Contacts of the helix formed by residues 181 - 196 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155G SER* 4.2 8.3 - - - +
156G GLY 3.3 13.7 - - - +
157G ASP 3.5 17.5 - - - +
158G GLY 3.9 0.4 - - - -
159G VAL 3.6 23.6 - - - +
160G THR* 4.1 1.8 - - - +
180G LEU* 1.3 78.5 - - - +
182G GLY* 1.4 56.4 + - - +
183G ARG 3.3 1.8 - - - -
184G ASP* 2.9 34.5 + - - +
185G LEU* 3.5 5.9 + - - +
261G LEU* 5.1 0.9 - - - -
303G THR* 4.2 6.3 - - - -
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Residues in contact with GLY 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156G GLY 2.9 6.0 + - - -
157G ASP* 3.8 7.6 + - - -
181G ALA* 1.4 71.9 - - - +
183G ARG* 1.3 55.5 + - - +
184G ASP 3.3 0.2 - - - -
185G LEU* 3.2 5.7 + - - +
186G THR* 3.0 31.2 + - - -
213G LYS* 3.2 14.6 + - - -
303G THR* 2.8 29.7 + - - -
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Residues in contact with ARG 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLU* 1.1 183.5 + - + +
73G HIS* 2.7 45.5 + - + +
75G ILE 3.5 0.4 + - - -
77G THR* 2.1 37.9 - - - +
157G ASP* 3.2 14.8 + - - +
181G ALA 3.0 2.4 + - - -
182G GLY* 1.3 69.9 - - - +
184G ASP* 1.3 69.4 + - - +
186G THR* 3.3 5.7 + - - +
187G ASP* 3.0 34.5 + - - +
206G ARG* 5.0 8.7 - - - +
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Residues in contact with ASP 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G HIS* 3.4 29.9 + - - -
157G ASP 4.3 0.9 - - - +
179G ASP 4.0 5.9 - - - +
180G LEU* 3.6 31.9 - - + -
181G ALA 2.9 22.7 + - - +
183G ARG* 1.3 77.3 - - - +
185G LEU* 1.3 57.6 + - - +
187G ASP* 3.6 7.0 - - - +
188G TYR* 3.1 28.8 + - - +
267G LEU* 4.1 9.9 - - + +
269G MET* 4.0 11.6 - - - +
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Residues in contact with LEU 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G LEU* 3.9 26.0 - - + -
181G ALA 3.5 2.6 + - - +
182G GLY* 3.2 9.6 + - - +
183G ARG 3.1 0.4 - - - -
184G ASP* 1.3 79.9 - - - +
186G THR* 1.3 62.2 + - - +
188G TYR* 4.1 3.1 - - + +
189G LEU* 3.2 8.7 + - - +
213G LYS* 3.6 5.4 - - + -
257G CYS* 3.2 37.1 - - - +
258G PRO* 4.2 3.6 - - + -
260G ALA* 4.0 22.2 - - + -
261G LEU* 3.9 20.2 - - + -
267G LEU* 4.9 0.4 - - + -
303G THR* 3.9 12.3 - - + -
306G TYR* 3.1 40.8 - - + +
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Residues in contact with THR 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182G GLY 3.0 10.2 + - - -
183G ARG* 3.8 6.8 - - - -
185G LEU* 1.3 74.3 - - - +
187G ASP* 1.3 61.6 + - - +
189G LEU* 3.4 5.6 + - - +
190G MET* 3.2 22.5 + - - +
206G ARG* 3.7 22.9 - - - +
209G VAL* 3.4 27.4 - - + +
210G ARG* 3.9 21.8 - - + +
213G LYS* 2.6 36.7 + - - +
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Residues in contact with ASP 187 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLU* 4.8 7.8 - - - +
183G ARG* 3.0 24.3 + - - +
184G ASP* 3.6 6.9 - - - +
186G THR* 1.3 76.2 - - - +
188G TYR* 1.3 61.7 - - - +
189G LEU 3.3 0.2 - - - -
190G MET* 3.7 15.0 + - - +
191G LYS* 3.4 20.4 + - - +
206G ARG* 3.1 32.2 + - - -
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Residues in contact with TYR 188 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G ASP 3.1 16.3 + - - +
185G LEU* 3.6 4.2 + - - +
187G ASP* 1.3 77.3 - - - +
189G LEU* 1.3 64.9 + - - +
191G LYS* 3.6 21.1 + - - +
192G ILE* 3.1 51.6 + - + +
256G ARG* 3.3 31.3 + - - +
257G CYS* 4.2 19.7 - - - -
260G ALA* 4.4 3.8 - - + -
266G PHE* 3.3 44.0 + + + +
267G LEU* 3.4 25.1 - - + -
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Residues in contact with LEU 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU 3.2 18.2 + - - +
186G THR 3.5 4.0 - - - +
188G TYR* 1.3 77.6 - - - +
190G MET* 1.3 50.0 + - - +
192G ILE* 3.2 15.6 + - + +
193G LEU* 2.8 48.2 + - + +
209G VAL* 3.2 39.0 - - + +
212G ILE* 4.1 13.9 - - + -
213G LYS* 3.6 21.1 - - + +
217G CYS* 4.5 9.9 - - - -
250G ILE* 5.3 2.0 - - + -
253G GLU* 4.6 13.9 - - + +
257G CYS* 3.6 21.5 - - + -
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Residues in contact with MET 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186G THR 3.2 6.4 + - - +
187G ASP* 3.7 28.5 - - - +
188G TYR 3.4 0.2 - - - -
189G LEU* 1.3 79.1 - - - +
191G LYS* 1.3 51.4 + - - +
193G LEU* 3.4 3.9 + - - +
194G THR* 2.8 43.6 + - - +
200G PHE* 4.3 20.4 - - + +
206G ARG* 3.7 44.4 - - + +
209G VAL* 3.8 33.7 - - + -
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Residues in contact with LYS 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G ASP 3.4 14.4 + - - +
188G TYR* 3.8 30.6 - - - +
189G LEU 3.3 0.2 - - - -
190G MET* 1.3 76.2 - - - +
192G ILE* 1.3 71.9 + - - +
194G THR* 3.8 7.5 - - + -
195G GLU* 2.9 52.3 + - + +
173H HIS 5.9 2.0 - - - -
175H ILE 6.1 0.7 - - - -
176H LEU* 5.2 14.4 - - + -
284H LYS* 5.1 17.2 - - - +
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Residues in contact with ILE 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G TYR* 3.1 58.6 + - + +
189G LEU* 3.3 18.4 - - + +
191G LYS* 1.3 77.8 - - - +
193G LEU* 1.3 60.9 + - - +
195G GLU* 3.2 26.0 + - - +
196G ARG* 3.3 12.0 + - - +
253G GLU* 3.9 44.7 - - + +
256G ARG* 3.8 33.9 + - + +
257G CYS* 4.3 7.6 - - + +
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Residues in contact with LEU 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G LEU* 2.8 31.0 + - + +
190G MET 3.6 4.9 - - - +
192G ILE* 1.3 75.8 - - - +
194G THR* 1.3 55.1 + - - +
196G ARG* 3.1 13.2 + - - +
198G TYR* 2.7 48.9 + - + +
200G PHE* 3.8 27.4 - - + -
209G VAL* 4.6 2.9 - - + -
212G ILE* 3.9 21.5 - - + -
248G ILE* 4.5 5.6 - - + -
250G ILE* 3.9 25.8 - - + -
253G GLU* 3.9 24.7 - - + +
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Residues in contact with THR 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G MET* 2.8 27.0 + - - +
191G LYS* 4.0 8.1 - - + +
193G LEU* 1.3 67.0 - - - +
195G GLU* 1.3 66.3 + - + +
196G ARG 3.1 1.6 - - - -
197G GLY* 3.0 14.8 + - - -
198G TYR* 3.5 23.9 + - - +
200G PHE* 3.8 18.7 + - - +
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Residues in contact with GLU 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191G LYS* 2.9 48.4 + - + +
192G ILE* 3.2 24.3 + - - +
194G THR* 1.3 73.5 - - + +
196G ARG* 1.3 56.9 + - - +
197G GLY* 2.8 11.3 + - - -
256G ARG* 5.4 3.2 + - - +
110H LEU* 6.4 3.1 - - + -
113H LYS* 3.5 11.3 + - - +
175H ILE 5.5 2.8 - - - +
177H ARG* 5.9 1.2 + - - -
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Residues in contact with ARG 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G ILE 3.3 9.2 + - - +
193G LEU 3.1 12.8 + - - +
195G GLU* 1.3 73.7 - - - +
197G GLY* 1.3 62.3 + - - +
198G TYR* 3.4 24.4 + - + -
237G GLU* 2.9 32.1 + - - -
249G THR* 3.0 35.4 + - - +
251G GLY* 4.1 1.0 - - - +
252G ASN 5.2 0.8 - - - +
253G GLU* 3.2 33.3 + - - +
113H LYS* 3.1 31.2 + - - +
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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