Contacts of the helix formed by residues 181 - 196 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C SER* 4.2 8.5 - - - +
156C GLY 3.3 13.7 - - - +
157C ASP 3.5 17.0 - - - +
158C GLY 3.9 0.2 - - - -
159C VAL 3.6 24.0 - - - +
160C THR* 4.1 1.8 - - - +
180C LEU* 1.3 77.3 - - - +
182C GLY* 1.4 56.0 + - - +
183C ARG 3.3 1.8 - - - -
184C ASP* 2.9 35.7 + - - +
185C LEU* 3.5 5.1 + - - +
261C LEU* 5.1 0.7 - - - -
303C THR* 3.9 6.7 - - - -
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Residues in contact with GLY 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156C GLY 2.9 6.2 + - - -
157C ASP* 4.3 8.5 - - - -
181C ALA* 1.4 71.9 - - - +
183C ARG* 1.3 55.0 + - - +
184C ASP 3.3 0.2 - - - -
185C LEU* 3.3 5.6 + - - +
186C THR* 3.0 31.1 + - - -
213C LYS* 3.2 14.2 + - - -
303C THR* 2.8 27.9 + - - -
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Residues in contact with ARG 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLU* 1.1 184.9 + - + +
73C HIS* 2.7 44.5 + - + +
75C ILE 3.5 0.4 + - - -
77C THR* 2.1 38.1 - - - +
157C ASP* 3.2 15.5 + - - +
181C ALA 3.0 2.6 + - - -
182C GLY* 1.3 70.1 - - - +
184C ASP* 1.3 68.3 + - - +
186C THR* 3.3 5.9 + - - +
187C ASP* 3.0 34.9 + - - +
206C ARG* 5.0 8.7 - - - +
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Residues in contact with ASP 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS* 3.4 28.7 + - - -
157C ASP 4.3 1.0 - - - +
179C ASP 4.0 5.7 - - - +
180C LEU* 3.6 32.4 - - + -
181C ALA 2.9 23.7 + - - +
183C ARG* 1.3 76.3 - - - +
185C LEU* 1.3 57.8 + - - +
187C ASP* 3.6 7.0 - - - +
188C TYR* 3.1 28.8 + - - +
267C LEU* 4.1 9.6 - - + +
269C MET* 4.0 12.0 - - - +
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C LEU* 3.9 25.6 - - + -
181C ALA 3.5 2.8 + - - +
182C GLY* 3.3 9.2 + - - +
183C ARG 3.1 0.6 - - - -
184C ASP* 1.3 80.3 - - - +
186C THR* 1.3 62.6 + - - +
188C TYR* 4.1 3.3 - - + +
189C LEU* 3.2 9.2 + - - +
213C LYS* 3.6 5.4 - - + -
257C CYS* 3.2 36.3 - - - +
258C PRO* 4.2 3.6 - - + -
260C ALA* 4.0 22.4 - - + -
261C LEU* 3.9 19.7 - - + -
267C LEU* 4.9 0.7 - - + -
303C THR* 3.9 11.9 - - + -
306C TYR* 3.1 40.8 - - + +
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Residues in contact with THR 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C GLY 3.0 10.2 + - - -
183C ARG* 3.8 6.4 - - - -
185C LEU* 1.3 74.1 - - - +
187C ASP* 1.3 61.9 + - - +
189C LEU* 3.4 5.4 + - - +
190C MET* 3.2 23.0 + - - +
206C ARG* 3.7 23.1 - - - +
209C VAL* 3.4 27.8 - - + +
210C ARG* 3.9 21.6 - - + +
213C LYS* 2.6 37.2 + - - +
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Residues in contact with ASP 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C GLU* 4.8 8.0 - - - +
183C ARG* 3.0 23.6 + - - +
184C ASP* 3.6 6.9 - - - +
186C THR* 1.3 77.3 - - - +
188C TYR* 1.3 62.6 - - - +
190C MET* 3.7 16.0 + - + +
191C LYS* 3.4 20.6 + - - +
206C ARG* 3.1 31.8 + - - -
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Residues in contact with TYR 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C ASP 3.1 15.9 + - - +
185C LEU* 3.6 4.0 + - - +
186C THR 3.4 0.2 - - - -
187C ASP* 1.3 76.5 - - - +
189C LEU* 1.3 66.2 + - - +
191C LYS* 3.6 21.2 + - - +
192C ILE* 3.1 51.3 + - + +
256C ARG* 3.3 30.7 + - - +
257C CYS* 4.2 18.8 - - - -
260C ALA* 4.4 4.5 - - + -
266C PHE* 3.3 43.9 + + + +
267C LEU* 3.4 24.2 - - + -
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Residues in contact with LEU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C LEU 3.2 17.8 + - - +
186C THR 3.5 3.6 - - - +
188C TYR* 1.3 78.2 - - - +
190C MET* 1.3 50.9 + - - +
192C ILE* 3.2 14.8 + - + +
193C LEU* 2.8 47.8 + - + +
209C VAL* 3.2 39.0 - - + +
212C ILE* 4.1 13.0 - - + -
213C LYS* 3.6 20.4 - - + +
217C CYS* 4.5 9.6 - - - -
250C ILE* 5.3 2.5 - - + -
253C GLU* 4.6 13.5 - - + +
257C CYS* 3.6 22.0 - - + -
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Residues in contact with MET 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C THR 3.2 6.6 + - - +
187C ASP* 3.7 27.4 - - - +
188C TYR 3.4 0.2 - - - -
189C LEU* 1.3 79.1 - - - +
191C LYS* 1.3 52.0 + - - +
193C LEU* 3.4 4.1 + - - +
194C THR* 2.8 43.0 + - - +
200C PHE* 4.3 19.9 - - + +
206C ARG* 3.7 44.0 - - + +
209C VAL* 3.8 33.9 - - + -
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Residues in contact with LYS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C ASP 3.4 14.3 + - - +
188C TYR* 3.8 30.6 - - - +
189C LEU 3.3 0.4 - - - -
190C MET* 1.3 75.8 - - - +
192C ILE* 1.3 71.0 + - - +
194C THR* 3.8 8.0 - - + -
195C GLU* 2.9 50.7 + - + +
173D HIS 5.9 1.6 - - - -
175D ILE 6.1 0.7 - - - -
176D LEU* 5.2 14.8 - - + -
284D LYS* 5.1 17.4 - - - +
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Residues in contact with ILE 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C TYR* 3.1 58.2 + - + +
189C LEU* 3.3 19.7 - - + +
191C LYS* 1.3 79.1 - - - +
193C LEU* 1.3 60.9 + - - +
195C GLU* 3.2 26.8 + - - +
196C ARG* 3.3 11.6 + - - +
253C GLU* 3.9 45.9 - - + +
256C ARG* 3.8 33.4 + - + +
257C CYS* 4.3 6.3 - - + +
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Residues in contact with LEU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LEU* 2.8 30.6 + - + +
190C MET 3.6 4.5 - - - +
192C ILE* 1.3 75.5 - - - +
194C THR* 1.3 55.2 + - - +
196C ARG* 3.1 13.3 + - - +
198C TYR* 2.7 48.6 + - + +
200C PHE* 3.8 26.7 - - + -
209C VAL* 4.6 3.1 - - + -
212C ILE* 3.9 21.1 - - + -
248C ILE* 4.5 5.8 - - + -
250C ILE* 3.9 26.5 - - + -
253C GLU* 3.9 24.9 - - + +
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Residues in contact with THR 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C MET* 2.8 27.5 + - - +
191C LYS* 4.0 7.4 - - + +
193C LEU* 1.3 67.0 - - - +
195C GLU* 1.3 65.2 + - + +
196C ARG 3.1 1.8 - - - -
197C GLY* 3.0 14.7 + - - -
198C TYR 3.5 24.1 + - - +
200C PHE* 3.8 18.0 + - - +
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Residues in contact with GLU 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C LYS* 2.9 48.4 + - + +
192C ILE* 3.2 24.5 + - - +
194C THR* 1.3 72.6 - - + +
196C ARG* 1.3 56.7 + - - +
197C GLY* 2.8 11.5 + - - -
256C ARG* 5.4 3.3 + - - +
110D LEU* 6.4 3.1 - - + -
113D LYS* 3.5 12.0 + - - +
175D ILE 5.5 2.8 - - - +
177D ARG* 5.9 1.2 + - - -
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Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ILE 3.3 10.1 + - - +
193C LEU 3.1 13.2 + - - +
195C GLU* 1.3 73.2 - - - +
197C GLY* 1.3 61.9 + - - +
198C TYR* 3.4 24.2 + - + -
237C GLU* 2.9 31.3 + - - -
249C THR* 3.0 35.2 + - - +
251C GLY* 4.1 1.0 - - - +
252C ASN 5.2 0.6 - - - +
253C GLU* 3.2 33.1 + - - +
113D LYS* 3.1 31.9 + - - +
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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