Contacts of the helix formed by residues 170 - 192 (chain A) in PDB entry 3UJK
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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125A MET 3.7 23.4 + - - -
126A GLU* 3.9 18.2 + - - +
169A GLY* 1.3 73.3 - - - -
171A GLN* 1.3 60.6 + - - +
172A VAL 3.3 2.5 - - - -
173A ALA* 3.4 2.8 + - - -
174A ASN* 2.8 54.1 + - - -
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Residues in contact with GLN 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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168A GLY 5.2 0.5 - - - +
169A GLY* 3.2 27.7 - - - -
170A SER* 1.3 74.6 + - - +
172A VAL* 1.3 60.1 + - - +
174A ASN* 3.9 5.7 - - - +
175A TYR* 3.0 27.2 + - - +
224A ALA* 5.0 5.7 - - + +
226A ALA* 3.9 20.6 - - + -
227A PRO* 3.6 28.4 - - + +
230A VAL* 3.4 9.6 - - + +
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Residues in contact with VAL 172 (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 3.3 0.2 - - - -
171A GLN* 1.3 73.4 - - - +
173A ALA* 1.3 61.9 + - - +
174A ASN 3.2 0.2 - - - -
175A TYR* 3.6 5.4 - - - +
176A CYS* 2.9 28.5 + - - -
220A ILE* 3.7 17.0 - - + -
226A ALA* 3.7 23.3 - - + -
230A VAL* 3.6 28.7 - - + +
231A GLY 3.8 9.9 - - - +
232A SER* 3.5 17.5 - - - -
305A ILE* 3.6 35.7 - - + +
306A GLY* 4.8 0.2 - - - -
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Residues in contact with ALA 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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126A GLU 3.3 25.6 - - - +
128A SER* 3.5 17.3 - - - +
164A TYR* 3.7 16.8 - - + +
166A GLY* 3.8 6.5 - - - +
170A SER* 3.4 7.4 + - - +
172A VAL* 1.3 75.8 - - - +
174A ASN* 1.3 62.6 + - - +
176A CYS* 3.3 3.0 + - - +
177A ARG 3.1 18.2 + - - -
231A GLY 4.7 1.2 + - - -
232A SER* 3.5 23.4 - - - +
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Residues in contact with ASN 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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127A ASP 5.1 0.2 - - - +
128A SER* 2.9 20.7 + - - -
170A SER* 2.8 44.2 + - - +
171A GLN* 3.9 6.2 - - - +
173A ALA* 1.3 78.4 - - - +
175A TYR* 1.3 61.6 + - - +
177A ARG* 3.4 26.1 + - - +
178A GLU* 3.1 30.8 + - - +
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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 GLN 3.0 19.4 + - - +
172A VAL* 3.2 7.8 + - - +
174A ASN* 1.3 74.4 - - - +
176A CYS* 1.3 58.8 + - - +
178A GLU* 3.1 8.7 + - + +
179A ARG* 2.8 57.7 + - + +
216A VAL* 3.9 15.3 - - + -
219A GLU* 2.5 48.5 + - + +
220A ILE* 3.7 18.4 - - + -
223A VAL* 3.6 28.6 - - + +
224A ALA* 3.6 23.1 - - + -
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Residues in contact with CYS 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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164A TYR* 3.5 35.1 + - + -
172A VAL* 2.9 23.0 + - - +
173A ALA 3.6 0.9 - - - +
175A TYR* 1.3 78.1 - - - +
177A ARG* 1.3 62.8 + - - +
180A MET* 2.9 44.1 + - + +
181A HIS 4.8 0.2 + - - -
216A VAL* 4.1 13.5 - - - -
232A SER* 4.7 4.5 - - - -
234A SER* 4.9 0.2 - - - -
305A ILE* 4.0 32.8 - - - -
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Residues in contact with ARG 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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127A ASP 5.3 0.8 + - - -
128A SER* 3.5 26.3 + - - +
129A VAL 3.5 26.4 - - - +
130A SER* 3.3 15.2 + - - +
164A TYR* 3.7 5.9 - - + -
173A ALA 3.1 13.7 + - - +
174A ASN* 3.5 32.2 + - - +
176A CYS* 1.3 74.9 - - - +
178A GLU* 1.3 86.7 + - - +
181A HIS* 3.1 23.7 - - - -
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Residues in contact with GLU 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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174A ASN* 3.1 16.9 + - - +
175A TYR* 3.1 11.9 + - + +
177A ARG* 1.3 122.8 + - - +
179A ARG* 1.3 59.6 + - + +
181A HIS* 3.6 6.8 + - - -
182A LEU* 3.2 24.4 - - - +
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Residues in contact with ARG 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* 2.8 46.8 + - + +
176A CYS* 4.9 0.2 - - - -
178A GLU* 1.3 75.5 - - + +
180A MET* 1.3 66.5 + - - +
181A HIS 3.3 2.0 - - - -
182A LEU* 2.9 28.6 + - - +
183A ALA* 2.9 31.1 + - - +
186A GLU* 2.9 40.1 + - - -
215A ARG* 4.4 6.1 - - - +
216A VAL* 4.0 10.5 - - + -
219A GLU* 2.7 43.7 + - - +
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Residues in contact with MET 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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160A PHE* 3.9 10.5 - - + -
164A TYR* 3.5 19.1 - - + +
176A CYS* 2.9 45.2 + - - +
178A GLU 4.0 0.4 - - - -
179A ARG* 1.3 72.7 - - - +
181A HIS* 1.3 56.5 + - - +
183A ALA* 3.3 3.5 + - - +
184A LEU* 3.0 27.1 + - + +
212A SER* 4.1 11.0 - - - +
213A PHE* 3.7 32.3 - - + -
216A VAL* 3.9 28.7 - - + -
234A SER* 3.4 24.2 - - - +
236A VAL* 4.0 8.7 - - + -
305A ILE* 4.6 2.9 - - + -
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Residues in contact with HIS 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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130A SER* 4.4 4.8 + - - -
132A ILE* 3.5 32.8 - - + +
135A PHE* 3.8 9.1 - + + -
138A VAL* 5.7 4.1 - - + +
139A SER* 3.6 21.0 + - - -
160A PHE* 3.7 38.2 - - + -
176A CYS 4.8 0.6 + - - -
177A ARG 3.1 26.8 + - - -
178A GLU* 3.6 15.1 + - - -
180A MET* 1.3 80.0 + - - +
182A LEU* 1.3 74.8 + - + +
184A LEU* 3.7 3.8 - - - +
185A THR* 2.9 31.5 + - - -
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Residues in contact with LEU 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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138A VAL* 6.5 0.2 - - + -
139A SER* 3.7 27.1 - - - +
178A GLU 3.2 27.6 - - - +
179A ARG* 2.9 29.2 + - - +
181A HIS* 1.3 94.9 - - + +
183A ALA* 1.3 64.9 + - - +
185A THR* 3.3 6.0 + - - -
186A GLU* 3.0 31.0 + - - +
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Residues in contact with ALA 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 ARG* 2.9 20.1 + - - +
180A MET 3.6 7.9 - - - +
182A LEU* 1.3 76.7 - - - +
184A LEU* 1.3 61.3 + - - +
186A GLU* 3.2 14.0 + - - +
187A GLU* 3.0 27.2 + - - +
212A SER* 4.0 15.7 - - - +
215A ARG* 3.9 10.9 + - + +
216A VAL* 3.7 26.5 - - + -
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Residues in contact with LEU 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 PHE* 3.7 23.6 - - + -
160A PHE* 3.7 24.7 - - + -
180A MET* 3.0 17.2 + - + +
181A HIS 3.7 5.2 - - - +
182A LEU 3.2 0.2 - - - -
183A ALA* 1.3 77.2 - - - +
185A THR* 1.3 56.2 + - - +
187A GLU* 3.1 2.0 + - - +
188A ILE* 2.9 28.3 + - + +
205A TRP* 4.2 10.5 - - + -
208A ALA* 3.7 33.4 - - + +
209A LEU* 3.7 32.8 - - + +
212A SER* 3.6 11.1 - - - +
238A VAL* 3.9 7.4 - - + -
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.6 2.4 - - - -
136A LEU* 3.5 31.4 - - + +
139A SER* 3.2 25.4 + - - +
140A SER* 4.0 24.9 - - - +
152A PHE* 4.2 8.7 - - + -
181A HIS 2.9 23.2 + - - -
182A LEU 3.6 5.4 - - - -
184A LEU* 1.3 75.0 - - - +
186A GLU* 1.3 65.1 + - + +
188A ILE* 3.3 1.4 + - - +
189A VAL* 3.1 27.3 + - + +
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Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ARG* 2.9 36.5 + - - -
182A LEU* 3.0 18.2 + - - +
183A ALA* 3.4 7.0 - - - +
185A THR* 1.3 79.9 - - + +
187A GLU* 1.3 62.2 + - - +
189A VAL* 3.6 7.3 + - - +
190A LYS* 3.4 27.6 + - - +
215A ARG* 2.6 43.2 + - - +
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Residues in contact with GLU 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 ALA 3.0 16.8 + - - +
184A LEU 3.1 6.0 + - - +
186A GLU* 1.3 73.8 - - - +
188A ILE* 1.3 65.8 + - - +
190A LYS* 3.0 38.2 + - - +
191A GLU* 3.3 21.0 + - + +
208A ALA* 3.7 32.8 - - + +
211A ASN* 3.4 29.4 + - + +
212A SER* 4.0 11.2 - - - +
215A ARG* 2.8 30.3 + - - +
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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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136A LEU* 4.2 12.3 - - + -
152A PHE* 3.9 28.0 - - + -
184A LEU* 2.9 19.1 + - + +
185A THR* 3.3 6.0 + - - +
187A GLU* 1.3 76.9 - - - +
189A VAL* 1.3 63.0 + - - +
191A GLU* 3.1 4.5 + - + +
192A LYS 3.0 19.1 + - - -
193A PRO* 3.2 26.5 - - + +
204A LYS 4.5 2.2 - - - +
205A TRP* 3.3 63.0 - - + +
208A ALA* 3.7 17.0 - - + -
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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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150A ASN* 5.6 0.2 - - + -
151A GLY* 4.0 23.2 - - - +
152A PHE* 3.7 32.1 - - + -
185A THR* 3.1 21.7 + - + +
186A GLU* 3.7 7.2 - - - +
187A GLU 3.3 0.2 - - - -
188A ILE* 1.3 75.1 - - - +
190A LYS* 1.3 63.0 + - + +
192A LYS* 3.0 35.1 + - - +
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Residues in contact with LYS 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 GLU* 3.4 17.5 + - - +
187A GLU* 3.0 40.9 + - - +
189A VAL* 1.3 81.8 - - + +
191A GLU* 1.3 68.4 + - - +
192A LYS* 3.6 15.0 + - - +
215A ARG* 4.0 19.4 - - - +
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Residues in contact with GLU 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 GLU* 3.3 18.7 + - - +
188A ILE* 3.1 8.3 + - + +
190A LYS* 1.3 81.8 - - - +
192A LYS* 1.3 73.8 + - - +
193A PRO* 3.4 2.2 - - + -
204A LYS* 3.2 62.4 + - + +
207A LYS* 2.9 45.6 + - + +
208A ALA* 4.6 6.1 + - + +
211A ASN* 4.5 5.0 + - - -
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Residues in contact with LYS 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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151A GLY* 3.7 19.7 - - - +
188A ILE 3.0 6.7 + - - -
189A VAL* 3.0 26.2 + - - +
190A LYS* 3.8 12.9 + - - +
191A GLU* 1.3 80.8 - - - +
193A PRO* 1.3 70.9 - - - +
194A GLU* 3.7 12.0 + - - +
204A LYS* 4.3 3.8 - - - -
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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