Contacts of the helix formed by residues 186 - 201 (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 LEU 186 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159F CYS* 3.9 29.8 - - + +
160F ILE* 5.5 3.1 - - + -
173F LEU* 3.6 35.9 - - + -
175F TYR 5.4 7.4 - - - +
179F GLU* 5.3 3.6 - - + +
184F ARG* 4.6 12.0 - - + +
185F GLN* 1.3 77.0 - - - +
187F THR* 1.3 71.4 + - - +
190F GLU* 3.1 37.5 - - + +
194F ILE* 5.5 3.6 - - + -
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Residues in contact with THR 187 (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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185F GLN* 2.4 24.9 + - - +
186F LEU* 1.3 81.7 - - - +
188F ASP* 1.3 79.6 + - + +
189F ARG* 3.0 34.9 + - + +
190F GLU* 3.8 3.9 + - - +
191F LYS* 4.0 7.3 + - - +
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Residues in contact with ASP 188 (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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185F GLN* 6.0 1.6 - - - +
187F THR* 1.3 80.5 - - + +
189F ARG* 1.3 65.2 + - + +
191F LYS* 3.6 16.4 - - - +
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Residues in contact with ARG 189 (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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187F THR* 3.0 18.1 - - + +
188F ASP* 1.3 79.0 - - + +
190F GLU* 1.3 57.7 + - + +
191F LYS 2.5 17.8 + - - -
192F GLU* 2.8 27.2 + - - +
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Residues in contact with GLU 190 (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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172F ASP 5.7 1.0 - - - +
173F LEU* 3.4 29.2 - - - +
186F LEU* 3.1 41.1 + - + +
187F THR* 3.8 2.3 + - - +
189F ARG* 1.3 79.4 - - + +
191F LYS* 1.3 58.4 + - - +
192F GLU* 2.9 8.2 + - - -
193F ILE* 2.8 47.9 - - - +
194F ILE* 3.7 8.4 + - + +
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Residues in contact with LYS 191 (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* 3.2 25.3 + - - -
156F THR* 3.6 23.5 - - + +
187F THR 4.0 6.3 + - - +
188F ASP* 3.6 20.6 + - - +
189F ARG 2.5 6.3 + - - -
190F GLU* 1.3 74.3 - - - +
192F GLU* 1.3 55.4 + - - +
193F ILE 3.4 0.2 + - - -
194F ILE* 3.3 36.4 + - + +
195F ARG* 3.1 38.7 + - + +
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Residues in contact with GLU 192 (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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188F ASP 4.8 0.2 + - - -
189F ARG* 2.8 29.7 + - + +
190F GLU* 3.5 8.0 - - - +
191F LYS* 1.3 71.5 - - - +
193F ILE* 1.3 94.5 + - - +
195F ARG* 4.8 3.1 - - - +
196F GLN* 2.8 29.5 + - - +
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Residues in contact with ILE 193 (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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170F HIS* 4.4 23.5 - - + +
172F ASP* 4.3 27.4 - - + +
173F LEU* 5.6 4.0 - - + +
190F GLU* 2.8 51.1 - - - +
192F GLU* 1.3 94.0 - - - +
194F ILE* 1.3 69.8 + - + +
196F GLN* 3.2 10.2 + - - +
197F ALA* 2.6 38.0 + - - +
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Residues in contact with ILE 194 (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* 4.5 2.9 - - - +
155F MET* 3.6 26.5 - - + +
156F THR* 4.1 12.1 - - + +
159F CYS* 3.1 39.9 - - + -
169F VAL* 4.2 12.1 - - + -
170F HIS* 6.4 1.3 - - + -
173F LEU* 5.2 1.6 - - + -
186F LEU* 5.5 5.2 - - + -
190F GLU* 4.5 9.6 - - + +
191F LYS* 3.3 30.9 + - + +
193F ILE* 1.3 90.6 - - + +
195F ARG* 1.3 60.0 + - - +
197F ALA* 2.9 9.7 + - - +
198F ALA* 2.8 27.5 + - - +
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Residues in contact with ARG 195 (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* 3.4 25.1 - - + -
152F GLU* 2.7 41.0 + - - +
191F LYS* 3.1 27.0 + - + +
192F GLU* 4.6 3.6 - - - +
194F ILE* 1.3 80.0 - - - +
196F GLN* 1.3 57.2 + - - +
198F ALA* 3.1 13.3 + - - +
199F VAL* 2.9 21.9 - - + +
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Residues in contact with GLN 196 (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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192F GLU* 2.8 22.6 + - - +
193F ILE* 3.6 10.2 - - - +
194F ILE 3.2 0.6 - - - -
195F ARG* 1.3 76.4 - - - +
197F ALA* 1.3 65.2 + - - +
199F VAL* 2.8 28.8 + - + +
200F GLN* 3.6 25.9 + - - +
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Residues in contact with ALA 197 (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* 5.5 4.8 + - + -
155F MET* 3.3 25.1 - - + +
169F VAL 4.0 7.9 - - - +
170F HIS* 5.0 7.6 - - + -
193F ILE 2.6 22.5 + - - +
194F ILE* 2.9 9.2 + - - +
196F GLN* 1.3 74.3 + - - +
198F ALA* 1.3 59.7 + - - +
199F VAL 3.1 6.2 + - - -
200F GLN* 3.7 3.3 + - - +
201F GLN* 3.5 25.3 + - - +
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Residues in contact with ALA 198 (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 19.1 - - + -
151F LEU* 3.3 24.9 - - + +
152F GLU* 3.6 19.3 - - - +
155F MET* 3.8 13.2 - - - -
194F ILE 2.8 10.8 + - - +
195F ARG 3.1 10.9 + - - +
197F ALA* 1.3 79.0 - - - +
199F VAL* 1.3 55.2 + - - +
200F GLN 3.7 0.2 - - - -
202F THR* 2.9 24.7 - - - +
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Residues in contact with VAL 199 (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* 3.3 18.2 - - + -
195F ARG* 2.9 21.5 - - + +
196F GLN* 2.8 35.4 - - + +
197F ALA 3.1 0.8 - - - -
198F ALA* 1.3 79.7 - - - +
200F GLN* 1.3 87.1 + - - +
202F THR* 3.3 18.3 - - - +
203F LYS* 4.1 7.4 - - - +
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Residues in contact with GLN 200 (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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196F GLN* 3.6 24.6 + - - +
197F ALA* 3.7 3.1 + - - +
199F VAL* 1.3 105.6 + - - +
201F GLN* 1.3 63.0 + - - +
202F THR 3.5 0.2 - - - -
203F LYS* 3.9 14.8 + - - +
204F GLU* 3.0 22.8 + - - +
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Residues in contact with GLN 201 (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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99F THR* 4.8 5.2 - - + +
105F HIS* 2.7 50.8 + - + +
106F LEU* 2.6 38.2 + - - +
151F LEU* 4.8 8.6 - - + +
155F MET* 5.0 3.4 - - - +
168F LEU 4.4 0.6 + - - -
197F ALA 3.5 17.4 + - - +
200F GLN* 1.3 75.6 - - - +
202F THR* 1.3 53.6 + - - +
203F LYS 3.0 4.9 - - - -
204F GLU* 3.1 20.8 - - + +
205F MET* 2.7 61.3 + - - +
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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