Contacts of the helix formed by residues 146 - 152 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82E ASP* 6.4 1.8 - - + -
83E VAL* 5.0 9.9 - - + -
84E GLU* 5.8 3.1 - - + +
141E ILE* 3.8 25.0 + - + +
145E GLY* 1.3 71.0 - - - -
147E GLN* 1.3 63.8 + - + +
149E TYR* 3.1 10.5 + - + +
150E LEU* 2.9 52.5 + - + +
250E SO4 3.2 17.1 + - - +
143I LYS 5.7 1.3 - - - +
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Residues in contact with GLN 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E GLY 3.5 0.4 - - - -
146E LEU* 1.3 76.3 - - + +
148E ASN* 1.3 62.9 + - - +
150E LEU* 3.3 1.4 + - - +
151E GLN* 3.1 19.2 + - - +
250E SO4 3.1 27.0 + - - +
142I GLN 4.5 4.2 + - - -
143I LYS 3.5 17.7 + - - +
144I MET* 3.3 46.1 - - - +
145I GLY* 3.6 8.9 - - - +
148I ASN* 3.8 7.8 - - - +
250I SO4 4.6 8.7 + - - -
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Residues in contact with ASN 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E MET* 3.4 37.7 - - + +
145E GLY 3.6 1.4 + - - -
146E LEU 3.4 0.4 - - - -
147E GLN* 1.3 76.2 - - - +
149E TYR* 1.3 66.7 + - - +
151E GLN* 3.4 11.0 + - - +
152E ALA* 3.2 22.5 + - - +
250E SO4 4.7 1.0 + - - -
148I ASN* 2.7 40.3 + - - +
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Residues in contact with TYR 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 3.5 14.3 - - + +
83E VAL* 4.0 15.5 - - + -
87E LEU* 3.9 4.7 - - - +
137E GLU* 2.5 47.0 + - + +
140E LEU* 4.2 13.5 - - + -
141E ILE* 3.6 45.3 - - + -
144E MET* 3.8 15.2 - - + +
145E GLY 3.0 19.6 + - - +
146E LEU* 3.1 9.2 + - + +
148E ASN* 1.3 77.3 - - - +
150E LEU* 1.3 77.0 + - + +
152E ALA* 3.2 7.0 + - - +
153E GLN* 2.9 50.4 + - + -
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Residues in contact with LEU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LEU* 4.0 23.9 - - + +
83E VAL* 3.9 28.0 - - + -
146E LEU* 2.9 45.4 + - + +
147E GLN* 3.7 3.6 - - - +
149E TYR* 1.3 86.0 - - + +
151E GLN* 1.3 63.3 + - - +
153E GLN* 2.8 21.2 + - + +
154E ILE* 3.7 6.9 + - - +
140I LEU* 5.8 0.9 - - + -
143I LYS* 4.0 40.8 - - + +
144I MET* 4.4 12.3 - - + -
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Residues in contact with GLN 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLN 3.1 15.1 + - - +
148E ASN* 3.9 11.6 + - - +
149E TYR 3.3 0.2 - - - -
150E LEU* 1.3 76.1 - - - +
152E ALA* 1.3 61.7 + - - +
153E GLN 3.1 1.4 + - - -
154E ILE* 3.4 16.3 + - - +
155E ARG* 4.9 0.9 + - - +
144I MET* 3.7 26.4 - - - +
148I ASN* 3.4 40.6 + - + +
151I GLN* 3.0 36.4 + - - +
152I ALA* 3.8 16.8 - - + +
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Residues in contact with ALA 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E ARG* 4.5 11.5 + - - +
144E MET* 4.9 8.5 - - + -
148E ASN 3.2 13.2 + - - +
149E TYR* 3.4 12.6 - - - +
150E LEU 3.1 1.2 - - - -
151E GLN* 1.3 77.0 - - - +
153E GLN* 1.3 68.6 + - - +
154E ILE 3.5 0.4 - - - -
155E ARG 4.5 7.1 + - - +
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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