Contacts of the helix formed by residues 145 - 157 (chain F) in PDB entry 1LE9
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 LYS 145 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143F THR* 3.0 41.1 + - + +
144F LYS* 1.3 81.9 - - - +
146F LYS* 1.3 60.7 + - + +
147F VAL* 3.2 6.5 + - - +
148F PHE* 4.7 1.7 + - - +
149F GLU* 4.3 12.0 + - - +
809G T 5.7 7.0 - - - -
810G C 5.1 4.4 + - - +
820H G 5.5 1.6 + - - -
821H T 5.0 6.5 + - - -
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Residues in contact with LYS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F VAL* 3.5 19.3 - - + +
143F THR* 3.1 26.2 + - - +
145F LYS* 1.3 81.0 - - + +
147F VAL* 1.3 56.7 + - - +
148F PHE 3.7 0.7 - - - -
149F GLU* 3.8 25.9 + - - +
150F THR* 2.9 51.3 + - - +
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Residues in contact with VAL 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ALA* 4.0 19.4 - - + +
142F VAL* 4.1 7.6 - - + -
143F THR 3.5 5.3 + - - +
144F LYS* 3.1 21.5 - - + +
145F LYS 3.2 2.2 - - - +
146F LYS* 1.3 75.0 - - - +
148F PHE* 1.3 60.4 + - + +
151F LEU* 2.7 39.4 + - + +
202F THR* 2.8 38.4 - - - +
205F MET* 4.0 22.0 - - + -
207F LEU* 4.6 8.5 - - + -
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Residues in contact with PHE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F LYS 4.7 1.7 + - - +
147F VAL* 1.3 80.5 - - + +
149F GLU* 1.3 73.1 + - + +
151F LEU* 3.2 7.4 - - - +
152F GLU* 2.9 50.7 + - + +
195F ARG* 3.4 40.4 - - + -
198F ALA* 2.9 23.1 - - + -
199F VAL* 3.3 29.8 - - + -
202F THR* 3.4 17.2 + - + +
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Residues in contact with GLU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F LYS 4.3 7.0 + - - +
146F LYS* 3.8 37.8 + - + +
147F VAL 4.3 0.2 - - - +
148F PHE* 1.3 90.1 - - + +
150F THR* 1.3 62.1 + - - +
152F GLU* 3.5 15.5 + - - +
153F ALA* 4.2 2.6 + - - +
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Residues in contact with THR 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108F ALA* 3.6 25.8 - - - +
110F SER* 5.9 1.1 - - - -
142F VAL* 4.3 10.2 - - + +
146F LYS* 2.9 51.8 + - - +
147F VAL 4.3 0.4 - - - -
149F GLU* 1.3 72.1 - - - +
151F LEU* 1.3 67.3 + - - +
153F ALA* 3.5 14.5 + - + +
154F ARG* 3.5 24.2 + - - +
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Residues in contact with LEU 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 3.2 34.1 - - + +
108F ALA* 5.2 5.4 - - + +
147F VAL* 2.7 27.2 + - + +
148F PHE* 3.2 7.0 - - - +
150F THR* 1.3 74.6 - - - +
152F GLU* 1.3 67.3 + - - +
154F ARG* 3.0 18.0 + - - +
155F MET* 3.2 33.8 + - + +
198F ALA* 3.3 30.5 - - + +
201F GLN* 4.7 9.2 - - + +
202F THR* 3.4 28.7 - - - +
205F MET* 4.9 6.5 - - + -
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Residues in contact with GLU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F PHE* 2.9 36.3 + - + +
149F GLU* 3.6 10.8 - - - +
150F THR 3.3 0.2 - - - -
151F LEU* 1.3 76.5 - - - +
153F ALA* 1.3 53.1 + - - +
155F MET* 3.1 4.6 + - - +
156F THR* 2.7 42.3 + - + +
191F LYS* 3.2 16.2 + - - +
194F ILE* 4.5 0.8 - - - +
195F ARG* 2.7 65.3 + - - +
198F ALA* 3.6 8.4 - - - +
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F GLU 4.2 2.8 + - - +
150F THR* 3.5 11.7 + - + +
151F LEU 3.3 0.8 - - - -
152F GLU* 1.3 78.9 - - - +
154F ARG* 1.3 57.3 + - - +
156F THR* 2.5 25.1 + - - +
157F GLU* 2.6 25.7 + - - +
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Residues in contact with ARG 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F GLN* 3.3 33.7 + - - +
97F LEU* 4.3 7.5 - - - +
106F LEU* 3.7 24.1 - - + +
107F HIS 3.4 10.4 + - - +
108F ALA* 3.4 4.7 + - - -
109F HIS 3.3 22.8 + - - -
110F SER* 4.0 13.4 - - - -
118F ASP* 3.0 34.4 + - - +
119F GLY* 4.8 1.3 - - - -
120F VAL* 5.3 4.5 - - - -
150F THR* 3.5 27.1 + - - +
151F LEU* 3.0 11.0 + - - +
153F ALA* 1.3 79.8 - - - +
155F MET* 1.3 57.0 + - - +
157F GLU* 3.1 22.8 - - - +
158F ALA* 4.0 7.0 - - - +
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Residues in contact with MET 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F HIS* 5.1 2.0 - - + -
106F LEU* 3.2 26.7 - - + -
151F LEU* 3.4 25.4 - - + +
152F GLU 3.1 3.9 + - - +
154F ARG* 1.3 71.4 - - - +
156F THR* 1.3 60.4 + - - +
157F GLU 2.6 17.8 - - - +
158F ALA* 4.8 0.4 - - - +
159F CYS* 2.8 22.7 - - - -
168F LEU 4.1 6.1 - - - +
169F VAL* 3.2 42.8 - - + +
194F ILE* 3.6 33.0 - - + +
197F ALA* 3.3 22.4 - - + +
198F ALA* 3.8 9.0 - - - -
201F GLN* 5.0 5.8 - - - +
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Residues in contact with THR 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F GLU* 2.7 35.2 + - + +
153F ALA* 2.5 28.6 + - - +
155F MET* 1.3 73.0 - - - +
157F GLU* 1.3 66.7 + - - +
159F CYS* 2.9 15.6 + - - +
160F ILE* 3.4 15.2 - - - +
191F LYS* 3.6 34.5 - - - +
194F ILE* 4.1 8.5 - - + +
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Residues in contact with GLU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ASP* 3.7 25.2 - - + +
120F VAL* 4.4 13.4 - - - +
153F ALA 2.6 22.3 + - - +
154F ARG* 3.1 12.6 - - - +
155F MET 2.6 12.8 - - - +
156F THR* 1.3 69.7 + - - +
158F ALA* 1.3 88.1 + - + +
159F CYS 2.4 20.4 + - - -
160F ILE* 3.8 9.4 - - + +
161F ARG* 2.7 47.1 + - - +
163F TYR* 5.3 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