Contacts of the helix formed by residues 181 - 196 (chain H) in PDB entry 3LUE
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 ALA 181 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155H SER* 4.2 8.3 - - - +
156H GLY 3.3 14.4 - - - +
157H ASP 3.5 16.8 - - - +
158H GLY 3.9 0.2 - - - -
159H VAL 3.6 23.6 - - - +
160H THR* 4.1 1.8 - - - +
180H LEU* 1.3 78.8 - - - +
182H GLY* 1.4 55.6 + - - +
183H ARG 3.3 1.6 - - - -
184H ASP* 2.9 35.6 + - - +
185H LEU* 3.5 5.7 + - - +
261H LEU* 5.1 0.4 - - - -
303H THR* 3.9 7.6 - - - -
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Residues in contact with GLY 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H GLY 2.9 6.0 + - - -
157H ASP* 4.3 7.9 - - - -
181H ALA* 1.4 72.4 - - - +
183H ARG* 1.3 54.3 + - - +
184H ASP 3.3 0.2 - - - -
185H LEU* 3.3 6.0 + - - +
186H THR* 3.0 30.7 + - - -
213H LYS* 3.2 14.8 + - - -
303H THR* 2.8 29.8 + - - -
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Residues in contact with ARG 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H GLU* 1.1 183.0 + - + +
73H HIS* 2.7 44.6 + - - +
75H ILE 3.5 0.4 + - - -
77H THR* 2.1 38.1 - - - +
157H ASP* 3.2 14.4 + - - +
181H ALA 3.0 2.4 + - - -
182H GLY* 1.3 70.1 - - - +
184H ASP* 1.3 66.9 + - - +
186H THR* 3.3 5.6 + - - +
187H ASP* 3.0 34.0 + - - +
206H ARG* 5.0 8.7 - - - +
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Residues in contact with ASP 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H HIS* 3.4 29.0 + - - -
157H ASP 4.3 1.4 - - - +
179H ASP 4.0 5.9 - - - +
180H LEU* 3.6 31.8 - - + -
181H ALA 2.9 23.2 + - - +
183H ARG* 1.3 77.7 - - - +
185H LEU* 1.3 57.7 + - - +
187H ASP* 3.6 7.3 - - - +
188H TYR* 3.1 28.6 + - - +
267H LEU* 4.1 10.2 - - + +
269H MET* 4.0 11.6 - - - +
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Residues in contact with LEU 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H LEU* 3.9 25.8 - - + -
181H ALA 3.5 3.1 + - - +
182H GLY* 3.3 9.2 + - - +
183H ARG 3.1 0.4 - - - -
184H ASP* 1.3 80.9 - - - +
186H THR* 1.3 61.7 + - - +
188H TYR* 4.5 2.9 - - + +
189H LEU* 3.2 9.4 + - - +
213H LYS* 3.6 5.2 - - + -
257H CYS* 3.2 37.2 - - - +
258H PRO* 4.2 3.4 - - + -
260H ALA* 4.0 22.2 - - + -
261H LEU* 3.9 20.4 - - + -
267H LEU* 4.9 0.4 - - + -
303H THR* 3.9 11.9 - - + -
306H TYR* 3.1 40.6 - - + +
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Residues in contact with THR 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H GLY 3.0 10.3 + - - -
183H ARG* 3.8 6.4 - - - -
185H LEU* 1.3 74.7 - - - +
187H ASP* 1.3 62.0 + - - +
189H LEU* 3.4 5.4 + - - +
190H MET* 3.2 22.7 + - - +
206H ARG* 3.7 22.9 - - - +
209H VAL* 3.4 27.7 - - + +
210H ARG* 3.9 21.9 - - + +
213H LYS* 2.6 37.2 + - - +
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Residues in contact with ASP 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H GLU* 4.8 7.8 - - - +
183H ARG* 3.0 23.4 + - - +
184H ASP* 3.6 7.5 - - - +
186H THR* 1.3 76.8 - - - +
188H TYR* 1.3 62.2 + - - +
189H LEU 3.3 0.2 - - - -
190H MET* 3.7 15.3 + - + +
191H LYS* 3.4 21.1 + - - +
206H ARG* 3.1 31.8 + - - -
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Residues in contact with TYR 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184H ASP 3.1 16.1 + - - +
185H LEU* 3.6 3.8 + - - +
186H THR 3.4 0.2 - - - -
187H ASP* 1.3 76.3 - - - +
189H LEU* 1.3 65.8 + - - +
191H LYS* 3.6 21.0 + - - +
192H ILE* 3.1 49.8 + - + +
256H ARG* 3.3 31.0 + - - +
257H CYS* 4.2 18.6 - - - -
260H ALA* 4.4 4.7 - - + -
266H PHE* 3.3 44.6 + + + +
267H LEU* 3.4 25.1 - - + -
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Residues in contact with LEU 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185H LEU 3.2 18.3 + - - +
186H THR 3.5 3.6 - - - +
187H ASP 3.3 0.2 - - - -
188H TYR* 1.3 78.8 - - - +
190H MET* 1.3 50.5 + - - +
192H ILE* 3.2 15.3 + - + +
193H LEU* 2.8 49.1 + - + +
209H VAL* 3.2 39.3 - - + +
212H ILE* 4.1 12.8 - - + -
213H LYS* 3.6 20.6 - - + +
217H CYS* 4.5 9.6 - - - -
250H ILE* 5.3 2.7 - - + -
253H GLU* 4.6 13.5 - - + +
257H CYS* 3.6 22.2 - - + -
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Residues in contact with MET 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H THR 3.2 7.0 + - - +
187H ASP* 3.7 28.5 - - - +
188H TYR 3.4 0.2 - - - -
189H LEU* 1.3 78.0 - - - +
191H LYS* 1.3 53.6 + - - +
193H LEU* 3.4 4.0 + - - +
194H THR* 2.8 43.3 + - - +
200H PHE* 4.3 20.5 - - + +
206H ARG* 3.7 44.6 - - + +
209H VAL* 3.8 33.4 - - + -
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Residues in contact with LYS 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H ASP 3.4 14.5 + - - +
188H TYR* 3.8 30.4 - - - +
189H LEU 3.3 0.2 - - - -
190H MET* 1.3 75.6 - - - +
192H ILE* 1.3 70.7 + - - +
194H THR* 3.4 7.7 + - + -
195H GLU* 2.9 50.9 + - + +
173I HIS 5.9 1.3 - - - -
175I ILE 6.1 0.7 - - - -
176I LEU* 5.2 14.1 - - + -
284I LYS* 5.1 18.3 - - - +
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Residues in contact with ILE 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188H TYR* 3.1 57.5 + - + +
189H LEU* 3.2 19.7 + - + +
191H LYS* 1.3 79.0 - - - +
193H LEU* 1.3 60.5 + - - +
195H GLU* 3.2 25.9 + - - +
196H ARG* 3.3 11.8 + - - +
253H GLU* 3.9 44.2 - - + +
256H ARG* 3.8 33.1 + - + +
257H CYS* 4.3 7.9 - - + +
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Residues in contact with LEU 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H LEU* 2.8 31.6 + - + +
190H MET 3.6 5.2 - - - +
192H ILE* 1.3 76.7 - - - +
194H THR* 1.3 55.0 + - - +
196H ARG* 3.1 13.2 + - - +
198H TYR* 2.7 46.8 + - + +
200H PHE* 3.8 26.9 - - + -
209H VAL* 4.6 2.7 - - + -
212H ILE* 3.9 21.1 - - + -
248H ILE* 4.5 5.2 - - + -
250H ILE* 3.9 26.9 - - + -
253H GLU* 3.9 24.9 - - + +
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Residues in contact with THR 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190H MET* 2.8 27.4 + - - +
191H LYS* 4.0 7.9 - - + +
193H LEU* 1.3 66.5 - - - +
195H GLU* 1.3 65.6 + - + +
196H ARG 3.1 2.0 - - - -
197H GLY* 3.0 14.5 + - - -
198H TYR 3.5 23.2 + - - +
200H PHE* 3.8 18.2 + - - +
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Residues in contact with GLU 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191H LYS* 2.9 48.6 + - + +
192H ILE* 3.2 24.7 + - - +
194H THR* 1.3 73.0 - - + +
196H ARG* 1.3 56.7 + - - +
197H GLY* 2.8 11.8 + - - -
256H ARG* 5.4 3.0 + - - +
110I LEU* 6.4 2.9 - - + -
113I LYS* 3.5 12.2 + - - +
175I ILE 5.5 2.8 - - - +
177I ARG* 5.9 1.0 + - - -
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Residues in contact with ARG 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192H ILE 3.3 9.2 + - - +
193H LEU 3.1 13.2 + - - +
195H GLU* 1.3 72.8 - - - +
197H GLY* 1.3 62.8 + - - +
198H TYR* 3.4 25.0 + - + -
237H GLU* 2.9 31.3 + - - -
249H THR* 3.0 34.6 + - - +
251H GLY* 4.1 1.2 - - - +
252H ASN 5.2 1.0 - - - +
253H GLU* 3.2 33.3 + - - +
113I LYS* 3.1 30.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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