Contacts of the helix formed by residues 157 - 186 (chain D) in PDB entry 1W8D
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 157 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B LEU* 3.9 1.8 - - - -
181B LYS* 4.1 2.7 - - - +
155D ARG 3.8 2.2 + - - -
156D LEU* 1.3 76.9 - - - +
158D PRO* 1.3 76.2 - - - +
159D ASN* 3.7 8.5 + - - +
160D ALA* 3.1 26.2 + - - +
161D TRP* 3.1 21.1 + - - +
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Residues in contact with PRO 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B PRO* 3.7 34.3 - - + +
174B PHE* 3.4 26.0 - - + -
177B LEU* 3.7 17.7 - - + -
178B GLU* 5.8 4.7 - - - +
181B LYS* 4.3 7.0 - - - +
157D SER* 1.3 86.9 - - - +
159D ASN* 1.3 56.4 + - - +
161D TRP* 3.3 4.8 + - + +
162D LYS* 2.9 26.9 + - - +
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Residues in contact with ASN 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D SER* 3.2 8.1 + - - +
158D PRO* 1.3 75.7 - - - +
160D ALA* 1.3 60.7 + - - +
162D LYS* 4.4 11.4 - - - +
163D THR* 2.7 45.3 + - - -
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Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D PHE* 3.3 37.3 - - + -
156D LEU* 3.9 19.7 - - + -
157D SER* 3.1 25.1 + - - +
159D ASN* 1.3 78.4 - - - +
161D TRP* 1.3 62.8 + - - +
163D THR* 3.7 3.4 - - - -
164D ILE* 3.4 12.1 + - - +
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Residues in contact with TRP 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 4.1 4.5 - - + +
170B ASN* 3.1 20.2 + - - +
173B ALA* 3.2 32.6 - - + +
174B PHE* 4.4 6.7 - + + -
177B LEU* 5.0 15.5 - - + -
220B MSE 3.7 21.5 - - + -
224B LEU* 6.0 0.4 - - + -
153D THR* 4.9 6.5 - - + -
156D LEU* 4.5 10.2 - - + +
157D SER 3.1 10.8 + - - +
158D PRO* 3.4 11.9 - - + +
160D ALA* 1.3 75.0 - - - +
162D LYS* 1.3 68.2 + - - +
164D ILE* 3.1 7.6 + - - +
165D THR* 3.0 39.9 + - - -
208D VAL* 3.6 28.0 - - + -
209D PRO* 3.6 34.7 - - + +
212D SER* 3.6 26.7 - - - -
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Residues in contact with LYS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG 5.7 3.1 - - - -
121B PRO* 6.0 1.8 - - + -
162B LYS* 3.4 28.0 - - - +
166B ASP* 4.5 8.7 - - - -
170B ASN* 3.9 20.2 - - - +
174B PHE* 4.2 18.6 - - + -
158D PRO 2.9 16.8 + - - +
159D ASN* 3.8 12.1 - - - +
161D TRP* 1.3 84.1 - - - +
163D THR* 1.3 53.0 + - - +
165D THR* 3.3 3.9 + - - -
166D ASP* 2.7 61.2 + - - +
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Residues in contact with THR 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ARG* 4.6 17.0 + - - +
149D PHE* 4.7 10.3 - - + -
159D ASN* 2.7 35.9 + - - -
160D ALA* 3.7 8.2 - - - -
162D LYS* 1.3 75.6 - - - +
164D ILE* 1.3 62.0 + - + +
166D ASP* 3.1 7.0 + - - +
167D ILE* 2.9 53.0 + - + +
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Residues in contact with ILE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D GLY* 3.6 18.2 - - - +
148D ASN* 3.5 27.4 - - - +
149D PHE* 3.5 33.4 - - + +
160D ALA 3.4 14.4 - - - +
161D TRP 3.1 6.6 + - - +
163D THR* 1.3 79.2 - - + +
165D THR* 1.3 61.6 + - - +
167D ILE* 3.4 4.4 + - + -
168D VAL* 3.0 30.6 + - + +
209D PRO* 3.7 15.3 - - + +
210D SER* 3.5 35.9 - - - +
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Residues in contact with THR 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B THR* 4.2 12.8 - - + -
169B LEU* 3.8 25.0 - - + +
170B ASN* 3.4 27.4 - - - +
161D TRP* 3.0 31.6 + - - -
162D LYS* 3.5 8.1 - - - -
164D ILE* 1.3 78.8 - - - +
166D ASP* 1.3 62.0 + - - +
169D LEU* 3.1 23.5 + - + -
170D ASN* 3.2 8.7 + - - +
209D PRO 4.6 5.0 + - - -
213D ALA* 4.1 8.7 - - + -
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Residues in contact with ASP 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LYS* 3.8 12.1 - - - -
170B ASN* 4.7 3.5 + - - -
119D ARG* 3.4 35.2 + - + +
162D LYS* 2.7 51.0 + - - +
163D THR* 3.1 6.9 + - - +
165D THR* 1.3 73.5 - - - +
167D ILE* 1.3 56.1 + - - +
170D ASN* 3.1 25.0 + - - +
171D GLY 2.9 25.5 + - - -
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Residues in contact with ILE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ARG* 6.1 2.9 - - - +
118D VAL* 3.4 23.5 - - + +
119D ARG* 3.5 23.1 - - - +
145D ALA 4.2 5.4 - - - +
146D ALA* 3.9 8.1 - - - -
147D GLY* 3.9 31.2 - - - +
163D THR* 2.9 40.1 + - + +
164D ILE* 4.0 4.5 - - + +
166D ASP* 1.3 74.8 - - - +
168D VAL* 1.3 64.9 + - - +
171D GLY* 3.4 7.3 - - - -
172D THR* 3.9 1.4 + - - -
1329D NAP 3.8 37.2 - - + +
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Residues in contact with VAL 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D ALA 4.6 4.9 - - - +
146D ALA* 4.0 11.2 - - + -
147D GLY 3.9 32.1 - - - +
164D ILE* 3.0 22.3 + - + +
167D ILE* 1.3 76.8 - - - +
169D LEU* 1.3 59.9 + - - +
172D THR* 2.8 31.3 + - - +
210D SER* 5.5 1.1 - - - -
213D ALA* 3.6 24.7 - - + +
214D LYS* 3.7 34.5 - - + +
217D VAL* 3.4 7.0 - - + +
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TRP* 4.3 2.9 - - + +
165B THR* 4.4 15.9 - - + +
169B LEU* 3.8 26.7 - - + -
212B SER* 4.0 18.4 - - - +
213B ALA* 4.5 1.6 - - - +
165D THR* 3.1 14.1 + - + +
168D VAL* 1.3 77.2 - - - +
170D ASN* 1.3 68.1 + - - +
172D THR 3.3 2.1 + - - -
173D ALA* 2.9 24.4 + - - +
213D ALA* 3.9 13.7 - - + +
216D GLY* 3.6 34.5 - - - +
217D VAL* 3.8 4.3 - - + +
220D MSE 3.6 23.1 - - + +
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Residues in contact with ASN 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B TRP* 3.3 19.1 + - - +
162B LYS* 3.4 24.8 - - - +
165B THR* 3.3 32.4 + - - +
166B ASP* 4.7 0.4 + - - -
170B ASN* 5.3 0.4 - - - +
119D ARG* 5.5 0.2 - - + -
165D THR* 3.2 5.3 + - - +
166D ASP* 3.1 34.6 + - + +
169D LEU* 1.3 78.9 - - - +
171D GLY* 1.3 53.6 + - - +
173D ALA* 3.1 6.0 + - - +
174D PHE* 2.7 58.6 + - + -
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Residues in contact with GLY 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 3.3 31.0 - - - -
143D ASN* 5.0 0.2 - - - -
166D ASP 2.9 13.6 + - - -
167D ILE 3.4 13.6 + - - -
169D LEU 3.3 0.8 - - - -
170D ASN* 1.3 76.3 - - - +
172D THR* 1.3 59.8 + - - +
174D PHE* 3.9 1.2 - - - +
175D VAL* 3.1 30.7 + - - +
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Residues in contact with THR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ASN* 3.6 40.7 + - + +
145D ALA 5.1 5.2 + - - -
167D ILE 3.9 1.5 + - - -
168D VAL* 2.8 25.1 + - - +
169D LEU 3.3 3.9 + - - -
170D ASN 3.3 0.2 - - - -
171D GLY* 1.3 72.0 - - - +
173D ALA* 1.3 60.8 + - - +
175D VAL* 3.6 1.0 + - - +
176D THR* 2.9 38.9 + - - +
194D SER* 4.0 12.1 - - - +
217D VAL* 3.9 16.6 - - + +
220D MSE 4.2 12.1 - - - -
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Residues in contact with ALA 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B TRP* 3.3 55.0 - - + +
169D LEU 2.9 10.4 + - - +
170D ASN 3.4 7.2 - - - +
172D THR* 1.3 76.2 - - - +
174D PHE* 1.3 54.7 + - + +
176D THR* 3.2 0.9 + - - -
177D LEU* 2.6 39.7 + - + +
220D MSE 3.6 12.2 - - + +
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Residues in contact with PHE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PRO* 3.3 47.1 - - + +
161B TRP* 4.6 10.5 - + + -
162B LYS* 4.4 15.9 - - + -
118D VAL 3.5 20.6 - - - +
119D ARG 3.7 21.1 - - - -
121D PRO* 4.0 24.7 - - + -
124D VAL* 3.6 13.9 - - + +
170D ASN* 2.7 43.7 + - + +
171D GLY 3.9 4.0 - - - +
173D ALA* 1.3 73.0 - - + +
175D VAL* 1.3 62.5 + - - +
177D LEU* 3.6 6.4 - - + +
178D GLU* 3.1 26.9 + - - +
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Residues in contact with VAL 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D PHE* 3.8 28.0 - - + -
65D THR* 4.3 5.6 - - + -
116D CYS* 5.8 1.8 - - - -
118D VAL* 4.1 20.6 - - + -
124D VAL* 3.9 22.7 - - + -
128D VAL* 5.6 1.3 - - + -
141D VAL* 4.4 2.5 - - + -
143D ASN* 3.6 26.5 - - - +
171D GLY 3.1 18.4 + - - +
172D THR 4.0 0.2 - - - +
174D PHE* 1.3 75.9 - - - +
176D THR* 1.3 58.5 + - - +
178D GLU* 4.1 0.9 - - - +
179D ILE* 3.1 42.4 + - + +
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Residues in contact with THR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ASN* 3.5 17.2 + - - -
172D THR* 2.9 24.0 + - - +
173D ALA 3.7 2.5 - - - -
175D VAL* 1.3 73.4 - - - +
177D LEU* 1.3 61.0 + - - +
180D GLY* 2.8 29.8 + - - -
192D PHE* 4.0 15.6 - - + -
220D MSE 4.4 7.8 - - - -
224D LEU* 3.5 31.2 - - + -
228D TRP* 3.9 4.1 - - + -
235D PHE* 3.5 21.9 - - + -
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B THR* 3.4 41.1 - - + +
154B GLU* 4.9 0.7 - - - -
156B LEU* 3.1 25.6 - - + +
157B SER 4.0 2.9 - - - +
158B PRO* 3.9 25.6 - - + -
161B TRP* 5.4 11.7 - - + -
173D ALA 2.6 23.1 + - - +
174D PHE* 3.6 8.3 - - + +
176D THR* 1.3 73.7 - - - +
178D GLU* 1.3 57.1 + - - +
180D GLY* 3.7 0.2 - - - -
181D LYS* 2.8 55.3 + - - +
228D TRP* 4.4 7.6 - - + -
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Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PRO* 5.7 5.2 - - - +
124D VAL* 4.1 5.6 - - + -
125D GLN* 3.9 41.8 + - - +
128D VAL* 3.6 29.6 - - + +
174D PHE 3.1 15.1 + - - +
175D VAL 4.2 0.2 - - - +
177D LEU* 1.3 75.0 - - - +
179D ILE* 1.3 66.8 + - - +
181D LYS* 3.1 21.8 + - - +
182D GLN* 3.0 52.4 + - - +
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Residues in contact with ILE 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D PHE* 3.8 29.6 - - + -
128D VAL* 3.6 27.8 - - + -
131D LEU* 4.2 12.1 - - + -
138D PRO* 3.8 17.3 - - + -
141D VAL* 3.9 19.1 - - + -
175D VAL* 3.1 21.7 + - + +
176D THR 4.4 0.9 - - - +
178D GLU* 1.3 74.9 - - - +
180D GLY* 1.3 63.1 + - - +
182D GLN* 3.1 4.3 + - + +
183D LEU* 2.9 42.7 + - + +
192D PHE* 3.8 14.6 - - + -
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D THR 2.8 21.1 + - - -
177D LEU 3.7 0.4 - - - -
179D ILE* 1.3 79.4 - - - +
181D LYS* 1.3 61.9 + - - +
183D LEU* 3.2 2.3 + - - +
184D ILE* 3.2 33.5 + - - +
192D PHE* 4.6 0.6 - - - -
228D TRP* 3.9 16.6 - - - -
233D MSE 3.9 14.9 - - - +
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Residues in contact with LYS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLU* 3.6 29.2 + - + +
156B LEU 2.8 30.2 + - - -
157B SER* 4.2 5.9 - - - +
158B PRO* 4.3 5.7 - - - +
177D LEU* 2.8 42.2 + - + +
178D GLU* 3.4 22.0 + - - +
180D GLY* 1.3 73.5 - - - +
182D GLN* 1.3 63.6 + - + +
184D ILE* 3.7 11.2 + - - +
185D LYS* 3.4 21.3 + - - +
228D TRP* 5.0 1.0 - - + -
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Residues in contact with GLN 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D VAL* 3.9 16.2 - - + +
129D SER* 5.9 3.0 + - - +
132D ILE* 3.6 29.0 - - + +
137D HIS* 4.1 9.7 + - + -
178D GLU* 3.0 35.9 + - - +
179D ILE* 3.6 8.3 - - - +
181D LYS* 1.3 78.7 - - - +
183D LEU* 1.3 65.0 + - + +
184D ILE 3.2 0.2 - - - -
185D LYS* 3.4 17.4 + - - +
186D ALA* 3.1 24.4 + - - +
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D HIS* 4.0 17.7 - - + -
138D PRO* 3.7 23.8 - - + +
179D ILE* 2.9 38.0 + - + +
180D GLY 3.2 4.2 + - - +
182D GLN* 1.3 73.2 - - + +
184D ILE* 1.3 59.8 + - - +
186D ALA* 4.6 2.0 - - - +
187D GLN* 3.0 6.2 + - - -
188D LYS* 2.8 62.2 + - + +
189D GLY 4.2 2.2 - - - +
190D ALA* 3.7 24.2 - - + +
192D PHE* 4.1 1.8 - - + -
233D MSE 4.0 24.0 - - + -
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLU* 3.4 34.1 - - + -
180D GLY 3.2 22.0 + - - +
181D LYS* 3.8 8.3 - - - +
183D LEU* 1.3 74.5 - - - +
185D LYS* 1.3 65.4 + - - +
187D GLN* 3.2 20.3 + - - +
188D LYS 5.1 0.4 - - - -
228D TRP* 4.5 3.4 - - + -
231D TYR* 3.6 48.7 - - + +
233D MSE 3.8 16.8 - - + -
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Residues in contact with LYS 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D LYS 3.4 11.7 + - - +
182D GLN* 3.4 21.7 + - - +
184D ILE* 1.3 83.0 - - - +
186D ALA* 1.3 58.1 + - + +
187D GLN* 3.5 9.4 + - - +
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Residues in contact with ALA 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D HIS* 3.5 38.1 - - + +
182D GLN 3.1 11.2 + - - +
183D LEU 4.3 2.5 - - - +
185D LYS* 1.3 75.0 - - + +
187D GLN* 1.3 70.0 + - - +
188D LYS* 3.2 16.9 + - + +
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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).
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