Contacts of the helix formed by residues 233 - 240 (chain A) in PDB entry 1EMU
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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229A THR* 3.1 13.5 + - + +
230A MET 3.3 0.6 + - - -
232A GLU* 1.3 80.7 - - + +
234A THR* 1.3 75.1 + - + +
235A TYR 3.4 1.3 - - - -
236A PRO* 3.3 5.1 - - - +
237A SER* 2.9 33.5 + - - -
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Residues in contact with THR 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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139A PHE* 4.1 3.1 - - - -
142A PHE* 3.5 9.2 - - + -
143A LEU* 3.5 32.4 - - + +
146A GLU* 5.6 2.5 - - + -
148A CYS* 3.8 18.4 - - - -
151A LEU* 4.3 8.3 - - + +
229A THR* 4.2 2.1 + - + +
230A MET* 3.4 25.3 - - - +
233A ASN* 1.3 84.0 - - + +
235A TYR* 1.3 62.3 + - - +
237A SER* 3.3 5.8 + - - -
238A PHE* 2.8 30.5 + - - +
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Residues in contact with TYR 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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122A TRP 2.6 29.8 + - - -
123A ALA 3.7 5.9 + - - -
124A GLU 4.1 0.2 - - - -
125A SER* 3.0 20.5 + - - -
126A LEU* 3.5 43.7 - - + -
129A LEU* 3.8 21.8 - - + -
139A PHE* 4.0 9.6 - - + -
230A MET 2.8 28.6 + - - +
231A GLU* 4.0 14.4 - - + +
234A THR* 1.3 72.6 + - - +
236A PRO* 1.3 70.3 - - + +
238A PHE* 3.1 13.6 + + - +
239A LEU* 3.1 33.5 + - + +
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Residues in contact with PRO 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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230A MET 3.5 1.8 - - - +
231A GLU 3.1 24.0 - - - +
232A GLU 4.2 7.9 - - - +
233A ASN 3.3 13.2 - - - +
235A TYR* 1.3 101.1 - - + +
237A SER* 1.3 61.8 + - - +
239A LEU* 3.2 19.3 + - + +
240A LYS* 3.3 32.4 + - - +
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Residues in contact with SER 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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142A PHE* 3.8 17.2 - - - -
233A ASN* 2.9 32.1 + - - -
234A THR* 3.7 6.1 - - - -
235A TYR 3.3 0.2 - - - -
236A PRO* 1.3 77.1 - - - +
238A PHE* 1.3 62.1 + - - +
240A LYS* 3.2 12.5 + - - +
241A SER* 3.0 22.5 + - - -
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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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122A TRP* 5.3 0.7 - + - -
129A LEU* 4.0 29.8 - - + -
138A LEU* 3.7 32.5 - - + -
139A PHE* 3.5 33.7 - + + -
142A PHE* 3.6 29.8 - + + -
234A THR 2.8 14.7 + - - +
235A TYR 3.1 8.9 + - - +
237A SER* 1.3 77.4 - - - +
239A LEU* 1.3 70.5 + - + +
240A LYS 3.0 0.2 - - - -
241A SER* 2.5 31.6 + - - -
243A ILE* 4.5 2.2 - - + -
244A TYR* 3.1 47.6 - + + +
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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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122A TRP* 4.2 6.7 - - + +
123A ALA* 3.9 31.9 - - + +
129A LEU* 5.6 0.2 - - + -
235A TYR* 3.1 41.3 + - + +
236A PRO* 3.2 12.3 + - + +
238A PHE* 1.3 91.2 - - + +
240A LYS* 1.3 61.7 + - + +
241A SER 3.5 0.2 - - - -
244A TYR* 3.2 45.7 - - + -
245A LEU* 3.6 5.9 - - - +
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Residues in contact with LYS 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 PRO* 3.3 32.1 + - - +
237A SER* 3.2 11.3 + - - +
238A PHE 3.0 0.6 - - - -
239A LEU* 1.3 81.0 - - + +
241A SER* 1.3 64.1 + - - +
245A LEU* 4.1 14.4 - - - +
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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