Contacts of the helix formed by residues 181 - 197 (chain F) in PDB entry 1NU9
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 HIS 181 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175F PHE* 4.0 21.5 - + + -
178F ASP* 2.7 36.6 + - - +
180F GLN* 1.3 107.9 + - + +
182F LYS* 1.3 62.8 + - - -
183F THR 3.5 2.0 - - - -
184F GLU* 3.2 12.4 + - - +
185F ALA* 3.1 19.1 + - - +
225F PHE* 4.2 0.7 - - + -
229F THR* 3.2 51.4 - - + +
231F LEU* 3.9 26.2 - - + +
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Residues in contact with LYS 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F PHE 3.7 9.2 - - - -
176F VAL* 3.8 24.7 + - - +
177F ARG* 5.9 0.4 - - - -
178F ASP 2.8 13.7 + - - +
179F THR* 4.1 12.2 + - - +
180F GLN 3.7 1.2 - - - -
181F HIS* 1.3 75.8 - - - +
183F THR* 1.3 62.1 + - - +
185F ALA* 2.7 21.9 + - - +
186F LEU* 2.8 40.1 + - + +
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Residues in contact with THR 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D MET* 4.1 8.7 - - - -
109D LYS* 3.9 36.8 - - + +
110D LYS* 4.0 17.3 - - + -
181F HIS 3.5 0.8 - - - -
182F LYS* 1.3 80.6 - - - +
184F GLU* 1.3 70.9 + - - +
186F LEU* 3.3 6.5 + - - +
187F GLU* 3.0 46.0 + - - +
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Residues in contact with GLU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LYS* 3.0 38.6 + - - +
180F GLN 4.1 5.6 - - - +
181F HIS* 3.4 20.3 - - - +
182F LYS 3.2 0.4 - - - -
183F THR* 1.3 81.8 + - - +
185F ALA* 1.3 57.3 + - - +
187F GLU* 4.0 8.7 - - - +
188F LEU* 3.0 26.5 + - - +
225F PHE* 3.4 12.7 - - + +
228F GLU* 4.2 18.9 - - + +
229F THR* 3.4 34.3 - - + +
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Residues in contact with ALA 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F TYR* 3.2 22.2 - - + +
175F PHE* 3.8 10.3 - - + -
176F VAL* 3.8 29.8 - - - +
181F HIS 3.1 10.8 + - - +
182F LYS 2.7 9.0 + - - +
184F GLU* 1.3 76.7 - - - +
186F LEU* 1.3 64.3 + - - +
188F LEU* 3.1 5.9 + - - +
189F LYS 3.0 19.4 + - - -
225F PHE* 3.7 8.9 - - + -
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Residues in contact with LEU 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D MET* 3.9 32.8 - - + -
172F TYR* 4.2 12.6 - - + +
176F VAL* 3.9 22.7 - - + -
182F LYS* 2.8 49.3 + - + +
183F THR* 3.8 4.5 - - - +
185F ALA* 1.3 76.3 - - - +
187F GLU* 1.3 56.5 + - - +
189F LYS* 3.4 5.7 + - + +
190F ALA* 3.0 27.3 + - - +
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Residues in contact with GLU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LYS* 4.3 7.7 + - - -
82D ILE* 4.2 12.6 - - + +
83D SER* 3.8 6.1 - - - -
84D MET* 3.2 43.4 + - + +
109D LYS* 5.2 0.3 - - - +
110D LYS* 4.0 22.4 - - - +
183F THR* 3.0 28.0 + - - +
184F GLU* 4.0 7.3 - - - +
186F LEU* 1.3 74.6 - - - +
188F LEU* 1.3 57.7 + - - +
190F ALA* 3.7 6.0 - - - -
191F LYS* 2.8 51.1 + - + +
228F GLU* 4.2 11.8 - - - +
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Residues in contact with LEU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ALA* 3.6 28.5 - - + +
171F VAL* 3.8 17.9 - - + -
172F TYR* 3.6 20.6 - - + +
184F GLU 3.0 15.4 + - - +
185F ALA 3.3 7.2 - - - +
187F GLU* 1.3 76.4 - - - +
189F LYS* 1.3 64.1 + - - +
191F LYS* 3.9 4.6 - - - +
192F VAL* 3.0 38.5 + - + +
221F ILE* 3.6 39.5 - - + +
222F ILE* 4.2 9.2 - - + -
225F PHE* 4.1 16.2 - - + -
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Residues in contact with LYS 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F TYR* 3.8 16.4 - - + -
172F TYR* 3.6 54.0 + - + +
173F PHE* 6.4 0.4 - - - -
185F ALA 3.0 6.5 + - - -
186F LEU* 3.6 8.1 - - + +
188F LEU* 1.3 79.8 - - - +
190F ALA* 1.3 58.5 + - - +
192F VAL* 3.2 5.8 + - - +
193F ASP* 2.9 61.7 + - - +
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Residues in contact with ALA 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LYS* 4.6 17.3 - - + +
65D LEU* 4.0 24.9 - - + +
82D ILE* 5.3 2.2 - - + -
84D MET* 6.2 3.1 - - + -
186F LEU 3.0 17.2 + - - +
187F GLU* 3.7 7.2 - - - +
189F LYS* 1.3 77.5 - - - +
191F LYS* 1.3 60.0 + - + +
193F ASP* 3.4 9.7 + - - +
194F LEU* 3.0 28.1 + - - +
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Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TYR* 4.2 14.6 + - + +
81D LYS* 5.8 5.1 - - - +
82D ILE* 3.8 45.5 - - + +
187F GLU* 2.8 34.4 + - + +
188F LEU* 4.7 2.2 - - - +
190F ALA* 1.3 70.1 - - - +
192F VAL* 1.3 65.8 + - - +
194F LEU* 3.5 7.5 + - - +
195F VAL* 3.2 29.5 + - - +
221F ILE* 3.7 29.1 + - + +
224F ASP* 2.6 41.8 + - - +
228F GLU* 4.8 5.1 + - - -
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Residues in contact with VAL 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F ALA* 4.0 15.3 - - + +
168F ALA* 3.6 25.1 - - + -
169F TYR* 3.5 32.5 - - + +
188F LEU* 3.0 25.1 + - + +
189F LYS* 3.7 4.3 - - - +
191F LYS* 1.3 75.0 - - - +
193F ASP* 1.3 63.4 + - - +
195F VAL* 3.2 21.3 - - - +
196F LEU* 3.2 21.1 + - + +
218F LEU* 4.1 10.3 - - + -
221F ILE* 3.9 16.4 - - + -
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Residues in contact with ASP 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLN* 3.6 2.9 + - - -
169F TYR* 2.3 38.6 + - - -
189F LYS* 2.9 48.4 + - - +
190F ALA* 3.6 8.9 - - - +
192F VAL* 1.3 78.1 - - - +
194F LEU* 1.3 61.6 + - - +
196F LEU* 3.4 2.9 + - - +
197F GLY 3.0 29.0 + - - +
199F GLU* 5.5 3.3 - - - +
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Residues in contact with LEU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D PHE* 3.3 38.6 - - + -
38D GLN* 2.7 25.6 + - - +
65D LEU* 5.0 9.9 - - + -
67D ARG* 3.6 39.9 - - - +
76D TYR* 4.3 11.2 - - + -
80D GLU* 4.8 0.2 - - - +
82D ILE* 5.1 7.0 - - + -
190F ALA 3.0 17.5 + - - +
191F LYS* 3.7 8.5 - - - +
192F VAL 3.3 0.2 - - - -
193F ASP* 1.3 77.4 - - - +
195F VAL* 1.3 78.4 + - + +
196F LEU 3.3 0.2 + - - -
197F GLY* 3.4 1.9 + - - -
203F HIS* 4.2 4.3 + - - -
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Residues in contact with VAL 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TYR* 3.7 38.8 - - + -
48F TYR* 4.7 1.9 + - - -
191F LYS 3.2 14.3 + - - +
192F VAL* 3.2 15.7 - - - +
194F LEU* 1.3 83.1 - - + +
196F LEU* 1.3 61.0 + - - +
203F HIS* 3.4 8.7 - - - -
214F MET* 3.2 32.1 - - - +
217F ASP* 4.8 6.1 - - + +
218F LEU* 3.7 26.2 - - + -
221F ILE* 3.8 13.0 - - + -
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Residues in contact with LEU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F VAL* 4.0 27.1 - - + -
162F ASP* 4.8 8.3 - - - +
165F ALA* 3.7 28.7 - - + -
169F TYR* 3.7 22.0 - - + +
192F VAL* 3.2 21.5 + - + +
193F ASP* 3.8 3.4 - - - +
195F VAL* 1.3 78.8 - - - +
197F GLY* 1.3 63.3 + - - +
202F PRO* 3.5 13.0 - - + +
203F HIS* 3.0 27.9 + - - +
205F ILE* 6.1 0.2 - - + -
214F MET* 4.3 13.4 - - + +
218F LEU* 4.4 7.4 - - + -
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Residues in contact with GLY 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLN* 3.5 14.8 - - - -
193F ASP* 3.0 17.0 + - - +
194F LEU 3.4 2.8 + - - -
196F LEU* 1.3 82.8 - - - +
198F ASP* 1.3 68.5 + - - +
199F GLU* 3.5 3.1 + - - +
202F PRO* 4.4 1.9 - - - +
203F HIS* 3.5 22.7 - - - -
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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
------------------------------------------------------------
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