Contacts of the helix formed by residues 146 - 152 (chain D) in PDB entry 3E1J
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 LEU 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D ASP* 6.4 1.8 - - + -
83D VAL* 5.0 10.8 - - + -
84D GLU* 5.7 2.9 - - + +
141D ILE* 3.8 24.4 + - + +
145D GLY* 1.3 71.3 - - - -
147D GLN* 1.3 63.2 + - + +
149D TYR* 3.1 10.5 + - + +
150D LEU* 2.9 53.7 + - + +
250D SO4 3.2 18.2 + - - +
143H LYS 5.7 1.8 - - - +
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Residues in contact with GLN 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLY 3.5 0.4 - - - -
146D LEU* 1.3 76.0 - - + +
148D ASN* 1.3 62.9 + - - +
150D LEU* 3.3 3.7 + - - +
151D GLN* 3.1 20.1 + - - +
250D SO4 3.1 26.9 + - - +
142H GLN 4.5 3.6 + - - -
143H LYS 3.5 18.1 + - - +
144H MET* 3.4 43.4 - - - +
145H GLY* 3.7 9.3 - - - +
148H ASN* 3.8 7.9 - - - +
250H SO4 4.7 7.8 + - - -
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Residues in contact with ASN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D MET* 3.4 38.1 - - + +
145D GLY 3.6 1.4 + - - -
146D LEU 3.4 0.4 - - - -
147D GLN* 1.3 74.5 - - - +
149D TYR* 1.3 66.8 + - - +
151D GLN* 3.4 11.4 + - - +
152D ALA* 3.2 21.8 + - - +
250D SO4 4.7 1.0 + - - -
148H ASN* 2.8 32.3 + - - +
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Residues in contact with TYR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU* 3.5 14.6 - - + +
83D VAL* 4.0 15.0 - - + -
87D LEU* 3.9 4.5 - - - +
137D GLU* 2.5 47.4 + - + +
140D LEU* 4.2 13.7 - - + -
141D ILE* 3.6 46.9 - - + -
144D MET* 3.8 14.8 - - + +
145D GLY 3.0 19.0 + - - +
146D LEU* 3.1 9.4 + - + +
148D ASN* 1.3 77.5 - - - +
150D LEU* 1.3 74.9 + - + +
152D ALA* 3.2 7.4 + - - +
153D GLN* 2.9 50.3 + - + -
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Residues in contact with LEU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 4.0 24.0 - - + +
83D VAL* 3.8 28.7 - - + -
146D LEU* 2.9 45.3 + - + +
147D GLN 3.7 3.4 - - - +
149D TYR* 1.3 85.5 - - + +
151D GLN* 1.3 64.8 + - - +
153D GLN* 2.8 21.3 + - + +
154D ILE* 3.7 7.4 + - - +
140H LEU* 5.9 0.9 - - + -
143H LYS* 4.0 40.4 - - + +
144H MET* 4.5 11.9 - - + -
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Residues in contact with GLN 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D GLN 3.1 14.4 + - - +
148D ASN* 3.9 11.6 + - - +
150D LEU* 1.3 74.7 - - - +
152D ALA* 1.3 62.6 + - - +
153D GLN 3.1 1.6 + - - -
154D ILE* 3.4 16.9 + - - +
155D ARG* 4.9 0.5 + - - +
144H MET* 3.7 26.8 - - - +
148H ASN* 3.5 40.2 + - + +
151H GLN* 2.9 37.3 + - - +
152H ALA* 3.9 15.5 - - + +
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Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ARG* 4.5 11.9 + - - +
144D MET* 4.9 8.7 - - + -
148D ASN 3.2 12.1 + - - +
149D TYR* 3.4 13.0 - - - +
150D LEU 3.1 1.4 + - - -
151D GLN* 1.3 77.0 - - - +
153D GLN* 1.3 68.7 + - - +
154D ILE 3.5 0.4 - - - -
155D ARG* 4.5 6.9 + - - +
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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