Contacts of the helix formed by residues 181 - 196 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B SER* 4.2 8.3 - - - +
156B GLY 3.3 14.1 - - - +
157B ASP 3.5 17.7 - - - +
158B GLY 5.0 0.2 - - - -
159B VAL 3.6 24.0 - - - +
160B THR* 4.1 1.8 - - - +
180B LEU* 1.3 79.0 - - - +
182B GLY* 1.4 54.6 + - - +
183B ARG 3.3 1.8 - - - -
184B ASP* 2.9 36.3 + - - +
185B LEU* 3.5 5.7 + - - +
261B LEU* 5.1 0.4 - - - -
303B THR* 4.2 6.3 - - - -
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Residues in contact with GLY 182 (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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156B GLY 2.9 5.9 + - - -
157B ASP* 3.8 7.4 + - - -
181B ALA* 1.4 71.9 - - - +
183B ARG* 1.3 56.5 + - - +
185B LEU* 3.2 6.2 + - - +
186B THR* 3.0 31.4 + - - -
213B LYS* 3.2 14.2 + - - -
303B THR* 2.8 29.0 + - - -
306B TYR* 5.6 0.2 - - - -
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Residues in contact with ARG 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLU* 1.1 185.1 + - + +
73B HIS* 2.7 46.0 + - + +
75B ILE 3.5 0.6 + - - -
77B THR* 2.1 36.9 - - - +
157B ASP* 3.2 13.9 + - - +
181B ALA 3.0 2.6 + - - -
182B GLY* 1.3 69.7 - - - +
184B ASP* 1.3 68.6 + - - +
186B THR* 3.3 5.8 + - - +
187B ASP* 3.0 33.5 + - - +
206B ARG* 5.0 8.7 - - - +
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Residues in contact with ASP 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B HIS* 3.4 29.0 + - - -
157B ASP 4.3 0.9 - - - +
179B ASP 4.0 5.9 - - - +
180B LEU* 3.6 30.7 - - + -
181B ALA 2.9 24.2 + - - +
183B ARG* 1.3 76.9 - - - +
185B LEU* 1.3 57.2 + - - +
187B ASP* 3.6 7.3 - - - +
188B TYR* 3.1 28.8 + - - +
267B LEU* 4.1 9.3 - - + +
269B MET* 4.0 11.6 - - - +
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B LEU* 3.9 25.6 - - + -
181B ALA 3.5 2.4 + - - +
182B GLY* 3.2 10.3 + - - +
183B ARG 3.1 0.2 - - - -
184B ASP* 1.3 78.5 - - - +
186B THR* 1.3 62.6 + - - +
188B TYR* 4.1 3.1 - - + +
189B LEU* 3.2 9.2 + - - +
213B LYS* 3.6 4.5 - - + -
257B CYS* 3.2 37.2 - - - +
258B PRO* 4.2 3.8 - - + -
260B ALA* 4.0 22.2 - - + -
261B LEU* 3.9 19.5 - - + -
267B LEU* 4.9 0.7 - - + -
303B THR* 3.9 12.6 - - + -
306B TYR* 3.1 40.6 - - + +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLY 3.0 10.5 + - - -
183B ARG* 3.3 6.6 + - - -
185B LEU* 1.3 73.4 - - - +
187B ASP* 1.3 62.1 + - - +
189B LEU* 3.4 5.6 + - - +
190B MET* 3.2 22.7 + - - +
206B ARG* 3.7 22.9 - - - +
209B VAL* 3.4 26.9 - - + +
210B ARG* 3.9 21.8 - - + +
213B LYS* 2.6 36.8 + - - +
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Residues in contact with ASP 187 (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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72B GLU* 4.8 8.1 - - - +
183B ARG* 3.0 23.4 + - - +
184B ASP* 3.6 7.1 - - - +
186B THR* 1.3 75.8 - - - +
188B TYR* 1.3 62.4 - - - +
190B MET* 3.7 15.6 + - - +
191B LYS* 3.4 20.3 + - - +
206B ARG* 3.1 31.3 + - - -
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Residues in contact with TYR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP 3.1 16.1 + - - +
185B LEU* 4.2 3.4 - - - +
187B ASP* 1.3 76.9 - - - +
189B LEU* 1.3 65.0 + - - +
191B LYS* 3.6 20.9 + - - +
192B ILE* 3.1 53.0 + - + +
256B ARG* 3.3 31.1 + - - +
257B CYS* 4.2 19.1 - - - -
260B ALA* 4.4 4.5 - - + -
266B PHE* 3.3 43.7 + + + +
267B LEU* 3.4 25.1 - - + -
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU 3.2 18.4 + - - +
186B THR 3.5 3.6 - - - +
187B ASP 3.3 0.2 - - - -
188B TYR* 1.3 77.8 - - - +
190B MET* 1.3 50.7 + - - +
192B ILE* 3.2 16.0 + - + +
193B LEU* 2.8 49.2 + - + +
209B VAL* 3.2 39.5 - - + +
212B ILE* 4.1 13.9 - - + -
213B LYS* 3.6 20.9 - - + +
217B CYS* 4.5 9.6 - - - -
250B ILE* 5.3 1.8 - - + -
253B GLU* 4.6 13.7 - - + +
257B CYS* 3.6 21.1 - - + -
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Residues in contact with MET 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR 3.2 5.1 + - - +
187B ASP* 3.7 28.9 - - - +
188B TYR 3.4 0.2 - - - -
189B LEU* 1.3 79.1 - - - +
191B LYS* 1.3 51.4 + - - +
193B LEU* 3.4 4.5 + - - +
194B THR* 2.8 43.8 + - - +
200B PHE* 4.3 20.4 - - + +
206B ARG* 3.7 44.6 - - + +
209B VAL* 3.8 33.9 - - + -
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ASP 3.4 14.4 + - - +
188B TYR* 3.8 30.1 - - - +
189B LEU 3.3 0.6 - - - -
190B MET* 1.3 75.0 - - - +
192B ILE* 1.3 72.2 + - - +
194B THR* 3.8 7.7 - - + -
195B GLU* 2.9 51.9 + - + +
173C HIS 5.9 1.8 - - - -
175C ILE 6.1 0.7 - - - -
176C LEU* 5.2 14.4 - - + -
284C LYS* 5.1 16.9 - - - +
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.1 57.9 + - + +
189B LEU* 3.3 18.8 - - + +
191B LYS* 1.3 78.0 - - - +
193B LEU* 1.3 61.9 + - - +
195B GLU* 3.2 26.1 + - - +
196B ARG* 3.3 12.1 + - - +
253B GLU* 3.9 45.5 - - + +
256B ARG* 3.8 34.0 + - + +
257B CYS* 4.3 6.7 - - + +
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Residues in contact with LEU 193 (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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189B LEU* 2.8 30.4 + - + +
190B MET 3.6 4.7 - - - +
192B ILE* 1.3 75.2 - - - +
194B THR* 1.3 55.2 + - - +
196B ARG* 3.1 13.0 + - - +
198B TYR* 2.7 48.5 + - + +
200B PHE* 3.8 27.6 - - + -
209B VAL* 4.6 2.7 - - + -
212B ILE* 3.9 21.5 - - + -
248B ILE* 4.5 5.8 - - + -
250B ILE* 3.9 26.2 - - + -
253B GLU* 3.9 25.1 - - + +
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Residues in contact with THR 194 (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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190B MET* 2.8 27.5 + - - +
191B LYS* 4.0 8.3 - - + +
193B LEU* 1.3 66.3 - - - +
195B GLU* 1.3 65.8 + - + +
196B ARG 3.1 2.0 - - - -
197B GLY* 3.0 14.7 + - - -
198B TYR* 3.5 24.3 + - - +
200B PHE* 3.8 17.8 + - - +
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Residues in contact with GLU 195 (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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191B LYS* 2.9 49.0 + - + +
192B ILE* 3.2 24.3 + - - +
194B THR* 1.3 73.4 - - + +
196B ARG* 1.3 57.2 + - - +
197B GLY 2.8 11.8 + - - -
256B ARG* 5.4 2.9 + - - -
110C LEU* 6.4 2.9 - - + -
113C LYS* 3.5 11.3 + - - +
175C ILE 5.5 2.9 - - - +
177C ARG* 5.9 0.9 + - - -
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ILE 3.3 9.8 + - - +
193B LEU 3.1 13.2 + - - +
195B GLU* 1.3 73.7 - - - +
197B GLY* 1.3 62.3 + - - +
198B TYR* 3.4 24.0 + - + -
237B GLU* 2.9 32.9 + - - -
249B THR* 3.0 34.1 + - - +
251B GLY* 4.1 1.0 - - - +
252B ASN* 5.2 1.0 - - - +
253B GLU* 3.2 33.8 + - - +
113C LYS* 3.1 32.3 + - - +
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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
------------------------------------------------------------
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