Contacts of the helix formed by residues 179 - 206 (chain D) in PDB entry 3H90
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 179 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D HIS* 4.1 23.0 + - - +
110D PRO* 4.6 11.7 - - - +
111D MET 5.1 0.7 + - - -
112D THR* 4.7 17.0 + - - -
164D ILE* 3.7 26.5 - - + +
178D ALA* 1.3 81.3 - - - +
180D ALA* 1.3 54.9 + - - +
181D LEU 3.5 0.2 - - - -
182D PHE* 2.9 10.5 + - + +
183D ALA* 2.6 41.8 + - + -
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Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D GLY 3.7 10.1 - - - +
104D HIS* 3.7 23.9 + - - +
105D LEU* 3.7 30.3 - - + -
106D ILE* 5.8 0.4 - - + -
178D ALA* 3.2 9.2 - - + +
179D ASP* 1.3 76.9 - - - +
181D LEU* 1.3 55.7 + - - +
182D PHE 2.9 1.0 + - - -
183D ALA* 4.5 2.9 - - - +
184D LEU* 2.7 40.1 + - - +
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Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU* 5.4 1.1 - - - +
177D ARG* 6.0 5.4 - - + +
178D ALA 4.5 5.1 + - - +
179D ASP 3.5 0.6 - - - -
180D ALA* 1.3 77.6 - - - +
182D PHE* 1.3 78.1 + - + +
184D LEU* 4.8 7.9 - - + +
185D GLY* 3.5 19.0 + - - -
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Residues in contact with PHE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ASN* 3.2 37.5 - - - +
163D ALA* 4.6 19.3 - - + -
164D ILE* 6.3 1.3 - - + -
178D ALA 5.1 3.6 + - - -
179D ASP* 2.9 12.2 + - + +
181D LEU* 1.3 100.5 - - + +
183D ALA* 1.3 63.1 + - - +
184D LEU 3.2 2.0 - - - -
185D GLY* 4.0 0.6 - - - -
186D ILE* 3.2 34.0 + - + +
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Residues in contact with ALA 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 3.1 39.4 - - + +
100D THR* 5.4 1.3 - - - +
101D GLY* 4.3 10.1 - - - +
104D HIS* 4.8 8.7 - - + +
179D ASP* 2.6 31.4 + - + +
180D ALA* 4.2 1.3 - - - +
182D PHE* 1.3 71.7 - - - +
184D LEU* 1.3 58.4 + - - +
186D ILE* 5.0 2.5 - - - -
187D GLY 3.5 11.4 + - - -
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU 4.6 0.4 - - - -
98D PHE* 3.7 22.1 - - + +
101D GLY* 3.8 13.9 - - - +
102D ILE* 3.5 40.2 - - + +
105D LEU* 4.7 8.5 - - + -
180D ALA 2.7 18.7 + - - +
181D LEU* 4.9 7.6 - - + +
183D ALA* 1.3 78.0 - - - +
185D GLY* 1.3 60.4 + - - +
186D ILE 3.2 0.2 - - - -
187D GLY* 3.0 3.5 + - - -
188D ILE* 3.0 46.0 + - + +
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Residues in contact with GLY 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D LEU 3.5 19.3 + - - -
182D PHE* 3.5 1.3 + - - -
184D LEU* 1.3 84.5 - - - +
186D ILE* 1.3 59.9 + - - +
188D ILE* 3.9 7.8 + - - +
189D TYR* 3.4 22.5 + - - +
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Residues in contact with ILE 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 4.0 19.7 - - + -
156D SER* 5.0 7.2 - - - +
159D MET* 3.6 51.4 - - + +
161D ASN* 4.4 13.2 - - - +
182D PHE* 3.2 23.9 + - + +
183D ALA* 5.0 2.2 - - - -
185D GLY* 1.3 75.3 - - - +
187D GLY* 1.3 59.4 + - - +
189D TYR* 3.1 4.6 + - - -
190D ILE* 2.8 52.3 + - + +
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Residues in contact with GLY 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ALA* 3.4 25.6 - - - +
97D LEU* 4.2 6.0 - - - +
98D PHE* 3.9 14.6 - - - +
183D ALA 3.5 10.5 + - - -
184D LEU 3.0 7.6 + - - -
186D ILE* 1.3 79.0 - - - +
188D ILE* 1.3 59.2 + - - +
190D ILE* 5.2 0.2 - - - -
191D LEU* 3.2 25.5 + - - +
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Residues in contact with ILE 188 (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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98D PHE* 3.6 33.2 - - + -
184D LEU* 3.0 27.4 + - + +
185D GLY* 4.0 7.2 - - - +
187D GLY* 1.3 72.9 - - - +
189D TYR* 1.3 69.6 + - + +
191D LEU* 3.0 7.9 + - - +
192D TYR* 2.9 27.7 + - + +
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Residues in contact with TYR 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LEU* 5.9 1.6 - - + -
155D GLN* 5.4 4.7 + - + -
159D MET* 4.1 26.9 - - + -
185D GLY 3.4 14.0 + - - +
186D ILE* 3.1 4.1 + - - +
188D ILE* 1.3 82.2 - - + +
190D ILE* 1.3 76.2 + - + +
192D TYR* 3.8 13.3 + + - +
193D SER* 3.1 50.9 + - - -
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Residues in contact with ILE 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ILE* 4.0 23.1 - - + +
93D SER* 6.4 0.2 - - - -
94D ALA* 3.8 17.0 - - + +
152D LEU* 4.3 19.2 - - + +
155D GLN* 4.7 2.7 - - + -
156D SER* 4.2 34.5 - - - +
159D MET* 4.3 5.6 - - - -
186D ILE* 2.8 40.0 + - + +
187D GLY* 5.2 0.2 - - - -
189D TYR* 1.3 92.0 - - + +
191D LEU* 1.3 54.1 + - - +
193D SER* 3.1 3.1 + - - -
194D ALA* 2.7 33.4 + - - +
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Residues in contact with LEU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D SER* 3.3 40.4 - - - +
94D ALA* 3.4 10.9 - - + +
95D LEU* 4.5 24.2 - - + +
98D PHE* 5.7 8.3 - - + -
187D GLY 3.2 20.0 + - - +
188D ILE* 3.0 5.9 + - - +
190D ILE* 1.3 76.7 - - - +
192D TYR* 1.3 62.9 + - - +
194D ALA* 3.4 3.2 + - - -
195D LEU* 3.1 47.3 + - + +
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Residues in contact with TYR 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D ILE* 2.9 20.7 + - + +
189D TYR* 3.9 13.9 - + - +
191D LEU* 1.3 77.5 - - - +
193D SER* 1.3 71.0 + - - +
195D LEU* 3.3 7.3 + - - +
196D ARG* 3.0 55.3 + - + +
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Residues in contact with SER 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LEU* 3.6 24.6 - - - +
189D TYR* 3.1 42.0 + - - -
190D ILE* 3.1 5.6 + - - -
192D TYR* 1.3 84.9 - - - +
194D ALA* 1.3 57.5 + - - +
195D LEU 3.3 0.2 - - - -
196D ARG* 4.1 5.2 - - - +
197D MET* 3.1 25.5 + - - +
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Residues in contact with ALA 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D SER* 2.6 32.5 + - - +
90D ILE* 3.8 27.1 - - + -
91D SER* 3.7 26.3 + - - +
152D LEU* 3.6 8.5 - - + +
190D ILE 2.7 16.3 + - - +
191D LEU 3.8 1.6 - - - +
192D TYR 3.2 0.4 - - - -
193D SER* 1.3 75.5 - - - +
195D LEU* 1.3 58.5 + - - +
197D MET* 3.6 3.4 - - - +
198D GLY 3.3 4.9 + - - -
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Residues in contact with LEU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D SER* 4.8 1.3 - - - +
91D SER* 3.5 18.8 - - - +
191D LEU* 3.1 39.2 + - + +
192D TYR* 3.9 5.8 - - - +
194D ALA* 1.3 77.1 - - - +
196D ARG* 1.3 61.2 + - - +
197D MET 3.0 1.1 - - - -
198D GLY* 3.0 1.7 + - - -
199D TYR* 2.9 33.1 + - - +
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Residues in contact with ARG 196 (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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192D TYR* 3.0 44.3 + - + +
193D SER* 4.2 6.5 - - - +
195D LEU* 1.3 75.9 - - - +
197D MET* 1.3 61.4 + - - +
199D TYR* 4.0 34.6 - - - +
200D GLU* 3.5 39.1 + - - +
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Residues in contact with MET 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ALA* 4.1 11.9 - - + +
87D SER* 4.2 15.9 - - - -
90D ILE* 6.3 0.2 - - + -
145D GLN* 3.7 26.2 - - + +
148D ARG* 3.9 35.4 - - - +
149D ALA* 3.8 29.6 - - + +
152D LEU* 4.3 13.2 - - + -
193D SER 3.1 20.5 + - - +
194D ALA* 3.6 8.5 - - - +
196D ARG* 1.3 77.8 - - - +
198D GLY* 1.3 61.7 + - - +
200D GLU* 3.4 12.4 - - - +
201D ALA* 3.3 17.5 + - + +
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Residues in contact with GLY 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU* 3.4 6.6 - - - +
87D SER* 3.1 26.0 - - - -
194D ALA 3.3 4.0 + - - -
195D LEU* 3.0 5.8 + - - -
197D MET* 1.3 77.4 - - - +
199D TYR* 1.3 59.8 + - - +
201D ALA* 3.2 10.9 - - - +
202D VAL* 3.0 31.9 + - - +
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Residues in contact with TYR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D LEU 2.9 16.3 + - - +
196D ARG* 4.0 33.9 - - - +
198D GLY* 1.3 73.5 - - - +
200D GLU* 1.3 62.1 + - + +
201D ALA 3.0 1.1 - - - -
202D VAL* 2.9 18.4 + - + +
203D GLN* 2.8 71.0 + - + +
208D ARG* 4.9 4.8 + - - -
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D GLN* 3.8 11.4 + - - +
148D ARG* 2.8 39.1 + - - +
196D ARG* 3.5 31.3 + - + +
197D MET* 3.4 12.4 + - - +
199D TYR* 1.3 83.3 - - + +
201D ALA* 1.3 61.2 + - - +
203D GLN* 3.5 8.8 + - - +
204D SER* 3.1 26.2 + - - -
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Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D SER* 3.6 21.5 - - - +
83D ALA* 4.4 8.1 - - + -
84D LEU* 3.9 19.1 - - + +
145D GLN* 4.1 11.8 - - - +
197D MET* 3.3 7.0 + - + +
198D GLY* 3.2 14.8 + - - +
199D TYR 3.0 0.6 - - - -
200D GLU* 1.3 77.2 - - - +
202D VAL* 1.3 64.3 + - - +
204D SER* 3.1 5.0 + - - -
205D LEU* 3.0 28.0 + - - +
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Residues in contact with VAL 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.9 17.5 - - + -
84D LEU* 3.6 25.4 - - + -
198D GLY 3.0 14.4 + - - +
199D TYR* 2.9 28.6 + - + +
201D ALA* 1.3 72.6 - - - +
203D GLN* 1.3 67.0 + - + +
205D LEU* 2.8 25.6 + - - +
206D LEU* 2.8 28.3 + - + +
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Residues in contact with GLN 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 4.4 4.8 + - - -
71B HIS* 2.9 28.5 + - - -
199D TYR* 2.8 62.7 + - + +
200D GLU* 3.6 9.6 - - - +
202D VAL* 1.3 75.8 - - - +
204D SER* 1.3 52.0 + - - +
206D LEU* 2.5 32.9 - - - +
208D ARG* 2.7 60.7 + - - +
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Residues in contact with SER 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LYS* 3.3 21.9 - - - -
80D SER* 3.7 18.8 - - - -
145D GLN* 4.0 12.1 + - - -
200D GLU 3.1 14.2 + - - -
201D ALA 3.6 7.6 - - - -
202D VAL 3.0 0.6 - - - -
203D GLN* 1.3 73.9 - - - +
205D LEU* 1.3 60.4 + - - +
206D LEU 2.9 13.4 - - - +
207D ASP* 4.2 2.3 - - - -
208D ARG* 4.7 3.1 + - - +
238D GLN* 4.7 13.1 + - - +
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 3.5 30.5 + - - +
81B LEU* 3.9 18.6 - - + -
205B LEU* 4.3 18.0 - - + +
77D LYS* 3.7 17.8 + - + +
80D SER* 4.1 21.8 - - - +
81D LEU* 3.5 32.1 - - + +
84D LEU* 3.5 31.2 - - + -
201D ALA 3.0 17.2 + - - +
202D VAL* 2.8 8.4 + - - +
204D SER* 1.3 74.9 - - - +
206D LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 4.3 23.1 - - + -
71B HIS* 4.2 15.7 - - + +
75B HIS* 5.3 6.7 - - - +
77B LYS* 3.9 9.2 - - + -
78B ALA* 3.6 30.3 - - + +
81B LEU* 3.4 26.7 - - + -
202D VAL* 2.8 28.2 + - + +
203D GLN* 2.5 48.7 - - - +
204D SER 2.9 7.1 - - - +
205D LEU* 1.3 72.9 - - - +
207D ASP* 1.3 55.1 + - - +
208D ARG 2.6 7.1 + - - -
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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