.0 - - + -
293A ILE* 2.9 10.5 + - + +
294A THR* 3.6 6.5 - - - +
296A LEU* 1.3 73.8 - - - +
298A GLU* 1.3 64.4 + - + +
300A PHE* 3.0 10.7 + - + +
301A LYS* 2.8 41.4 + - + +
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Residues in contact with GLU 298 (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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294A THR* 2.9 38.4 + - + +
295A ARG* 4.0 9.8 - - - +
297A VAL* 1.3 78.1 - - + +
299A THR* 1.3 63.6 + - - +
301A LYS* 3.4 8.1 + - - +
302A LYS* 3.0 37.9 + - + +
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Residues in contact with THR 299 (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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273A ILE* 4.0 30.3 - - + +
276A LEU* 3.8 29.5 + - + -
277A ALA* 3.4 19.1 + - - +
295A ARG* 2.6 25.7 + - - +
296A LEU* 3.3 5.8 - - - -
298A GLU* 1.3 75.3 - - - +
300A PHE* 1.3 65.2 + - - +
302A LYS* 3.0 5.7 + - - +
303A TYR* 2.9 24.6 + - + +
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Residues in contact with PHE 300 (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 PRO* 3.7 32.3 - - + +
234A TYR* 3.4 17.3 - - - -
236A VAL* 3.7 25.6 - - + +
241A ILE* 3.5 28.9 - - + -
258A LEU* 4.0 14.4 - - + -
262A PHE* 4.1 13.0 - + - -
265A ILE* 4.2 15.7 - - + -
273A ILE* 4.3 9.9 - - + -
296A LEU* 2.7 44.7 + - + -
297A VAL* 3.2 12.6 - - + +
299A THR* 1.3 75.0 - - - +
301A LYS* 1.3 65.0 + - + +
302A LYS 3.0 1.2 + - - -
303A TYR 3.2 7.3 + - - -
306A PHE* 3.7 15.2 - + - -
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Residues in contact with LYS 301 (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 PRO 5.1 0.7 - - - -
234A TYR* 2.6 48.4 + - + +
235A GLY* 4.5 4.6 + - - -
236A VAL 4.0 20.0 + - - -
237A ASP* 5.8 0.4 - - - +
297A VAL* 2.8 31.9 + - + +
298A GLU* 3.8 7.6 - - - +
299A THR 3.3 0.2 - - - -
300A PHE* 1.3 72.9 - - + +
302A LYS* 1.3 61.9 + - + +
346A GLN* 6.2 0.6 - - - +
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Residues in contact with LYS 302 (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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298A GLU* 3.0 23.4 + - + +
299A THR* 3.0 7.3 + - - +
301A LYS* 1.3 82.3 - - + +
303A TYR* 1.3 61.2 + - - +
304A GLU* 3.7 15.0 + - - +
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Residues in contact with TYR 303 (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 TYR* 2.3 35.2 + - - -
269A THR* 3.6 36.3 + - + +
272A LYS* 4.3 27.3 - - + +
273A ILE* 3.7 19.7 - - + -
276A LEU* 5.4 10.8 - - + -
299A THR* 2.9 17.4 + - + +
300A PHE 3.2 1.2 + - - -
302A LYS* 1.3 78.6 - - - +
304A GLU* 1.3 54.3 + - - +
305A ASP* 3.4 57.7 + - + +
306A PHE* 3.5 34.2 - + + -
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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