Contacts of the helix formed by residues 152 - 157 (chain C) in PDB entry 1LJ2
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 ILE 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A TYR* 3.3 46.4 - - + +
142C ILE* 2.8 24.3 + - + +
143C ARG 3.5 11.9 - - - +
144C ASP* 4.0 20.2 - - + +
147C GLN* 4.1 9.9 - - - +
150C LYS* 3.9 11.7 - - + +
151C ASP* 1.3 74.7 - - - +
153C THR* 1.3 63.5 + - - +
154C GLU 3.7 1.1 - - - -
155C GLU* 3.2 31.1 - - - +
156C ILE* 3.0 25.3 + - + +
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Residues in contact with THR 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B MET* 4.2 11.2 - - - -
140C ILE 4.2 11.9 - - - +
141C ARG* 3.2 19.2 + - - +
142C ILE* 2.7 27.0 + - - +
151C ASP* 2.5 35.0 + - - -
152C ILE* 1.3 75.6 - - - +
154C GLU* 1.3 67.2 + - - +
156C ILE* 3.0 6.8 + - - +
157C MET* 2.9 46.5 + - + +
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Residues in contact with GLU 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ARG* 4.5 7.6 - - - +
151C ASP* 4.5 1.0 + - - -
153C THR* 1.3 79.3 - - - +
155C GLU* 1.3 66.1 + - - +
157C MET* 3.2 30.3 + - + +
158C SER* 3.2 12.5 + - - -
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A TYR* 5.2 5.4 + - - -
147C GLN* 5.7 0.2 - - - +
152C ILE* 3.2 33.7 + - - +
153C THR 3.1 0.6 - - - -
154C GLU* 1.3 77.4 - - - +
156C ILE* 1.3 65.7 + - - +
158C SER* 2.8 29.1 + - - -
159C GLY* 3.5 5.4 + - - +
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Residues in contact with ILE 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A TYR* 3.5 35.0 - - + -
298B MET* 3.9 9.9 - - - +
301B GLY* 3.2 38.5 - - - +
302B LEU* 3.7 16.2 - - + +
305B ARG* 5.8 4.0 - - + -
142C ILE* 3.6 31.2 - - + -
152C ILE* 3.0 17.4 + - + +
153C THR 3.6 6.3 - - - +
155C GLU* 1.3 79.7 - - - +
157C MET* 1.3 59.1 + - - +
158C SER 2.8 11.1 + - - -
159C GLY* 3.1 17.2 + - - +
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Residues in contact with MET 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LYS* 4.6 6.5 - - - +
297B LEU* 4.3 37.5 - - + +
298B MET* 3.6 37.5 - - + +
301B GLY* 5.5 0.4 - - - -
141C ARG* 4.9 5.8 - - - +
153C THR* 2.9 27.8 + - + +
154C GLU* 3.2 32.2 + - + +
156C ILE* 1.3 74.0 - - - +
158C SER* 1.3 56.7 + - - +
159C GLY 3.7 0.2 - - - -
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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