Contacts of the helix formed by residues 173 - 207 (chain A) in PDB entry 4K71
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 ASP 173 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA* 3.7 3.2 - - - +
172A ALA* 1.3 75.2 - - + +
174A LYS* 1.3 63.1 + - - +
175A ALA* 3.4 10.4 + - - +
176A ALA* 3.1 35.8 + - + +
177A CYS* 3.3 21.8 + - - +
188D GLU* 3.0 13.3 + - - +
292D GLU* 3.1 41.5 - - - +
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 3.6 17.5 - - + -
121A ASP* 4.4 19.8 + - - +
124A CYS* 4.2 20.5 - - + +
168A CYS* 3.9 16.5 - - - +
169A CYS* 3.3 30.1 + - - +
170A GLN* 5.0 2.4 + - - +
171A ALA* 3.6 15.3 - - - +
172A ALA 3.9 0.4 + - - -
173A ASP* 1.3 73.1 + - - +
175A ALA* 1.3 57.4 + - - +
177A CYS* 3.3 2.6 + - - +
178A LEU* 2.8 33.5 + - + +
160D ARG* 3.8 28.7 - - - +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 3.8 29.1 - - + +
173A ASP* 3.4 7.7 + - - +
174A LYS* 1.3 78.9 - - - +
176A ALA* 1.3 57.8 + - - +
179A LEU* 2.9 43.8 + - + +
180A PRO* 3.6 0.5 - - - +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 3.1 31.6 + - + +
175A ALA* 1.3 79.6 - - - +
177A CYS* 1.3 57.1 + - - +
180A PRO* 3.3 23.2 - - - +
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Residues in contact with CYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 4.4 0.7 - - - -
168A CYS* 2.0 55.6 - - + -
171A ALA* 3.9 3.4 - - + -
173A ASP 3.3 13.6 + - - +
174A LYS 3.6 6.1 - - - +
175A ALA 3.2 0.4 - - - -
176A ALA* 1.3 79.4 - - - +
178A LEU* 1.3 62.5 + - - +
180A PRO* 3.9 4.2 - - - +
181A LYS* 3.5 26.9 + - - +
184D GLU* 3.5 33.2 - - - +
188D GLU* 5.3 0.2 - - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 4.0 23.3 - - + -
123A MET* 4.1 10.1 - - + -
124A CYS* 4.5 6.3 - - - -
164A ALA* 3.8 37.0 - - + +
165A PHE* 3.7 33.7 - - + +
168A CYS* 3.5 10.3 - - + -
174A LYS* 2.8 17.4 + - + +
175A ALA* 4.3 0.4 - - - +
177A CYS* 1.3 77.8 - - - +
179A LEU* 1.3 66.4 + - + +
180A PRO 3.4 0.2 - - - -
181A LYS* 3.1 5.8 + - - +
182A LEU* 3.0 42.1 + - + +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 4.6 15.4 + - + +
120A VAL* 3.6 29.8 - - + -
123A MET* 4.2 17.0 - - + -
175A ALA* 2.9 31.3 + - + +
178A LEU* 1.3 78.7 - - + +
180A PRO* 1.4 58.8 - - + +
182A LEU* 3.2 10.4 + - + +
183A ASP* 2.9 39.9 + - - +
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Residues in contact with PRO 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA 3.6 2.2 - - - +
176A ALA* 3.3 28.9 - - - +
177A CYS 3.9 2.9 - - - +
178A LEU 3.6 2.2 - - - -
179A LEU* 1.4 95.2 - - + +
181A LYS* 1.3 61.1 + - + +
183A ASP* 4.1 7.5 - - + +
184A GLU* 3.2 23.4 + - - +
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Residues in contact with LYS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.9 27.1 - - + -
167A GLU* 3.4 33.2 + - - +
168A CYS* 3.7 17.7 - - - -
177A CYS* 3.5 22.0 - - - +
178A LEU 3.1 7.9 + - - +
180A PRO* 1.3 77.8 - - + +
182A LEU* 1.3 65.1 + - - +
184A GLU* 3.4 9.5 + - - +
185A LEU* 3.1 27.2 + - + +
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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
----------------------------------------------------------
117A ARG* 3.5 39.8 + - - +
123A MET* 4.1 8.3 - - + -
161A TYR* 3.9 33.7 - - + -
164A ALA* 4.4 10.5 - - + -
165A PHE* 4.0 15.3 - - + -
178A LEU* 3.0 45.9 + - + +
179A LEU* 3.2 6.5 + - + +
181A LYS* 1.3 73.6 - - - +
183A ASP* 1.3 61.4 + - - +
185A LEU* 3.5 9.0 + - + +
186A ARG* 3.0 28.8 + - - +
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Residues in contact with ASP 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ARG* 3.0 31.8 + - - +
179A LEU* 2.9 23.8 + - - +
180A PRO* 3.6 7.8 + - + +
182A LEU* 1.3 75.6 - - - +
184A GLU* 1.3 61.7 + - - +
186A ARG* 3.3 9.8 + - - +
187A ASP* 3.0 32.2 + - - +
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 4.5 13.5 + - - -
180A PRO 3.2 18.3 + - - +
181A LYS* 3.6 8.4 - - - +
182A LEU 3.3 0.2 - - - -
183A ASP* 1.3 75.8 - - - +
185A LEU* 1.3 58.4 + - + +
187A ASP* 3.2 8.0 + - - +
188A GLU* 2.8 57.3 + - + +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 4.8 8.0 + - + +
142A ILE* 6.1 0.7 - - - +
157A PHE* 3.4 37.8 - - + +
160A ARG* 3.8 27.6 - - + +
161A TYR* 3.5 47.3 - - + +
164A ALA* 5.3 2.2 - - + -
181A LYS* 3.1 14.2 + - + +
182A LEU* 3.7 13.9 - - + +
184A GLU* 1.3 76.5 - - + +
186A ARG* 1.3 65.3 + - - +
188A GLU* 3.8 10.0 - - - +
189A GLY* 2.9 22.9 + - - -
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ARG* 4.5 24.2 - - - +
115A LEU* 5.7 4.9 + - - +
117A ARG* 4.3 15.7 - - - +
142A ILE* 6.4 2.2 - - - -
182A LEU 3.0 17.7 + - - +
183A ASP* 3.5 9.2 - - - +
185A LEU* 1.3 75.7 - - - +
187A ASP* 1.3 76.4 + - - +
189A GLY* 3.3 1.4 + - - -
190A LYS* 3.0 66.4 + - + +
432A LYS* 5.9 3.0 - - - +
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Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASP* 3.0 21.1 + - - +
184A GLU* 3.6 9.1 - - - +
186A ARG* 1.3 93.7 + - - +
188A GLU* 1.3 62.8 + - + +
190A LYS* 3.5 9.1 + - - +
191A ALA* 3.1 23.4 + - - +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 3.5 22.0 - - + -
160A ARG* 5.7 3.8 + - - -
184A GLU* 2.8 48.3 + - + +
185A LEU* 3.9 9.7 - - - +
187A ASP* 1.3 73.8 - - + +
189A GLY* 1.3 57.4 + - - +
191A ALA* 3.8 5.8 - - - +
192A SER* 2.9 30.3 + - - -
288A HIS* 6.0 2.4 - - - -
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Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 6.0 4.9 - - - -
146A HIS* 5.7 2.0 - - - -
149A PHE* 3.2 24.7 - - - -
157A PHE* 3.5 13.4 - - - -
185A LEU 2.9 16.2 + - - -
186A ARG 3.8 1.6 - - - -
188A GLU* 1.3 75.4 - - - +
190A LYS* 1.3 59.7 + - - +
193A SER* 2.9 26.7 + - - -
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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
----------------------------------------------------------
114A ARG* 5.8 1.4 - - - +
146A HIS* 4.6 23.7 - - + +
186A ARG* 3.0 64.6 + - + +
187A ASP* 3.8 8.3 - - - +
189A GLY* 1.3 75.5 - - - +
191A ALA* 1.3 62.6 + - - +
193A SER* 3.7 5.0 - - - -
194A ALA* 2.9 25.4 + - - +
432A LYS* 5.9 5.3 - - - +
459A GLN* 5.5 0.3 + - - -
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Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ASP 3.1 17.8 + - - +
188A GLU* 3.8 6.7 - - - +
190A LYS* 1.3 73.6 - - - +
192A SER* 1.3 63.8 + - - +
194A ALA* 3.2 7.4 + - - +
195A LYS* 2.9 37.2 + - - +
436A LYS* 4.3 20.6 - - - +
455A VAL* 5.6 0.3 - - - +
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Residues in contact with SER 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PHE* 4.0 15.5 - - - -
150A TYR* 5.1 4.5 - - - +
153A GLU* 4.6 9.2 - - - +
157A PHE* 4.0 19.3 - - - -
188A GLU 2.9 19.6 + - - -
189A GLY 3.7 4.3 - - - -
191A ALA* 1.3 76.2 - - - +
193A SER* 1.3 63.6 + - - +
195A LYS* 3.4 10.5 + - - +
196A GLN* 3.0 23.9 + - - +
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A HIS* 3.3 34.6 + - - +
148A TYR* 5.0 2.6 + - - +
149A PHE* 3.7 26.7 + - - +
189A GLY 2.9 17.8 + - - -
190A LYS 3.7 3.8 - - - -
192A SER* 1.3 75.0 - - - +
194A ALA* 1.3 66.2 + - - +
196A GLN* 3.3 6.2 + - - +
197A ARG* 3.0 25.1 + - - +
459A GLN* 5.9 0.4 + - - -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A LYS 2.9 19.3 + - - +
191A ALA* 3.5 7.2 - - - +
193A SER* 1.3 78.1 - - - +
195A LYS* 1.3 61.8 + - - +
197A ARG* 3.3 6.2 + - - +
198A LEU* 3.2 20.8 + - - +
455A VAL* 3.4 33.5 - - + +
458A ASN* 4.9 1.4 + - - -
459A GLN* 3.8 26.5 - - - +
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ALA* 2.9 28.6 + - - +
192A SER* 3.5 9.2 - - - +
193A SER 3.2 0.2 - - - -
194A ALA* 1.3 76.7 - - - +
196A GLN* 1.3 56.3 + - - +
198A LEU* 3.3 6.3 + - + +
199A LYS* 3.0 50.7 + - - +
451A ASP* 6.5 0.9 - - + -
455A VAL* 4.2 19.2 - - + +
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Residues in contact with GLN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR 3.1 26.0 - - - +
150A TYR* 3.6 36.4 - - + +
192A SER 3.0 17.0 + - - +
193A SER* 3.8 3.6 - - - +
195A LYS* 1.3 74.6 - - - +
197A ARG* 1.3 61.0 + - - +
199A LYS* 3.1 14.1 + - - +
200A CYS* 2.8 31.3 + - - -
242A HIS* 3.0 40.4 + - - +
245A CYS* 4.8 3.4 - - - +
246A CYS* 3.6 23.4 - - - -
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Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASP* 2.6 37.6 + - - +
148A TYR* 3.2 50.3 + - + +
193A SER* 3.0 17.7 + - - +
194A ALA* 3.6 8.7 - - - +
195A LYS 3.3 0.2 - - - -
196A GLN* 1.3 76.3 - - - +
198A LEU* 1.3 56.4 + - - +
200A CYS* 3.4 8.3 + - - +
201A ALA* 2.9 46.2 + - - +
204A GLN* 4.3 6.3 + - - -
458A ASN* 3.6 13.0 - - - +
459A GLN* 5.3 9.6 - - + +
462A VAL* 3.7 24.8 - - + +
466A LYS* 5.6 4.4 - - - +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA 3.2 9.1 + - - +
195A LYS* 3.5 9.6 - - + +
196A GLN 3.2 0.4 - - - -
197A ARG* 1.3 75.8 - - - +
199A LYS* 1.3 66.1 + - + +
201A ALA* 3.3 1.5 + - + +
202A SER* 3.0 22.1 + - - -
214A TRP* 6.5 1.6 - - + -
454A SER* 3.3 32.3 - - - +
455A VAL* 4.1 15.3 - - + -
458A ASN* 3.3 32.0 - - + +
481A LEU* 4.0 30.1 - - + -
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A LYS* 3.0 36.1 + - - +
196A GLN* 3.1 34.1 + - - +
198A LEU* 1.3 76.9 - - + +
200A CYS* 1.3 62.1 + - - +
202A SER* 2.7 23.5 + - - -
203A LEU* 3.2 12.3 + - - +
211A PHE* 3.9 19.4 - - + -
214A TRP* 3.0 49.0 - - + +
242A HIS* 3.7 20.6 - - + +
246A CYS* 4.6 2.0 - - - -
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Residues in contact with CYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 4.0 27.6 - - + -
196A GLN* 2.8 32.7 + - - +
197A ARG* 3.8 8.1 - - - +
199A LYS* 1.3 72.0 - - - +
201A ALA* 1.3 57.2 + - - +
203A LEU* 3.4 2.8 + - - +
204A GLN* 2.9 40.6 + - - +
246A CYS* 2.0 57.9 - - + -
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Residues in contact with ALA 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ARG* 2.9 28.5 + - - +
198A LEU* 3.8 4.5 - - + +
200A CYS* 1.3 76.5 - - - +
202A SER* 1.3 58.6 + - - +
204A GLN* 4.7 1.1 - - - -
205A LYS* 2.8 46.8 + - + +
206A PHE* 4.0 4.3 - - + -
458A ASN* 3.3 27.1 - - - +
462A VAL* 4.4 5.2 - - + -
481A LEU* 6.1 0.4 - - + -
484A ARG* 5.5 2.5 - - - +
----------------------------------------------------------
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Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU* 3.0 12.3 + - - -
199A LYS* 2.7 22.5 + - - -
201A ALA* 1.3 78.2 - - - +
203A LEU* 1.3 57.2 + - - +
206A PHE* 3.0 10.0 + - - +
207A GLY 2.9 29.8 + - - +
210A ALA* 4.3 10.5 - - - -
211A PHE* 4.0 15.8 - - - +
214A TRP* 5.9 1.5 - - - +
481A LEU* 3.4 33.1 - - - +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LYS 3.2 8.6 + - - +
200A CYS* 3.7 5.6 - - - +
202A SER* 1.3 81.5 + - - +
204A GLN* 1.3 66.0 + - + +
207A GLY* 3.2 23.8 + - - -
208A GLU* 4.1 18.4 + - + +
211A PHE* 3.4 36.1 - - + -
239A THR* 4.5 5.4 - - + +
242A HIS* 3.8 33.7 - - + +
243A THR* 3.7 31.0 - - + +
246A CYS* 4.2 9.6 - - + -
----------------------------------------------------------
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Residues in contact with GLN 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A TYR* 4.4 12.3 + - - -
197A ARG* 4.3 10.2 + - - -
200A CYS* 2.9 30.3 + - - +
201A ALA* 4.3 1.9 - - - +
203A LEU* 1.3 84.0 - - + +
205A LYS* 1.3 78.1 + - + +
206A PHE 3.8 0.2 - - - -
207A GLY* 4.9 0.7 + - - -
246A CYS* 3.0 34.5 + - + +
247A HIS* 4.8 4.8 - - - +
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Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ALA* 2.8 29.9 + - + +
204A GLN* 1.3 93.2 - - + +
206A PHE* 1.3 78.6 + - + +
207A GLY 3.7 0.7 - - - -
462A VAL* 6.5 0.7 - - + -
465A GLU* 2.9 40.2 + - - +
466A LYS* 5.9 2.6 - - - +
484A ARG* 5.9 0.4 - - - +
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ALA* 4.0 12.1 - - + -
202A SER* 3.0 10.0 + - - +
205A LYS* 1.3 91.5 - - + +
207A GLY* 1.3 63.2 + - - +
209A ARG* 5.1 0.7 + - - +
210A ALA* 3.7 21.0 + - + +
477A CYS 3.5 22.4 - - - -
478A THR* 3.7 21.5 - - - -
479A GLU 4.9 0.4 - - - -
480A SER* 4.3 2.2 - - - -
481A LEU* 3.7 50.9 - - + -
484A ARG* 3.4 19.7 - - - -
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Residues in contact with GLY 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER 2.9 14.5 + - - +
203A LEU* 3.2 17.0 + - - -
204A GLN 4.6 0.6 - - - -
205A LYS 3.7 0.8 - - - -
206A PHE* 1.3 78.4 - - - +
208A GLU* 1.3 65.9 + - - +
209A ARG 3.3 2.7 - - - -
210A ALA* 3.1 12.5 + - - +
211A PHE 3.8 1.7 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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