Contacts of the helix formed by residues 145 - 169 (chain D) in PDB entry 3BUW
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 145 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D ARG* 2.8 32.9 + - - -
142D GLU* 2.8 21.6 + - - -
143D GLU 3.1 2.6 + - - -
144D ASN* 1.3 82.3 - - - +
146D GLN* 1.3 59.2 + - - +
147D PRO* 3.5 8.4 - - - +
148D ARG* 3.2 13.7 + - - +
149D ARG* 3.0 26.8 + - - +
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Residues in contact with GLN 146 (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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203B LYS* 4.6 23.8 - - + +
139D ARG* 5.2 7.5 - - - +
144D ASN 4.0 0.6 + - - +
145D SER* 1.3 69.1 - - - +
147D PRO* 1.3 75.5 - - + +
149D ARG* 3.1 16.6 + - - +
150D ASN* 2.8 45.9 + - - +
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Residues in contact with PRO 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LEU* 3.4 19.4 - - + +
136D GLY* 4.3 11.9 - - - -
139D ARG* 3.5 45.8 - - + +
140D MET* 3.4 25.5 - - - +
145D SER* 3.5 14.8 - - - +
146D GLN* 1.3 92.5 - - + +
148D ARG* 1.3 60.0 + - - +
150D ASN* 3.4 9.7 + - - +
151D LEU* 3.1 17.8 + - - +
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Residues in contact with ARG 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 2.7 38.6 + - - +
76D ALA 4.4 1.8 + - - -
77D LEU* 3.6 27.5 - - - +
78D LYS* 6.1 2.6 - - - +
139D ARG 4.8 0.2 + - - -
140D MET* 3.1 30.6 + - - +
141D TYR* 4.4 10.3 + - - +
142D GLU 4.1 6.1 - - - +
143D GLU* 3.6 34.7 + - - +
144D ASN 4.9 0.2 - - - +
145D SER* 3.2 22.0 + - - +
146D GLN 3.1 0.2 - - - -
147D PRO* 1.3 80.0 - - - +
149D ARG* 1.3 64.3 + - - +
151D LEU* 3.1 20.5 + - - +
152D THR* 3.0 28.5 + - - +
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Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ASN 5.8 1.3 - - - +
145D SER 3.0 13.3 + - - +
146D GLN* 3.6 24.0 - - - +
148D ARG* 1.3 75.3 - - - +
150D ASN* 1.3 61.3 + - - +
152D THR* 3.1 6.4 + - - -
153D LYS* 2.9 65.1 + - - +
271D PHE* 3.2 33.6 + - - +
272D LEU* 4.6 7.3 - - - +
276D GLU* 3.3 25.8 + - - -
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Residues in contact with ASN 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LEU* 3.9 20.1 - - + +
146D GLN* 2.8 42.6 + - - +
147D PRO* 3.5 11.6 - - - +
148D ARG 3.2 0.2 - - - -
149D ARG* 1.3 80.8 + - - +
151D LEU* 1.3 54.6 + - - +
153D LYS* 3.3 8.1 + - - +
154D LEU* 2.7 43.0 + - + +
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Residues in contact with LEU 151 (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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70D CYS* 4.2 13.7 - - - -
75D LEU* 4.5 4.5 - - + -
77D LEU* 4.4 19.1 - - + -
84D ILE* 5.5 4.3 - - + -
129D THR* 3.9 28.5 - - + -
132D LEU* 3.6 9.8 - - + +
133D PHE* 4.1 27.1 - - + -
140D MET* 4.2 7.2 - - + -
147D PRO 3.1 13.4 + - - +
148D ARG* 3.1 24.0 + - - +
150D ASN* 1.3 76.0 - - - +
152D THR* 1.3 59.9 + - - +
154D LEU* 3.2 4.9 + - + +
155D SER* 2.8 39.1 + - - +
158D PHE* 6.4 0.2 - - + -
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Residues in contact with THR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D LYS* 5.9 0.7 + - - -
82D PRO* 5.5 0.4 - - + -
148D ARG* 3.0 19.1 + - - +
149D ARG* 3.3 12.4 - - - +
151D LEU* 1.3 74.2 - - - +
153D LYS* 1.3 60.2 + - - +
155D SER* 3.1 14.1 + - - -
156D LEU* 2.7 29.5 - - + +
271D PHE 5.5 0.2 - - - +
273D THR* 3.6 19.3 - - + +
276D GLU* 3.5 36.2 + - + +
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Residues in contact with LYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ARG* 2.9 38.6 + - - +
150D ASN* 3.7 10.3 - - - +
152D THR* 1.3 76.6 - - - +
154D LEU* 1.3 69.3 + - + +
156D LEU* 3.1 12.0 + - - +
157D ILE* 3.0 31.4 + - + +
232D CYS* 4.4 10.8 - - - -
271D PHE* 2.8 54.8 - - + -
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Residues in contact with LEU 154 (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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125D LYS* 3.9 31.0 - - + +
128D GLN* 3.9 17.7 - - + +
129D THR* 3.9 28.0 - - - +
132D LEU* 5.3 4.0 - - + -
150D ASN* 2.7 37.6 + - + +
151D LEU* 3.5 12.3 - - + +
153D LYS* 1.3 86.9 - - + +
155D SER* 1.3 56.4 + - - +
157D ILE* 3.1 9.8 + - + +
158D PHE* 2.8 40.9 + - + -
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Residues in contact with SER 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PRO* 3.7 25.5 + - - +
84D ILE* 3.8 24.4 + - - +
87D LEU* 3.5 12.0 - - - +
151D LEU* 2.8 24.3 + - - +
152D THR* 3.1 12.9 + - - -
154D LEU* 1.3 77.1 - - - +
156D LEU* 1.3 61.2 + - - +
158D PHE* 3.3 10.1 + - - +
159D SER 3.0 17.3 + - - -
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D PRO* 3.2 16.8 - - + -
152D THR* 2.7 28.9 + - + +
153D LYS* 3.1 6.9 + - - +
155D SER* 1.3 72.6 - - - +
157D ILE* 1.3 65.7 + - - +
159D SER* 3.0 4.7 + - - -
160D HIS* 2.9 42.1 + - + +
271D PHE* 3.3 49.1 - - + +
272D LEU 3.7 14.4 - - - +
273D THR* 3.0 29.6 - - + -
297D CYS* 5.5 5.6 - - + -
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LYS* 3.9 14.4 - - + -
153D LYS* 3.0 27.9 + - + +
154D LEU* 3.1 13.9 + - + +
156D LEU* 1.3 76.3 - - - +
158D PHE* 1.3 57.3 + - - +
160D HIS* 3.1 3.4 + - - +
161D MET* 2.8 51.9 + - + +
230D LEU 2.9 29.8 - - - +
231D THR 3.8 21.5 - - - +
232D CYS* 3.3 18.8 - - + -
271D PHE* 3.2 26.9 - - + -
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Residues in contact with PHE 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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66D VAL* 5.1 0.7 - - + -
84D ILE* 3.2 35.0 - - + -
87D LEU* 4.3 10.7 - - + +
88D LEU* 3.8 23.1 - - + -
91D THR* 4.9 5.3 + - + -
122D LEU* 4.0 9.9 - - + -
125D LYS* 3.9 25.4 - - + -
126D THR* 4.0 17.7 - - + -
129D THR* 3.6 28.7 - - + -
151D LEU* 6.4 0.4 - - + -
154D LEU* 2.8 32.6 + - + -
155D SER 3.6 6.5 - - - +
156D LEU 3.2 0.2 - - - -
157D ILE* 1.3 74.6 - - - +
159D SER* 1.3 62.3 + - - +
161D MET* 3.0 34.1 + - + +
162D LEU* 3.0 23.9 + - - +
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Residues in contact with SER 159 (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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82D PRO* 4.1 10.2 - - - +
87D LEU* 3.7 28.0 - - - +
155D SER 3.0 13.0 + - - -
156D LEU* 3.0 9.6 + - - -
158D PHE* 1.3 78.1 - - - +
160D HIS* 1.3 65.3 + - - +
162D LEU* 3.3 3.5 + - - +
163D ALA* 3.0 23.3 + - - +
297D CYS* 3.8 27.4 + - - +
300D LEU* 5.6 0.2 - - - -
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Residues in contact with HIS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D LEU* 2.9 34.7 + - + +
157D ILE 3.6 5.4 - - - +
159D SER* 1.3 78.4 + - - +
161D MET* 1.3 57.5 + - - +
163D ALA* 3.4 2.8 + - - +
164D GLU* 3.0 29.5 + - - +
230D LEU* 3.7 48.8 - - + +
231D THR* 4.3 3.4 - - + +
239D PHE* 4.3 3.5 - - + -
271D PHE* 4.3 14.0 - + - -
295D LEU* 5.0 10.4 - - + +
296D SER 5.0 0.7 - - - -
297D CYS* 4.6 19.5 + - + -
300D LEU* 3.7 37.5 - - + +
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Residues in contact with MET 161 (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 THR* 6.5 0.2 - - + -
118D PHE* 3.4 29.2 - - + -
121D ASN* 3.6 23.1 - - - +
122D LEU* 5.2 8.1 - - + -
125D LYS* 4.0 11.7 - - + -
157D ILE* 2.8 31.9 + - + +
158D PHE* 3.0 64.6 - - + +
159D SER 3.2 0.2 - - - -
160D HIS* 1.3 74.3 - - - +
162D LEU* 1.3 60.0 + - - +
164D GLU* 3.3 1.6 + - - +
165D LEU* 2.9 23.7 + - - +
231D THR* 3.8 27.6 - - + -
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Residues in contact with LEU 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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87D LEU* 4.1 20.9 - - + +
90D ASP* 3.8 28.5 - - + +
91D THR* 3.7 36.5 + - + +
94D HIS* 4.5 5.8 - - + -
118D PHE* 5.1 1.5 - - - -
158D PHE 3.0 16.7 + - - +
159D SER* 3.3 4.2 + - - +
161D MET* 1.3 75.9 - - - +
163D ALA* 1.3 64.0 + - - +
165D LEU* 3.3 7.4 + - + +
166D LYS* 3.0 57.6 + - + +
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Residues in contact with ALA 163 (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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159D SER* 3.0 15.4 + - - +
160D HIS 3.6 1.1 - - - +
162D LEU* 1.3 79.1 - - - +
164D GLU* 1.3 56.8 + - - +
166D LYS* 3.5 5.3 + - - +
167D GLY 3.0 23.0 + - - -
239D PHE* 3.5 13.5 - - + -
297D CYS 5.8 1.6 - - - +
300D LEU* 3.4 34.1 - - + -
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Residues in contact with GLU 164 (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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114D TYR* 2.6 35.8 + - + +
118D PHE* 3.9 10.4 - - - -
160D HIS 3.0 17.9 + - - +
161D MET* 3.5 3.6 - - - +
163D ALA* 1.3 74.9 - - - +
165D LEU* 1.3 59.4 + - - +
167D GLY* 3.1 1.7 + - - -
168D ILE* 2.9 35.4 + - + +
199D ILE* 5.8 0.5 - - - +
231D THR* 3.9 17.3 + - + +
233D ASN* 5.5 4.2 + - - -
237D SER* 2.7 27.9 + - - +
239D PHE* 3.5 30.1 - - + -
240D GLU* 3.7 16.3 - - - +
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Residues in contact with LEU 165 (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 THR* 4.6 7.9 - - + -
94D HIS* 3.7 29.6 - - + +
95D LEU* 4.1 19.7 - - + -
98D ILE* 4.0 16.2 - - + -
114D TYR* 3.5 10.7 + - + +
115D PHE* 4.8 2.7 - - + -
118D PHE* 3.9 42.8 - - + -
161D MET 2.9 17.6 + - - +
162D LEU* 3.3 7.6 + - + +
164D GLU* 1.3 76.3 - - - +
166D LYS* 1.3 56.6 + - - +
168D ILE 3.8 0.2 - - - -
169D PHE* 2.8 47.2 + - + +
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Residues in contact with LYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ASP* 4.9 11.4 + - - +
94D HIS* 3.7 40.8 - - + +
162D LEU* 3.0 49.9 + - + +
163D ALA* 4.0 6.3 - - - +
165D LEU* 1.3 75.8 - - - +
167D GLY* 1.3 61.1 + - - +
170D PRO* 3.3 26.2 - - - +
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Residues in contact with GLY 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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163D ALA 3.0 15.5 + - - -
164D GLU 3.1 4.2 + - - -
166D LYS* 1.3 79.2 - - - +
168D ILE* 1.3 63.5 + - - +
170D PRO* 3.6 9.9 - - - +
175D GLN* 5.3 2.1 - - - +
179D PHE* 3.8 19.2 - - - -
239D PHE* 4.4 13.0 - - - -
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Residues in contact with ILE 168 (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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114D TYR* 3.6 35.2 - - + -
164D GLU* 2.9 20.7 + - + +
165D LEU 4.1 0.7 - - - +
167D GLY* 1.3 76.7 - - - +
169D PHE* 1.3 53.4 + - + +
170D PRO* 3.2 8.1 - - - +
174D PHE* 3.4 32.9 - - + -
175D GLN* 2.8 31.7 + - - -
176D GLY* 3.6 10.3 + - - +
179D PHE* 3.9 23.6 - - + -
198D THR* 3.9 18.4 - - + -
237D SER* 5.7 0.7 - - - +
238D VAL* 3.9 10.8 - - + -
239D PHE* 4.2 8.7 - - + -
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Residues in contact with PHE 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D HIS* 3.0 13.0 - - + -
98D ILE* 3.6 28.3 - - + -
102D TYR* 4.0 3.4 - + - -
109D LEU* 3.9 30.1 - - + -
112D ASN* 4.6 2.9 - - - -
114D TYR* 3.7 25.6 - + - -
115D PHE* 4.0 21.3 - + + -
165D LEU* 2.8 23.6 + - + +
166D LYS 3.6 3.8 - - - -
168D ILE* 1.3 83.1 - - + +
170D PRO* 1.3 64.8 - - - +
172D GLY 2.9 23.7 + - - -
173D LEU 3.4 4.0 - - - -
174D PHE* 3.3 47.6 - + + -
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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