Contacts of the helix formed by residues 174 - 199 (chain A) in PDB entry 5DQZ
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 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A THR 4.5 5.9 - - - +
160A TRP* 5.3 0.3 - - - -
161A ASN* 5.0 12.5 + - - +
162A GLY 5.0 0.7 - - - +
173A GLY* 1.3 77.3 - - - +
175A THR* 1.3 64.7 + - - +
176A ILE* 3.4 17.6 - - + +
177A ASN* 2.3 42.2 + - - +
178A GLN* 3.2 18.6 + - - +
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Residues in contact with THR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ASP* 1.3 75.3 - - - +
176A ILE* 1.3 58.2 + - - +
178A GLN* 3.1 12.9 + - - +
179A CYS* 2.9 32.2 + - - -
236A ALA* 4.7 16.2 - - - +
239A ASN* 5.0 14.3 + - - +
240A PRO* 5.4 3.8 - - + +
243A PRO* 3.9 27.6 - - + -
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Residues in contact with ILE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 4.0 12.6 - - + -
159A THR 4.2 10.8 - - - +
160A TRP* 3.8 31.6 - - + -
174A ASP* 3.2 29.2 - - + +
175A THR* 1.3 78.7 - - - +
177A ASN* 1.3 56.4 + - - +
179A CYS* 3.3 1.1 + - - +
180A ILE* 2.9 34.6 + - + +
232A ALA 3.9 3.8 - - - +
233A PHE* 3.7 41.7 - - + +
236A ALA* 3.6 26.4 - - + +
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Residues in contact with ASN 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TRP* 4.2 5.5 - - - -
162A GLY 3.7 14.3 + - - -
163A ARG* 2.9 32.8 + - - +
164A ARG* 2.9 41.1 + - - +
165A TYR* 5.0 2.0 - - + -
173A GLY* 4.8 2.2 - - - -
174A ASP* 2.3 50.3 + - - +
176A ILE* 1.3 74.7 - - - +
178A GLN* 1.3 61.0 + - - +
180A ILE* 3.5 2.0 + - - -
181A SER* 2.9 34.3 + - - -
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TRP* 3.5 52.8 + - + +
171A GLU* 3.5 28.7 + - - +
173A GLY* 4.2 13.5 + - - +
174A ASP 3.2 11.1 + - - +
175A THR* 3.1 12.8 + - - +
177A ASN* 1.3 77.9 - - - +
179A CYS* 1.3 58.5 + - - +
181A SER* 3.2 4.1 + - - -
182A ALA* 2.9 30.7 + - - +
243A PRO* 3.9 19.9 - - + +
244A ASP* 4.8 9.3 - - + +
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Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A THR* 2.9 26.4 + - - -
176A ILE 3.5 7.6 - - - +
177A ASN 3.3 0.2 - - - -
178A GLN* 1.3 76.7 - - - +
180A ILE* 1.3 62.5 + - - +
182A ALA* 3.3 2.7 + - - +
183A ALA* 2.9 25.5 + - - +
232A ALA* 3.5 28.5 - - + +
235A ILE* 4.5 0.9 - - - -
236A ALA* 4.2 10.8 - - - -
243A PRO* 3.7 26.2 - - - -
244A ASP* 5.3 1.3 - - - +
247A VAL* 3.6 25.7 - - + +
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR* 4.0 23.6 - - + +
160A TRP* 3.7 36.1 - - + -
163A ARG* 3.7 26.2 - - - +
176A ILE* 2.9 34.0 + - + +
177A ASN* 3.7 5.4 - - - +
179A CYS* 1.3 75.8 - - - +
181A SER* 1.3 57.7 + - - +
183A ALA* 3.6 2.1 - - - +
184A THR* 2.9 46.7 + - + +
229A VAL* 4.6 8.7 - - + -
232A ALA* 3.8 12.5 - - + +
233A PHE* 4.2 10.3 - - + -
34G C 5.1 0.4 - - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 2.9 24.9 + - - +
165A TYR* 4.7 0.3 - - - +
170A TRP* 3.4 21.8 - - - -
177A ASN 2.9 18.3 + - - -
178A GLN* 3.6 1.6 - - - -
180A ILE* 1.3 78.1 - - - +
182A ALA* 1.3 56.3 + - - +
184A THR* 2.9 20.2 + - - -
185A SER* 2.9 17.0 + - - -
33G T 3.1 33.6 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 5.2 0.2 + - - -
170A TRP* 3.9 1.5 - - + -
178A GLN 2.9 16.5 + - - +
179A CYS 3.8 3.4 - - - +
181A SER* 1.3 73.6 - - - +
183A ALA* 1.3 65.7 + - - +
185A SER* 3.1 4.0 - - - -
186A CYS* 3.0 29.2 + - - -
244A ASP* 3.9 34.1 - - + +
247A VAL* 4.2 5.8 - - + -
248A ARG* 5.1 2.0 - - + +
32G T 3.8 22.4 - - - +
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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
----------------------------------------------------------
179A CYS 2.9 16.9 + - - +
180A ILE* 3.6 3.8 - - - +
182A ALA* 1.3 77.0 - - - +
184A THR* 1.3 63.8 + - + +
186A CYS* 3.1 6.1 + - - +
187A LEU* 2.9 21.5 + - - +
228A VAL* 3.7 30.1 - - + +
229A VAL* 4.8 1.6 - - - +
232A ALA* 4.1 4.7 - - + -
247A VAL* 3.6 17.7 - - + +
251A CYS* 3.9 14.4 - - - -
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A TYR* 6.0 0.7 - - - +
180A ILE* 2.9 29.8 + - + +
181A SER* 2.9 22.9 + - - -
183A ALA* 1.3 74.8 - - - +
185A SER* 1.3 56.2 + - - +
187A LEU* 3.3 9.4 + - - +
188A TYR* 2.9 44.5 + - - -
224A LYS* 3.8 28.7 - - + -
228A VAL* 5.2 0.4 - - + -
229A VAL* 4.6 6.7 - - + -
33G T 3.6 1.7 - - - -
34G C 2.9 29.5 + - - +
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL 3.8 0.3 - - - +
84A ARG* 2.8 37.9 + - - -
181A SER 2.9 15.4 + - - -
182A ALA* 3.1 13.7 - - - -
184A THR* 1.3 76.5 + - - +
186A CYS* 1.3 63.6 + - - +
188A TYR* 3.1 6.3 + - - +
189A GLY 3.0 16.5 + - - -
32G T 3.3 25.2 + - - -
33G T 4.1 12.7 + - - -
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Residues in contact with CYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 3.5 34.1 - - + +
84A ARG* 3.9 6.5 - - - -
182A ALA* 3.0 20.3 + - - -
183A ALA 3.1 6.5 + - - +
185A SER* 1.3 75.1 - - - +
187A LEU* 1.3 58.1 + - - +
189A GLY* 2.9 16.3 + - - -
190A VAL 3.0 11.8 + - - -
248A ARG* 3.5 43.3 - - - -
251A CYS* 3.8 15.9 - - + -
255A PHE* 3.7 5.9 - - + -
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ALA 2.9 12.6 + - - +
184A THR* 3.5 11.9 - - - +
186A CYS* 1.3 75.5 - - - +
188A TYR* 1.3 56.0 + - + +
190A VAL* 3.3 15.2 - - + +
191A THR* 2.6 49.0 + - - +
220A ALA* 3.7 19.3 - - + +
223A ILE* 3.9 22.0 - - + +
224A LYS* 3.6 39.7 - - + -
228A VAL* 4.1 19.5 - - + -
255A PHE* 4.0 12.2 - - + -
260A THR* 5.2 0.7 - - + -
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Residues in contact with TYR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A THR* 2.9 28.5 + - - -
185A SER 3.3 6.5 - - - +
187A LEU* 1.3 75.4 - - + +
189A GLY* 1.3 66.3 + - - +
192A GLU* 3.0 27.5 + - - +
213A LEU* 5.4 7.4 - - + +
216A VAL* 3.5 14.0 - - + +
217A TYR* 3.6 39.1 - + + -
220A ALA* 3.7 26.9 - - + -
221A ASP* 4.1 13.6 + - - -
224A LYS* 4.3 8.5 + - + -
33G T 3.4 28.5 - - - +
34G C 2.8 44.2 + + - +
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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
----------------------------------------------------------
82A GLY 3.0 9.6 - - - +
83A VAL 3.4 17.5 - - - -
84A ARG* 4.1 7.9 - - - -
85A VAL* 3.5 11.1 - - - +
185A SER 3.0 7.5 + - - -
186A CYS 2.9 9.7 + - - -
188A TYR* 1.3 78.9 - - - +
190A VAL* 1.3 61.7 + - - -
192A GLU* 3.2 2.8 + - - +
193A ALA 3.0 17.7 + - - -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA 3.3 27.1 - - - +
82A GLY* 2.9 13.6 + - - +
186A CYS 3.0 3.6 + - - -
187A LEU* 3.3 18.8 - - + +
189A GLY* 1.3 73.5 - - - +
191A THR* 1.3 60.2 + - - +
193A ALA* 3.2 7.3 + - - +
194A ALA* 2.9 28.1 + - - +
255A PHE* 3.3 48.9 - - + -
260A THR* 4.4 3.4 - - + -
261A LEU* 4.0 15.8 - - + +
264A LEU* 4.0 12.6 - - + +
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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
----------------------------------------------------------
187A LEU* 2.6 29.9 + - - +
190A VAL* 1.3 73.8 - - - +
192A GLU* 1.3 61.4 + - - +
194A ALA* 3.3 2.6 + - - +
195A ILE* 2.9 31.2 + - + +
216A VAL* 3.6 33.7 - - + +
219A ILE* 3.8 28.9 - - + -
220A ALA* 3.8 12.6 - - - +
264A LEU* 3.8 19.2 - - + +
268A ILE* 5.5 0.9 - - + -
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A VAL* 3.7 24.1 + - + +
188A TYR 3.0 19.1 + - - +
189A GLY* 3.5 5.2 - - - +
191A THR* 1.3 77.0 - - - +
193A ALA* 1.3 61.5 + - - +
195A ILE* 3.3 3.0 + - - +
196A LEU* 2.9 34.2 + - + +
202A PRO* 4.2 9.4 - - + -
213A LEU* 3.5 29.5 - - + +
216A VAL* 4.0 16.5 - - + +
91B PRO* 3.3 12.5 - - - +
303B ARG* 3.0 34.3 + - - -
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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
----------------------------------------------------------
53A MET* 4.3 15.3 - - + +
76A VAL* 5.5 2.4 - - + +
78A VAL* 5.0 3.6 - - + -
82A GLY* 4.8 4.0 - - - +
85A VAL* 3.7 15.2 - - + +
189A GLY 3.0 12.9 + - - +
190A VAL* 3.3 12.3 - - - +
192A GLU* 1.3 76.7 - - - +
194A ALA* 1.3 57.0 + - - +
196A LEU* 3.3 8.2 + - - +
197A ALA* 2.9 28.1 + - - +
261A LEU* 3.8 23.1 - - + -
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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 VAL 2.9 15.4 + - - +
191A THR 3.6 4.7 - - - +
193A ALA* 1.3 76.7 - - - +
195A ILE* 1.3 58.7 + - - +
197A ALA* 3.1 4.9 + - - +
198A ALA* 2.9 29.5 + - - +
261A LEU* 3.7 21.0 - - + +
264A LEU* 3.6 31.2 - - + -
265A ILE* 4.0 6.9 - - + +
268A ILE* 4.0 9.9 - - + -
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A THR* 2.9 18.9 + - + +
192A GLU* 3.3 5.1 + - - +
194A ALA* 1.3 74.8 - - - +
196A LEU* 1.3 63.0 + - - +
198A ALA* 3.3 5.1 + - - +
199A GLY 3.1 5.0 + - - -
200A TYR* 3.1 48.8 + - + +
202A PRO* 4.1 16.4 - - + -
215A PHE* 3.5 31.0 - - + +
216A VAL* 3.7 37.7 - - + +
219A ILE* 4.3 4.9 - - + -
268A ILE* 3.8 20.2 - - + -
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 3.6 19.9 - - + +
76A VAL* 4.5 9.9 - - + -
85A VAL* 3.9 21.3 - - + -
88A SER* 4.2 17.5 - - - +
192A GLU* 2.9 23.2 + - + +
193A ALA* 3.6 5.4 - - - +
195A ILE* 1.3 75.7 - - - +
197A ALA* 1.3 61.5 + - - +
199A GLY* 3.1 13.9 + - - +
200A TYR 4.1 10.3 - - - +
202A PRO* 4.0 18.8 - - + -
91B PRO* 3.7 43.3 - - + +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.7 29.6 - - + -
51A CYS* 4.5 5.8 - - + -
53A MET* 4.5 5.6 - - + -
74A LEU* 4.2 12.1 - - - +
76A VAL* 5.9 0.2 - - - +
193A ALA 2.9 17.4 + - - +
194A ALA* 3.1 6.3 + - - +
196A LEU* 1.3 77.0 - - - +
198A ALA* 1.3 62.2 + - - +
199A GLY* 3.4 1.0 + - - -
265A ILE* 4.0 10.7 - - + +
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 5.9 0.2 - - - -
98A LYS* 2.8 33.0 + - - +
194A ALA 2.9 16.1 + - - +
195A ILE* 3.6 4.3 - - - +
196A LEU 3.2 0.2 - - - -
197A ALA* 1.3 77.7 - - - +
199A GLY* 1.3 59.7 + - - +
200A TYR* 3.5 26.2 - - + -
265A ILE* 4.4 18.1 - - + +
268A ILE* 4.8 8.1 - - + -
269A GLU* 4.1 7.4 - - - +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY* 5.3 8.2 - - - -
94A ALA 6.1 1.8 - - - -
95A ARG* 4.7 7.4 + - - +
98A LYS* 3.3 24.5 - - - +
99A LEU* 3.7 13.3 - - - +
195A ILE 3.1 0.4 + - - -
196A LEU 3.1 15.1 + - - -
197A ALA 3.2 1.3 - - - -
198A ALA* 1.3 79.6 - - - +
200A TYR* 1.3 63.1 + - - +
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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