Contacts of the helix formed by residues 181 - 196 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D SER* 4.2 8.1 - - - +
156D GLY 3.3 14.1 - - - +
157D ASP 3.5 17.3 - - - +
158D GLY 3.9 0.4 - - - -
159D VAL 3.6 23.6 - - - +
160D THR* 4.1 1.6 - - - +
180D LEU* 1.3 77.7 - - - +
182D GLY* 1.4 55.9 + - - +
183D ARG 3.3 2.0 - - - -
184D ASP* 2.9 35.6 + - - +
185D LEU* 3.5 6.5 + - - +
261D LEU* 5.1 0.7 - - - -
303D THR* 3.9 6.5 - - - -
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Residues in contact with GLY 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D GLY 2.9 6.2 + - - -
157D ASP* 4.3 7.6 - - - -
181D ALA* 1.4 72.3 - - - +
183D ARG* 1.3 54.8 + - - +
184D ASP 3.3 0.2 - - - -
185D LEU* 3.3 6.3 + - - +
186D THR* 3.0 30.7 + - - -
213D LYS* 3.2 14.3 + - - -
303D THR* 2.8 28.5 + - - -
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Residues in contact with ARG 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLU* 1.1 183.5 + - + +
73D HIS* 2.7 43.8 + - - +
75D ILE 3.5 0.4 + - - -
77D THR* 2.1 38.3 - - - +
157D ASP* 3.2 14.2 + - - +
181D ALA 3.0 2.4 + - - -
182D GLY* 1.3 69.5 - - - +
184D ASP* 1.3 67.6 + - - +
186D THR* 3.8 5.2 - - - +
187D ASP* 3.0 34.2 + - - +
206D ARG* 5.0 8.7 - - - +
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Residues in contact with ASP 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D HIS* 3.4 28.8 + - - -
157D ASP 4.3 1.2 - - - +
179D ASP 4.0 5.9 - - - +
180D LEU* 3.6 30.5 - - + -
181D ALA 2.9 23.5 + - - +
183D ARG* 1.3 77.3 - - - +
185D LEU* 1.3 57.6 + - - +
187D ASP* 3.6 6.7 - - - +
188D TYR* 3.1 27.9 + - - +
267D LEU* 4.1 11.5 - - + +
269D MET* 4.0 12.0 - - - +
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D LEU* 3.9 25.4 - - + -
181D ALA 3.5 2.8 + - - +
182D GLY* 3.3 8.7 + - - +
183D ARG 3.1 0.6 - - - -
184D ASP* 1.3 80.1 - - - +
186D THR* 1.3 62.1 + - - +
188D TYR* 4.5 2.9 - - + +
189D LEU* 3.2 9.7 + - - +
213D LYS* 3.6 4.7 - - + -
257D CYS* 3.2 38.5 - - - +
258D PRO* 4.2 3.8 - - + -
260D ALA* 4.0 22.0 - - + -
261D LEU* 3.9 20.2 - - + -
267D LEU* 4.9 0.4 - - + -
303D THR* 3.9 12.1 - - + -
306D TYR* 3.1 40.8 - - + +
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Residues in contact with THR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D GLY 3.0 10.0 + - - -
183D ARG* 3.8 6.6 - - - -
185D LEU* 1.3 73.4 - - - +
187D ASP* 1.3 62.3 + - - +
189D LEU* 3.4 6.0 + - - +
190D MET* 3.2 22.5 + - - +
206D ARG* 3.7 23.1 - - - +
209D VAL* 3.4 27.4 - - + +
210D ARG* 3.9 21.7 - - + +
213D LYS* 2.6 37.4 + - - +
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Residues in contact with ASP 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D GLU* 4.8 8.0 - - - +
183D ARG* 3.0 23.0 + - - +
184D ASP* 3.6 7.4 - - - +
186D THR* 1.3 76.4 - - - +
188D TYR* 1.3 61.6 + - - +
190D MET* 3.7 15.4 + - + +
191D LYS* 3.4 21.1 + - - +
206D ARG* 3.1 31.7 + - - -
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Residues in contact with TYR 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ASP 3.1 16.6 + - - +
185D LEU* 3.6 3.8 + - - +
186D THR 3.4 0.2 - - - -
187D ASP* 1.3 76.5 - - - +
189D LEU* 1.3 65.7 + - - +
191D LYS* 3.8 20.8 - - - +
192D ILE* 3.1 51.5 + - + +
256D ARG* 3.3 31.4 + - - +
257D CYS* 4.2 18.8 - - - -
260D ALA* 4.4 4.5 - - + -
266D PHE* 3.3 44.0 + + + +
267D LEU* 3.4 25.6 - - + -
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Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D LEU 3.2 18.5 + - - +
186D THR 3.5 3.8 - - - +
188D TYR* 1.3 78.2 - - - +
190D MET* 1.3 51.2 + - - +
192D ILE* 3.2 15.4 + - + +
193D LEU* 2.8 49.0 + - + +
209D VAL* 3.2 39.3 - - + +
212D ILE* 4.1 13.5 - - + -
213D LYS* 3.6 20.6 - - + +
217D CYS* 4.5 9.6 - - - -
250D ILE* 5.3 2.7 - - + -
253D GLU* 4.6 13.0 - - + +
257D CYS* 3.6 22.0 - - + -
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Residues in contact with MET 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D THR 3.2 7.0 + - - +
187D ASP* 3.7 28.3 - - - +
188D TYR 3.4 0.2 - - - -
189D LEU* 1.3 78.2 - - - +
191D LYS* 1.3 52.5 + - - +
193D LEU* 3.6 3.8 - - - +
194D THR* 2.8 43.7 + - - +
200D PHE* 4.3 20.7 - - + +
206D ARG* 3.7 45.1 - - + +
209D VAL* 3.8 33.9 - - + -
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Residues in contact with LYS 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D ASP 3.4 14.3 + - - +
188D TYR* 3.8 30.2 - - - +
189D LEU 3.3 0.2 - - - -
190D MET* 1.3 75.8 - - - +
192D ILE* 1.3 70.8 + - - +
194D THR* 3.4 7.2 + - + -
195D GLU* 2.9 51.4 + - + +
173E HIS 5.9 1.3 - - - -
175E ILE 6.1 0.7 - - - -
176E LEU* 5.2 14.1 - - + -
284E LYS* 5.1 18.1 - - - +
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Residues in contact with ILE 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D TYR* 3.1 58.1 + - + +
189D LEU* 3.3 20.0 - - + +
191D LYS* 1.3 78.3 - - - +
193D LEU* 1.3 59.5 + - - +
195D GLU* 3.2 26.0 + - - +
196D ARG* 3.3 11.8 + - - +
253D GLU* 3.9 45.1 - - + +
256D ARG* 3.8 33.0 + - + +
257D CYS* 4.3 7.4 - - - +
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D LEU* 2.8 31.9 + - + +
190D MET 3.6 4.9 - - - +
192D ILE* 1.3 76.2 - - - +
194D THR* 1.3 55.8 + - - +
196D ARG* 3.1 13.2 + - - +
198D TYR* 2.7 47.6 + - + +
200D PHE* 3.8 26.5 - - + -
209D VAL* 4.6 2.5 - - + -
212D ILE* 3.9 20.9 - - + -
248D ILE* 4.5 5.8 - - + -
250D ILE* 3.9 26.7 - - + -
253D GLU* 3.9 25.1 - - + +
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Residues in contact with THR 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D MET* 2.8 27.1 + - - +
191D LYS* 4.0 8.3 - - + +
193D LEU* 1.3 66.9 - - - +
195D GLU* 1.3 65.8 + - + +
196D ARG 3.1 1.6 - - - -
197D GLY* 3.0 14.7 + - - -
198D TYR* 3.5 23.4 + - - +
200D PHE* 3.8 18.2 + - - +
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Residues in contact with GLU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D LYS* 2.9 48.7 + - + +
192D ILE* 3.2 24.9 + - - +
194D THR* 1.3 72.8 - - + +
196D ARG* 1.3 57.1 + - - +
197D GLY 2.8 11.3 + - - -
256D ARG* 5.4 3.2 + - - +
110E LEU* 6.4 2.9 - - + -
113E LYS* 3.5 12.2 + - - +
175E ILE 5.5 2.8 - - - +
177E ARG* 5.9 1.0 + - - -
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Residues in contact with ARG 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D ILE 3.3 8.8 + - - +
193D LEU 3.1 12.6 + - - +
195D GLU* 1.3 73.4 - - - +
197D GLY* 1.3 63.2 + - - +
198D TYR* 3.4 24.3 + - + -
237D GLU* 2.9 32.1 + - - -
249D THR* 3.0 34.8 + - - +
251D GLY* 4.1 1.0 - - - +
252D ASN 5.2 1.0 - - - +
253D GLU* 3.2 34.7 + - - +
113E LYS* 3.1 30.8 + - - +
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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