Contacts of the helix formed by residues 146 - 157 (chain B) 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 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B TYR* 6.1 1.8 - - - -
58B VAL* 4.9 16.2 - - - +
141B HIS 5.1 1.4 + - - -
142B VAL* 3.1 17.3 - - + +
143B THR* 2.9 40.0 - - + +
145B LYS* 1.3 79.8 - - + +
147B VAL* 1.3 56.9 + - - +
148B PHE 3.7 0.4 - - - -
149B GLU* 4.0 20.2 - - + +
150B THR* 2.7 45.3 + - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA* 4.0 10.6 - - + +
142B VAL* 4.0 8.3 - - + -
143B THR 3.1 19.5 - - - +
144B LYS* 2.9 26.7 - - + +
145B LYS 3.3 2.4 - - - +
146B LYS* 1.3 74.6 - - - +
148B PHE* 1.3 57.6 + - + +
151B LEU* 2.7 37.4 + - - +
202B THR* 3.1 30.7 - - + +
205B MET* 4.9 6.7 - - + -
207B LEU* 3.3 32.3 - - + -
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Residues in contact with PHE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LYS 4.8 1.4 + - - +
147B VAL* 1.3 77.2 - - + +
149B GLU* 1.3 73.6 + - - +
151B LEU* 3.8 5.3 - - - +
152B GLU* 3.0 30.5 + - + +
195B ARG* 3.3 23.1 - - + -
198B ALA* 2.8 27.4 - - + -
199B VAL* 3.3 31.2 - - + -
202B THR* 3.1 20.4 + - + +
203B LYS* 5.3 3.4 - - - +
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LYS 4.4 5.7 + - - +
146B LYS* 4.0 28.3 - - + +
147B VAL 3.3 0.2 - - - -
148B PHE* 1.3 88.8 - - - +
150B THR* 1.3 72.2 + - - +
152B GLU* 3.5 13.4 + - - +
153B ALA* 4.2 3.3 + - - +
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA* 3.7 15.3 - - - +
110B SER* 5.9 1.1 - - - -
142B VAL* 3.5 15.4 - - + +
146B LYS* 2.7 37.9 + - - +
147B VAL 4.1 1.1 - - - -
149B GLU* 1.3 78.9 + - - +
151B LEU* 1.3 63.2 + - - +
152B GLU 3.4 0.2 + - - -
153B ALA* 3.5 11.2 + - + +
154B ARG* 2.9 48.3 - - - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.0 23.1 - - + +
108B ALA* 4.8 8.1 - - + +
147B VAL 2.7 23.9 + - - +
148B PHE* 3.2 6.7 + - - +
150B THR* 1.3 72.6 - - - +
152B GLU* 1.3 69.2 + - - +
154B ARG* 3.0 24.1 + - + +
155B MET* 3.2 23.3 + - + +
198B ALA* 4.3 16.6 - - + -
201B GLN* 4.2 22.4 - - + +
202B THR* 4.5 8.7 - - - +
205B MET* 3.9 26.9 - - - -
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Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B PHE* 3.0 23.6 + - + +
149B GLU* 3.7 11.2 - - - +
150B THR 3.3 0.2 - - - -
151B LEU* 1.3 75.2 - - - +
153B ALA* 1.3 71.0 + - - +
155B MET* 3.1 4.1 + - - +
156B THR* 2.5 65.1 + - - +
194B ILE* 4.3 8.9 - - + +
195B ARG* 5.4 9.9 - - + -
198B ALA* 4.4 11.1 - - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149B GLU 4.2 2.4 + - - +
150B THR* 3.5 12.0 + - + +
151B LEU 3.2 0.8 - - - -
152B GLU* 1.3 89.3 + - - +
154B ARG* 1.3 65.1 + - - +
156B THR* 3.3 2.9 - - - -
157B GLU* 2.6 43.8 + - + +
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Residues in contact with ARG 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 3.7 24.6 - - + +
107B HIS 4.5 13.2 - - - +
108B ALA 3.8 7.8 + - - -
109B HIS 5.3 1.1 - - - +
110B SER* 3.3 27.6 + - - +
118B ASP* 2.3 55.9 + - - +
119B GLY* 3.8 1.1 - - - +
150B THR* 2.9 45.1 - - - +
151B LEU* 3.0 20.7 + - + +
153B ALA* 1.3 82.1 - - - +
155B MET* 1.3 57.4 + - - +
157B GLU* 2.9 24.1 - - - +
158B ALA* 3.8 4.0 - - - +
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Residues in contact with MET 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 4.2 13.5 - - + -
151B LEU* 3.5 21.1 - - + +
152B GLU 3.1 3.0 + - - +
154B ARG* 1.3 71.9 - - - +
156B THR* 1.3 61.0 + - - +
157B GLU 2.5 17.1 - - - +
159B CYS* 2.7 22.1 - - - -
168B LEU 4.7 0.9 - - - +
169B VAL* 3.9 25.8 - - + -
194B ILE* 3.6 38.1 - - + +
197B ALA* 3.8 12.6 - - + +
198B ALA* 3.8 17.5 - - - -
201B GLN* 3.0 44.9 - - - +
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU* 2.5 48.5 + - - +
153B ALA* 3.3 4.9 - - - +
155B MET* 1.3 73.5 - - - +
157B GLU* 1.3 68.6 + - + +
159B CYS* 3.1 15.1 - - - +
160B ILE* 3.3 30.2 - - + +
186B LEU* 5.1 1.3 - - - +
191B LYS* 6.2 3.3 - - - +
194B ILE* 3.9 16.8 - - - +
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ASP* 3.0 30.8 - - + +
120B VAL* 6.4 1.6 - - + -
153B ALA* 2.6 26.1 + - + +
154B ARG* 2.9 10.6 - - - +
155B MET 2.5 18.5 - - - +
156B THR* 1.3 74.8 - - + +
158B ALA* 1.3 60.0 + - + +
159B CYS 2.5 19.9 + - - -
160B ILE* 3.8 13.6 - - + +
161B ARG* 3.2 44.9 + - - +
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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