Contacts of the helix formed by residues 170 - 193 (chain A) in PDB entry 1N0U
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 SER 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A GLN 3.8 0.6 + - - -
169A VAL* 1.3 81.7 - - - +
171A LYS* 1.3 64.4 + - - +
172A GLU* 3.7 6.2 + - - +
173A ASP* 2.7 36.5 + - - -
174A LEU* 3.0 21.3 + - - +
282A PHE* 4.0 3.4 - - - -
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A SER* 1.3 73.4 - - - +
172A GLU* 1.3 58.0 + - - +
174A LEU 3.3 0.3 + - - -
175A TYR* 2.9 24.9 + - - +
270A GLU* 2.7 27.8 + - - +
274A ASN* 3.7 15.9 - - + +
278A LEU* 3.3 21.4 - - + +
279A ASP* 2.9 48.7 + - - +
282A PHE* 3.6 37.8 - - + -
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A SER* 3.3 5.6 + - - +
171A LYS* 1.3 75.4 - - - +
173A ASP* 1.3 62.6 + - - +
175A TYR* 3.3 3.1 + - - +
176A GLN* 2.8 53.6 + - + +
271A ARG* 2.8 39.8 + - - +
274A ASN* 2.6 33.8 + - - +
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Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A VAL* 3.2 20.0 - - + +
170A SER* 2.7 26.6 + - - +
172A GLU* 1.3 79.4 - - - +
174A LEU* 1.3 58.1 + - - +
176A GLN* 3.3 8.5 + - - +
177A THR* 2.8 34.4 + - - +
180A ARG* 4.9 0.5 + - - -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A THR* 3.9 19.3 - - + -
160A VAL* 4.0 16.8 - - + -
163A ALA* 4.0 13.0 - - + -
164A LEU* 4.1 7.2 - - + -
169A VAL* 3.6 7.3 - - + +
170A SER 3.0 16.2 + - - +
171A LYS* 3.6 5.2 - - - +
173A ASP* 1.3 74.6 - - - +
175A TYR* 1.3 66.7 + - - +
177A THR* 3.0 7.8 + - - -
178A PHE* 2.8 65.6 + - + -
278A LEU* 4.0 20.9 - - + -
282A PHE* 4.0 16.6 - - + -
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Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LYS 2.9 9.4 + - - +
172A GLU* 3.5 8.5 - - - +
174A LEU* 1.3 76.0 - - - +
176A GLN* 1.3 80.5 + - - +
178A PHE* 3.0 12.3 + - - +
179A ALA* 2.9 34.3 + - + +
245A TRP* 3.5 38.5 + + - -
246A GLY* 3.1 26.7 - - - -
247A ASP* 4.8 1.6 + - - -
271A ARG* 3.1 45.7 + - - -
273A PHE* 3.6 20.0 - + + -
274A ASN* 3.5 18.2 - - - +
278A LEU* 4.4 0.6 - - - +
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Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLU* 2.8 51.9 + - + +
173A ASP* 3.6 8.3 - - - +
175A TYR* 1.3 90.5 - - - +
177A THR* 1.3 64.0 + - - +
179A ALA* 3.3 7.6 + - - +
180A ARG* 2.9 47.7 + - - +
271A ARG* 3.7 4.9 - - - +
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A THR* 3.1 37.9 - - + +
132A ILE* 5.2 2.5 - - - +
169A VAL* 5.5 1.7 - - - +
173A ASP* 2.8 26.7 + - - +
174A LEU* 3.4 13.9 - - - +
176A GLN* 1.3 73.2 - - - +
178A PHE* 1.3 66.5 + - + +
180A ARG* 3.2 28.1 + - - +
181A THR* 3.0 29.6 + - - +
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A THR* 3.9 12.1 - - + -
157A ILE* 3.9 34.3 - - + +
160A VAL* 3.9 18.2 - - + -
174A LEU* 2.8 53.4 + - + -
175A TYR 3.3 5.8 - - - +
177A THR* 1.3 77.7 - - + +
179A ALA* 1.3 56.7 + - - +
181A THR* 3.2 4.3 + - - -
182A VAL* 2.9 34.7 + - - +
211A PHE* 3.5 39.9 - + + -
220A PHE* 5.3 0.9 - + - -
245A TRP* 4.0 7.4 - - + -
273A PHE* 3.8 28.7 - + - -
278A LEU* 4.5 3.6 - - + -
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A TYR* 2.9 32.5 + - + +
176A GLN* 3.6 15.0 - - - +
178A PHE* 1.3 78.0 - - - +
180A ARG* 1.3 62.7 + - + +
182A VAL* 3.4 5.2 + - - +
183A GLU* 3.0 23.6 + - - +
245A TRP* 4.2 13.4 - - + -
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASP 5.0 0.2 + - - -
176A GLN* 2.9 41.6 + - + +
177A THR* 3.3 35.3 + - - +
179A ALA* 1.3 75.7 - - + +
181A THR* 1.3 59.4 + - - +
183A GLU* 3.1 8.0 + - - +
184A SER* 2.9 33.1 + - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 3.3 35.4 - - + -
130A ASP 4.4 2.3 + - - +
131A THR 4.4 4.0 + - - -
134A GLY* 4.2 14.2 - - - -
135A VAL* 4.8 1.6 - - + -
155A VAL* 5.8 1.1 - - + -
157A ILE* 4.1 21.7 - - + +
177A THR* 3.0 21.1 + - - +
178A PHE* 3.5 8.5 - - - -
180A ARG* 1.3 77.8 - - - +
182A VAL* 1.3 62.9 + - - +
184A SER* 3.3 7.4 + - - -
185A VAL* 3.1 25.2 + - + +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL* 6.1 1.6 - - + -
157A ILE* 4.2 15.9 - - + -
178A PHE 2.9 23.0 + - - +
179A ALA* 3.7 7.6 - - - +
181A THR* 1.3 76.3 - - + +
183A GLU* 1.3 57.3 + - - +
185A VAL* 3.4 7.9 + - + +
186A ASN* 3.0 43.9 + - - +
202A VAL* 3.9 12.8 - - + +
204A PRO* 4.1 29.8 - - + -
209A VAL* 4.3 12.1 - - + -
245A TRP* 4.8 4.3 - - + -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ALA 3.0 14.1 + - - +
180A ARG* 3.1 12.1 + - - +
182A VAL* 1.3 75.9 - - - +
184A SER* 1.3 65.7 + - - +
186A ASN* 3.1 14.3 + - - +
187A VAL* 2.9 37.1 + - - +
201A GLN* 4.9 2.6 + - - -
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Residues in contact with SER 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 4.1 17.3 - - - -
180A ARG* 2.9 17.4 + - - +
181A THR* 3.3 10.3 + - - -
183A GLU* 1.3 76.4 - - - +
185A VAL* 1.3 62.7 + - - +
187A VAL* 3.4 16.4 + - - +
188A ILE* 3.5 20.7 + - - +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A VAL* 5.8 1.8 - - + -
129A VAL* 4.1 17.9 - - + -
135A VAL* 3.7 21.1 - - + -
143A LEU* 4.4 11.9 - - + -
153A PRO* 6.1 1.3 - - + -
155A VAL* 4.0 26.7 - - + -
181A THR* 3.1 17.5 + - + +
182A VAL* 3.6 9.9 - - + +
183A GLU 3.2 0.2 - - - -
184A SER* 1.3 77.7 - - - +
186A ASN* 1.3 63.2 + - - +
188A ILE* 3.3 9.9 + - - +
189A VAL* 3.0 37.8 + - + +
202A VAL* 5.0 4.7 - - + -
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Residues in contact with ASN 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 3.0 29.9 + - - +
183A GLU* 3.1 13.3 + - - +
185A VAL* 1.3 78.0 - - - +
187A VAL* 1.3 53.5 + - - +
188A ILE 3.3 0.2 - - - -
189A VAL* 3.7 5.5 - - - +
190A SER* 2.7 38.9 + - - -
201A GLN* 3.1 32.8 + - - +
202A VAL* 2.8 46.9 + - - +
203A TYR* 5.3 4.2 - - - -
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Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLU* 2.9 36.3 + - - +
184A SER* 3.5 12.1 - - - +
185A VAL 3.2 0.2 - - - -
186A ASN* 1.3 76.6 - - - +
188A ILE* 1.3 64.3 + - + +
190A SER* 3.0 14.5 + - - -
191A THR* 2.7 32.4 + - - +
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Residues in contact with ILE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 3.9 23.1 - - + -
140A GLU* 3.4 48.0 - - + +
143A LEU* 3.9 25.6 - - + -
144A ARG 4.8 1.1 - - - +
147A LEU* 3.8 3.3 - - + +
184A SER 3.5 17.0 - - - +
185A VAL* 3.3 9.8 + - - +
186A ASN 3.3 0.2 - - - -
187A VAL* 1.3 81.5 - - + +
189A VAL* 1.3 61.8 + - - +
191A THR* 3.3 4.3 + - - -
192A TYR* 3.1 43.4 + - + +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.4 6.7 - - + -
147A LEU* 3.7 17.7 - - + -
153A PRO* 4.3 17.5 - - + -
185A VAL* 3.0 35.5 + - + +
186A ASN* 4.0 11.4 - - - +
187A VAL 3.3 0.2 - - - -
188A ILE* 1.3 76.2 - - - +
190A SER* 1.3 57.7 + - - +
193A ALA* 2.9 36.4 + - + +
200A VAL* 3.2 49.1 - - + +
201A GLN* 3.8 6.1 - - + +
202A VAL* 5.5 0.7 - - + -
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Residues in contact with SER 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ASN 2.7 27.6 + - - -
187A VAL* 3.0 12.6 + - - -
189A VAL* 1.3 75.6 - - - +
191A THR* 1.3 60.8 + - - +
193A ALA* 4.6 7.0 + - - +
200A VAL* 5.8 0.4 - - - -
201A GLN* 4.0 20.2 + - - +
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 2.7 29.6 + - - +
188A ILE* 3.6 4.9 - - - -
189A VAL 3.1 0.4 - - - -
190A SER* 1.3 81.1 + - - +
192A TYR* 1.3 91.1 + - + +
193A ALA 3.7 1.4 - - - +
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Residues in contact with TYR 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 5.5 7.7 + - + -
144A ARG* 3.0 67.8 + - + +
147A LEU* 3.9 28.0 - - + +
148A GLY* 4.9 2.3 + - - +
188A ILE* 3.1 40.7 + - + +
191A THR* 1.3 99.6 - - + +
193A ALA* 1.3 63.3 + - - +
194A ASP* 3.7 7.4 + - - +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LEU* 4.5 13.6 - - + +
189A VAL* 2.9 16.6 + - + +
190A SER* 4.8 6.9 - - - +
191A THR 3.7 1.8 - - - +
192A TYR* 1.3 78.3 - - - +
194A ASP* 1.3 67.2 + - - +
195A GLU* 3.6 4.2 + - - +
197A LEU* 5.3 4.5 - - + -
198A GLY 5.5 0.7 - - - +
200A VAL* 3.1 36.6 - - + -
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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