Contacts of the helix formed by residues 142 - 173 (chain C) in PDB entry 5YWB
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 CYS 142 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 6.2 0.4 - - + -
97C HIS* 4.2 5.8 - - + -
110C CYS* 2.0 55.4 - - + -
139C THR 4.2 3.6 + - - +
140C GLU 5.2 1.1 - - - -
141C GLU* 1.3 99.5 - - - +
143C PRO* 1.3 66.8 - - - +
144C LEU* 3.2 8.2 + - + +
145C ALA* 3.4 13.5 + - + +
146C ILE* 3.4 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU 6.1 0.2 - - - -
141C GLU 3.6 9.4 - - - +
142C CYS* 1.3 80.0 - - - +
144C LEU* 1.3 58.5 + - - +
145C ALA 3.3 0.2 - - - -
146C ILE* 3.1 16.9 + - + +
147C LEU* 3.0 26.2 + - - +
118E SER* 5.7 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ILE* 3.7 27.6 - - + -
142C CYS* 3.2 5.2 - - + -
143C PRO* 1.3 76.9 - - - +
145C ALA* 1.3 60.1 + - - +
147C LEU* 3.2 24.4 + - + +
148C ILE* 3.0 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TRP* 4.5 10.0 - - - +
93C ILE* 4.0 10.5 - - + +
110C CYS* 4.4 20.0 - - + +
111C VAL* 5.5 0.7 - - + -
138C VAL* 4.1 22.6 - - + +
139C THR 5.5 0.2 - - - +
142C CYS* 3.4 11.8 + - + +
143C PRO 3.3 0.4 - - - -
144C LEU* 1.3 74.4 - - - +
146C ILE* 1.3 66.1 + - - +
148C ILE* 3.1 15.1 - - + +
149C LEU* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C VAL* 4.4 5.6 - - + -
139C THR 4.0 11.4 - - - +
140C GLU* 5.2 3.8 - - - -
142C CYS 3.4 14.1 - - - +
143C PRO* 3.1 15.2 + - + +
145C ALA* 1.3 78.9 - - - +
147C LEU* 1.3 55.8 + - - +
149C LEU* 3.4 7.7 + - + +
150C ILE* 2.9 30.1 + - + +
118E SER* 5.2 12.3 - - - +
121E PHE* 4.2 28.5 - - + -
122E LEU* 3.5 37.2 - - + -
125E ILE* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C PRO 3.0 12.2 + - - +
144C LEU* 3.2 24.9 + - + +
146C ILE* 1.3 78.1 - - - +
148C ILE* 1.3 64.0 + - - +
150C ILE* 3.2 20.4 + - + +
151C VAL* 3.0 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 4.4 10.3 - - + -
89C VAL* 4.1 37.2 - - + -
90C TRP* 3.6 33.4 - - + +
93C ILE* 4.9 9.0 - - + -
144C LEU* 3.0 11.9 + - + +
145C ALA* 3.1 30.1 - - - +
147C LEU* 1.3 78.3 - - - +
149C LEU* 1.3 56.6 + - - +
151C VAL* 3.2 17.9 - - + +
152C GLN* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TRP* 4.0 18.6 - - + -
123C PHE* 5.3 0.2 - - + -
127C VAL* 4.1 25.6 - - + -
138C VAL* 4.1 29.6 - - + -
145C ALA 2.9 17.2 + - - +
146C ILE* 3.7 7.2 - - + +
148C ILE* 1.3 78.7 - - - +
150C ILE* 1.3 59.5 + - + +
152C GLN* 3.6 1.8 - - - +
153C ASN* 3.0 47.4 + - - +
122E LEU* 4.9 7.0 - - + -
125E ILE* 4.1 27.1 - - + -
131E ILE* 4.7 4.3 - - + -
133E PHE* 4.2 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ILE* 2.9 17.2 + - + +
147C LEU* 3.2 33.0 + - + +
149C LEU* 1.3 77.4 - - + +
151C VAL* 1.3 59.1 + - + +
153C ASN* 4.3 2.4 - - + +
154C ILE* 3.3 21.3 + - - +
80E LEU* 5.2 10.8 - - + +
83E TRP* 3.8 30.6 - - + -
121E PHE* 3.8 26.0 - - + -
125E ILE* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 4.6 7.9 - - + -
147C LEU* 3.0 21.8 + - + +
148C ILE* 3.2 30.1 - - + +
150C ILE* 1.3 80.8 - - + +
152C GLN* 1.3 68.5 + - - +
153C ASN 3.3 0.2 - - - -
154C ILE* 3.2 11.4 - - + +
155C VAL* 3.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TRP* 6.1 0.4 - - - +
86C PHE* 3.2 47.8 - - + +
90C TRP* 3.4 28.6 - - + -
124C SER* 4.0 6.5 + - - -
127C VAL* 3.8 20.6 - - + +
128C GLN* 2.5 42.6 + - - +
148C ILE 2.9 19.9 + - - +
149C LEU* 3.6 6.5 - - - +
151C VAL* 1.3 78.3 - - - +
153C ASN* 1.3 60.1 + - + +
155C VAL* 3.1 8.2 - - - +
156C GLY 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C VAL* 4.0 16.4 + - - +
128C GLN* 4.5 4.6 - - - +
130C THR* 4.2 12.3 - - - +
149C LEU* 3.0 36.5 + - + +
150C ILE* 4.8 3.8 - - - +
152C GLN* 1.3 81.1 - - - +
154C ILE* 1.3 57.9 + - - +
156C GLY* 3.3 1.7 + - - -
157C LEU* 2.9 31.2 + - - +
83E TRP* 5.0 8.5 - - + -
125E ILE* 4.5 4.6 - - + +
129E VAL* 3.4 39.9 - - + +
131E ILE* 4.1 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ILE 3.3 17.5 + - - +
151C VAL* 3.2 24.2 - - + +
153C ASN* 1.3 78.9 - - - +
155C VAL* 1.3 63.9 + - + +
157C LEU* 3.3 5.1 + - + +
158C MET* 2.9 28.7 + - + +
72E LEU* 6.5 0.7 - - + -
75E PHE* 6.1 0.2 - - + -
76E THR* 4.4 30.3 - - - +
79E PHE* 3.6 35.2 - - + -
80E LEU* 5.6 3.1 - - + -
83E TRP* 4.6 11.4 - - + -
163E MET* 5.1 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C SER* 6.2 3.4 - - - -
86C PHE* 3.5 34.3 - - + -
128C GLN* 5.1 0.4 - - - +
151C VAL* 3.0 21.0 + - + +
152C GLN* 3.1 13.0 - - - +
154C ILE* 1.3 78.5 - - + +
156C GLY* 1.3 65.6 + - - +
158C MET* 3.3 6.8 + - + +
159C ILE* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C GLN* 3.3 30.5 - - - +
152C GLN 2.9 15.6 + - - -
153C ASN* 3.7 1.3 - - - -
155C VAL* 1.3 79.1 - - - +
157C LEU* 1.3 55.2 + - - +
159C ILE* 3.1 7.7 - - - +
160C ASN* 2.9 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ASN 2.9 16.2 + - - +
154C ILE* 3.7 8.1 - - + +
156C GLY* 1.3 74.8 - - - +
158C MET* 1.3 59.3 + - - +
160C ASN* 3.4 6.0 + - + +
161C ALA* 2.9 31.6 + - + +
79E PHE* 3.7 36.6 - - + -
83E TRP* 5.7 2.5 - - + -
129E VAL* 4.3 23.3 - - + -
160E ASN* 3.9 26.9 - - - +
163E MET* 4.1 14.1 - - + -
164E LEU* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 158 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 2.9 23.0 + - + +
155C VAL* 3.8 7.9 - - + +
157C LEU* 1.3 77.9 - - - +
159C ILE* 1.3 62.3 + - - +
161C ALA* 3.2 6.4 + - - +
162C ILE* 3.0 25.8 + - + +
68E TRP* 4.0 29.6 - - + -
72E LEU* 4.6 26.5 - - + -
75E PHE* 3.8 29.2 - - + -
163E MET* 4.0 22.4 - - - -
167E ILE* 4.2 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C SER* 4.9 19.7 - - - +
79C PHE* 4.1 25.8 - - + -
82C SER* 5.1 10.8 - - - +
128C GLN* 4.7 4.5 - - - +
155C VAL* 3.0 20.7 + - + +
156C GLY* 3.1 21.3 - - - +
158C MET* 1.3 76.3 - - - +
160C ASN* 1.3 57.7 + - - +
162C ILE* 3.1 17.5 - - + +
163C MET* 2.9 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 160 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.9 32.1 - - - +
79C PHE* 4.5 12.7 - - + -
129C VAL* 5.9 1.4 - - - +
156C GLY 2.9 19.0 + - - +
157C LEU* 3.7 7.2 - - + +
159C ILE* 1.3 78.9 - - + +
161C ALA* 1.3 57.8 + - - +
163C MET* 3.3 1.7 + - - +
164C LEU* 2.9 38.3 + - - +
164E LEU* 5.6 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C LEU* 2.9 24.8 + - + +
158C MET* 3.2 10.5 + - - +
160C ASN* 1.3 77.0 - - - +
162C ILE* 1.3 57.4 + - - +
164C LEU* 3.3 2.8 + - - +
165C GLY 3.0 24.9 + - - -
163E MET* 5.3 2.9 - - + +
164E LEU* 4.5 24.4 - - + +
167E ILE* 3.5 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PHE* 5.8 7.2 - - + -
63C LEU* 5.7 8.7 - - + -
158C MET* 3.0 16.5 + - + +
159C ILE* 3.1 38.1 - - + +
161C ALA* 1.3 75.5 - - - +
163C MET* 1.3 57.9 + - - +
165C GLY* 6.1 0.2 - - - -
166C CYS* 2.9 40.5 + - + +
68E TRP* 5.1 20.6 - - + -
167E ILE* 3.9 9.1 - - + +
171E THR* 4.4 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 5.1 2.5 - - + -
157A LEU* 4.1 12.1 - - + -
158A MET* 4.0 22.2 - - + -
161A ALA* 5.3 2.6 - - + +
75C PHE* 3.5 54.7 - - + +
78C SER* 5.7 2.7 - - - -
79C PHE* 3.5 44.4 - - + -
159C ILE* 2.9 24.1 + - + +
160C ASN 4.0 3.1 - - - +
162C ILE* 1.3 77.3 - - + +
164C LEU* 1.3 56.8 + - - +
166C CYS* 3.7 6.7 - - - -
167C ILE* 3.1 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 6.5 1.1 - - + -
160A ASN* 5.6 2.2 - - - +
161A ALA* 4.5 24.7 - - + +
164A LEU* 4.0 35.2 - - + -
160C ASN* 2.9 25.6 + - - +
161C ALA* 3.8 3.8 - - - +
163C MET* 1.3 76.5 - - - +
165C GLY* 1.3 72.3 + - - +
166C CYS 3.2 1.1 - - - -
167C ILE* 3.2 9.5 - - + +
168C PHE* 3.0 25.7 + - + +
164E LEU* 4.0 34.3 - - + -
168E PHE* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C ALA 3.0 16.0 + - - -
162C ILE* 3.9 1.3 - - - -
164C LEU* 1.3 82.9 - - - +
166C CYS* 1.3 56.7 + - - +
168C PHE* 3.4 2.9 + - - +
169C MET* 2.9 24.8 + - - +
167E ILE* 5.4 0.4 - - - -
168E PHE* 3.4 41.3 - - - -
171E THR* 5.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PHE 5.7 0.2 - - - +
63C LEU* 4.6 9.0 - - + -
64C VAL* 4.2 19.0 - - + +
75C PHE* 3.4 37.2 - - - -
162C ILE* 2.9 32.8 + - + +
163C MET* 3.6 13.9 - - - -
165C GLY* 1.3 77.4 - - - +
167C ILE* 1.3 67.1 + - - +
169C MET* 3.3 6.5 + - - +
170C LYS* 2.9 30.5 + - - +
171E THR* 5.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 4.2 14.8 - - + -
161A ALA* 3.5 44.0 - - + +
162A ILE* 3.9 10.1 - - + +
165A GLY* 5.4 0.7 - - - -
68C TRP* 5.2 12.2 - - + -
75C PHE* 3.4 36.3 - - + -
163C MET* 3.1 21.5 - - + +
164C LEU* 3.2 13.2 - - + +
166C CYS* 1.3 78.5 - - - +
168C PHE* 1.3 66.6 + - + +
170C LYS* 3.9 5.5 - - - +
171C THR* 2.8 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 168 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 6.2 0.7 - - + -
165A GLY* 3.4 40.4 - - - -
168A PHE* 3.2 36.3 - + - -
169A MET* 3.5 29.4 - - + -
164C LEU* 3.0 22.0 + - + +
165C GLY* 3.8 3.8 - - - +
167C ILE* 1.3 78.5 - - + +
169C MET* 1.3 59.8 + - - +
171C THR* 2.2 38.9 - - + +
172C ALA* 3.0 14.1 + - + +
168E PHE* 3.2 40.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C THR* 5.6 8.7 - - - -
64C VAL* 4.8 17.9 - - + +
165C GLY 2.9 16.7 + - - +
166C CYS* 3.3 7.1 + - - +
168C PHE* 1.3 80.0 - - - +
170C LYS* 1.3 63.9 + - - +
172C ALA* 3.4 16.2 + - - +
173C GLN* 3.8 7.3 + - - +
168E PHE* 3.5 20.0 - - + -
171E THR* 3.7 15.0 - - - +
172E ALA* 2.8 54.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C VAL* 3.3 35.3 - - + +
68C TRP* 5.5 11.5 + - + +
71C THR* 6.0 5.8 - - + +
75C PHE* 6.5 0.4 - - + -
166C CYS 2.9 14.6 + - - +
167C ILE* 3.9 6.5 - - - +
169C MET* 1.3 77.5 - - - +
171C THR* 1.3 62.2 + - - +
173C GLN* 2.4 39.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 5.7 4.9 - - - +
61A THR* 5.0 7.3 - - - +
162A ILE* 4.4 20.3 - - + +
165A GLY* 5.2 4.0 - - - -
166A CYS* 5.6 3.8 + - - +
169A MET* 3.7 12.0 - - + +
68C TRP* 5.2 13.8 - - - +
167C ILE* 2.8 23.8 + - + +
168C PHE* 2.2 52.9 - - + +
170C LYS* 1.3 76.2 - - - +
172C ALA* 1.3 63.2 + - - +
173C GLN 3.1 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 5.6 2.3 - - - +
169A MET* 2.8 31.3 - - + +
168C PHE* 3.0 18.8 + - + +
169C MET* 3.7 12.6 - - - +
170C LYS 3.3 0.4 - - - -
171C THR* 1.3 72.5 - - - +
173C GLN* 1.3 68.1 + - - +
174C ALA* 4.8 1.0 - - - +
294C THR* 4.8 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 5.0 4.0 - - - +
64C VAL* 4.3 15.7 + - - +
65C ASP* 5.8 1.8 - - - +
68C TRP* 5.9 3.4 - - - +
169C MET 3.8 5.5 + - - +
170C LYS* 2.4 44.4 + - - +
171C THR 3.1 9.9 - - - +
172C ALA* 1.3 85.1 - - - +
174C ALA* 1.3 64.0 + - - +
175C HIS* 3.6 33.9 - - + +
294C THR* 6.0 1.3 - - - -
296C ILE* 6.3 3.8 - - + -
293E THR* 5.6 5.8 + - - +
----------------------------------------------------------
Back to top of page
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