Contacts of the helix formed by residues 151 - 173 (chain C) in PDB entry 3NDR
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 MSE 151 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLU* 4.5 0.4 + - - -
92C VAL* 4.0 14.1 - - + -
93C PRO* 3.8 23.1 - - + +
95C VAL* 3.7 3.6 + - - +
100C VAL* 6.1 0.2 - - - -
104C HIS* 6.1 1.6 - - - -
143C THR* 4.2 11.0 - - + -
148C THR* 4.0 22.7 - - + +
149C PRO 3.1 9.7 - - - +
150C ASN* 1.3 80.0 - - - +
152C ALA* 1.3 60.8 + - - +
153C ALA 3.5 2.5 - - - -
154C TYR* 3.2 49.4 + - + -
155C VAL* 2.9 41.2 + - + +
197C HIS* 3.6 21.1 - - + -
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 4.5 13.1 - - + -
167B ALA* 4.1 24.2 - - + +
168B LEU* 5.5 0.7 - - + +
171B GLU* 5.0 10.1 + - + +
97C TRP* 4.1 31.9 - - + -
100C VAL* 4.8 8.6 - - + +
105C TRP* 4.4 3.3 - - + -
150C ASN 5.0 0.2 - - - +
151C MSE 1.3 72.3 - - - +
153C ALA* 1.3 67.5 + - - +
155C VAL* 3.3 1.7 + - - +
156C ALA* 3.0 23.9 + - - +
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Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C VAL* 4.9 4.7 - - + +
104C HIS* 3.9 29.3 + - + +
105C TRP* 3.7 35.8 - - + +
108C ILE* 3.7 18.1 - - + +
109C ILE* 3.8 3.1 - - + +
151C MSE 3.5 0.6 - - - -
152C ALA* 1.3 77.4 - - - +
154C TYR* 1.3 58.2 + - - +
156C ALA* 3.4 3.5 + - - +
157C ALA* 2.9 29.5 + - - +
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Residues in contact with TYR 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ILE 3.3 27.1 - - - -
92C VAL* 4.1 11.8 - - + +
93C PRO* 3.4 23.7 - - + +
108C ILE* 3.6 9.5 - - + +
112C ASN* 3.4 9.9 - - - -
141C SER* 3.5 22.0 + - - -
143C THR* 3.7 11.9 - - + -
151C MSE 3.2 34.9 + - + +
153C ALA* 1.3 79.5 - - - +
155C VAL* 1.3 59.5 + - - +
157C ALA* 3.3 2.6 + - - +
158C LYS* 2.9 48.8 + - + +
251C NAD 2.8 52.6 + - - -
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Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLY* 3.5 24.8 - - - +
166B ARG* 5.4 0.2 - - + -
167B ALA* 3.9 13.5 - - + +
143C THR* 3.5 44.2 - - - +
144C PHE* 3.8 13.2 - - - +
147C GLY* 4.9 0.7 - - - -
148C THR 3.8 20.4 - - - +
151C MSE 2.9 22.9 + - + +
152C ALA 3.3 4.2 + - - +
154C TYR* 1.3 74.0 - - - +
156C ALA* 1.3 56.0 + - - +
158C LYS* 3.9 2.8 - - - +
159C GLY 2.9 22.7 + - - -
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Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 4.6 2.9 - - + -
160B GLY* 3.3 33.2 - - - +
164B PHE* 3.8 10.0 - - + +
105C TRP* 3.6 28.3 - - + -
109C ILE* 4.6 1.8 - - + -
152C ALA 3.0 14.0 + - - +
153C ALA 3.5 7.9 - - - +
155C VAL* 1.3 73.4 - - - +
157C ALA* 1.3 54.7 + - - +
159C GLY 2.9 3.1 + - - -
160C GLY* 2.8 30.3 + - - -
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ILE* 4.4 4.7 - - + +
109C ILE* 3.8 18.9 - - + +
112C ASN* 3.9 27.1 - - + -
113C LEU* 3.8 17.0 - - + +
153C ALA 2.9 17.6 + - - +
154C TYR 3.6 4.3 - - - +
156C ALA* 1.3 75.2 - - - +
158C LYS* 1.3 59.1 + - - +
160C GLY* 2.8 16.1 + - - -
161C VAL* 2.9 18.3 + - - +
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Residues in contact with LYS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C SER* 3.0 22.4 + - - -
112C ASN* 4.3 9.5 + - + +
139C ILE 3.1 19.6 + - - +
140C ALA* 3.5 22.7 - - + +
141C SER* 3.9 16.8 - - - +
143C THR* 5.0 0.2 - - - +
144C PHE* 4.7 7.2 - - + -
154C TYR* 2.9 47.0 + - + +
155C VAL* 4.0 5.6 - - - +
157C ALA* 1.3 74.2 - - + +
159C GLY* 1.3 66.2 + - - +
161C VAL* 3.2 19.9 + - + +
162C ILE* 3.2 21.6 + - - +
251C NAD 3.0 30.8 + - - -
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Residues in contact with GLY 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PHE* 4.1 1.2 - - - -
159B GLY* 3.6 17.0 - - - -
163B GLY* 4.5 0.2 - - - -
144C PHE* 3.3 33.7 - - - -
155C VAL 2.9 12.2 + - - -
156C ALA 2.9 4.9 + - - -
158C LYS* 1.3 75.3 - - - +
160C GLY* 1.3 62.2 + - - +
162C ILE* 3.2 6.0 + - - +
163C GLY 3.0 17.7 + - - -
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Residues in contact with GLY 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ALA* 3.2 24.5 - - - +
160B GLY* 3.7 3.9 - - - +
113C LEU* 3.6 16.8 - - - -
156C ALA 2.8 12.9 + - - -
157C ALA 2.8 6.4 + - - -
159C GLY* 1.3 76.1 - - - +
161C VAL* 1.3 51.8 + - - +
163C GLY* 3.1 1.6 + - - -
164C PHE* 2.7 35.7 + - - +
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Residues in contact with VAL 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASN 3.5 25.1 - - - +
113C LEU* 4.2 5.8 - - + -
116C THR* 3.9 18.8 - - + +
138C SER* 3.8 28.7 - - - +
139C ILE 4.8 3.4 - - - +
140C ALA* 4.5 18.2 - - + -
157C ALA 2.9 13.8 + - - +
158C LYS* 3.2 16.1 + - + +
160C GLY* 1.3 75.0 - - - +
162C ILE* 1.3 58.2 + - - +
164C PHE* 3.6 9.7 - - + +
165C THR* 2.7 33.3 + - - +
181C ALA* 5.1 1.1 - - + -
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Residues in contact with ILE 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PHE* 4.3 13.9 - - + -
140C ALA* 4.0 22.2 - - + -
144C PHE* 3.6 38.1 - - + -
145C PHE* 5.1 2.0 - - + -
158C LYS 3.2 14.9 + - - +
159C GLY 3.2 5.4 + - - +
161C VAL* 1.3 74.0 - - - +
163C GLY* 1.3 66.3 + - - +
165C THR* 3.1 6.8 + - - -
166C ARG* 2.9 45.3 + - + +
181C ALA* 4.7 4.3 - - + -
183C THR* 4.3 11.2 - - + -
238C THR* 3.8 24.7 - - + +
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Residues in contact with GLY 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PHE* 3.8 17.9 - - - -
155B VAL* 3.6 34.3 - - - +
156B ALA* 4.1 0.7 - - - -
159B GLY* 4.5 0.2 - - - -
159C GLY 3.0 12.6 + - - -
160C GLY 3.5 3.1 - - - -
162C ILE* 1.3 78.1 - - - +
164C PHE* 1.3 64.6 + - - +
166C ARG* 3.2 3.1 + - - +
167C ALA* 3.1 16.8 + - - +
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Residues in contact with PHE 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B TRP* 4.1 15.0 - + - -
105B TRP* 4.0 24.5 - + + -
152B ALA* 4.6 13.0 - - + -
156B ALA* 3.8 13.0 - - + +
87C ASN* 5.8 0.2 - - - -
113C LEU* 5.2 1.8 - - + -
116C THR* 4.2 13.0 - - - -
117C PHE* 4.0 24.2 - + - -
120C THR* 3.7 35.7 - - + -
138C SER* 5.7 4.0 - - - -
160C GLY 2.7 19.8 + - - +
161C VAL* 3.6 9.6 - - + +
163C GLY* 1.3 73.3 - - - +
165C THR* 1.3 60.9 + - - +
167C ALA* 3.2 1.7 + - - -
168C LEU* 2.8 62.4 + - + +
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Residues in contact with THR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C SER* 4.1 10.9 + - - -
161C VAL 2.7 24.6 + - - -
162C ILE* 3.1 8.3 + - - -
164C PHE* 1.3 78.4 - - - +
166C ARG* 1.3 61.1 + - + +
168C LEU* 3.2 7.6 + - - +
169C ALA* 2.9 28.4 + - - +
179C ALA* 3.4 26.0 - - + +
180C ASN* 3.6 24.0 + - - -
181C ALA* 3.8 15.4 - - + +
236C GLY* 4.5 5.4 - - - +
237C GLN 4.4 4.5 - - - +
238C THR* 5.5 1.1 - - - +
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Residues in contact with ARG 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ARG* 2.6 54.0 + - + +
248A HIS* 3.3 31.1 - - - +
144B PHE* 3.2 46.5 + - - +
145B PHE* 3.8 16.2 - - - +
147B GLY* 3.8 14.1 - - - -
155B VAL* 5.3 0.7 - - + -
144C PHE* 6.2 1.2 - - - -
145C PHE* 5.9 1.8 - - - -
162C ILE* 2.9 38.4 + - + +
163C GLY 3.2 5.6 + - - +
165C THR* 1.3 79.7 - - + +
167C ALA* 1.3 62.3 + - - +
169C ALA 3.4 2.6 + - - -
170C THR* 3.1 2.8 - - - +
236C GLY* 3.8 20.5 + - - +
238C THR* 4.8 3.0 + - - +
248C HIS* 4.4 8.1 - - - -
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Residues in contact with ALA 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLY* 3.6 13.0 - - - +
148B THR 4.0 11.2 - - - +
152B ALA* 4.0 19.7 - - + +
155B VAL* 3.9 22.9 - - + -
163C GLY 3.1 11.3 + - - +
164C PHE 3.8 6.3 - - - +
166C ARG* 1.3 76.3 - - - +
168C LEU* 1.3 58.0 + - - +
170C THR* 3.3 6.4 + - - +
171C GLU* 2.9 32.5 + - - +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TRP* 3.7 44.2 - - + -
152B ALA* 5.4 0.9 - - + +
120C THR* 3.5 28.5 - - + -
136C VAL* 4.6 7.0 - - + -
164C PHE* 2.8 33.7 + - + +
165C THR* 3.5 6.5 - - - +
167C ALA* 1.3 74.8 - - - +
169C ALA* 1.3 66.8 + - - +
171C GLU* 2.8 6.1 + - + +
172C LEU* 2.8 45.2 + - + +
179C ALA* 4.0 17.5 - - + -
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Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 3.6 6.1 - - - +
247A ARG* 3.8 4.5 - - - +
165C THR 2.9 9.3 + - - +
166C ARG 3.5 8.1 - - - +
167C ALA 3.3 0.2 - - - -
168C LEU* 1.3 75.1 - - - +
170C THR* 1.3 57.2 + - - +
172C LEU* 3.8 0.7 - - - -
173C GLY* 3.0 27.7 + - - -
177C ILE 4.5 2.2 - - - +
179C ALA* 3.8 9.3 - - - +
235C THR* 3.2 30.7 + - + +
236C GLY* 3.3 28.5 - - - +
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Residues in contact with THR 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 3.7 15.9 - - - +
247A ARG* 2.8 38.4 - - - +
146B ALA 4.6 0.2 - - - +
147B GLY 2.7 30.4 + - - +
149B PRO* 3.7 21.4 - - - +
166C ARG 3.1 4.5 - - - +
167C ALA 3.5 2.5 + - - +
169C ALA* 1.3 72.1 - - - +
171C GLU* 1.3 66.8 + - - +
172C LEU 3.3 0.9 + - - -
173C GLY* 3.6 7.8 + - - -
174C LYS* 4.8 4.3 + - - +
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Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TRP* 3.1 53.0 + - + +
148B THR 4.8 0.3 - - - +
149B PRO* 3.4 18.1 - - - +
150B ASN* 3.1 27.7 + - - +
151B MSE 4.5 2.3 + - - -
152B ALA* 4.9 7.7 - - + +
167C ALA* 2.9 16.7 + - - +
168C LEU* 2.8 20.4 + - + +
170C THR* 1.3 79.0 + - - +
172C LEU* 1.3 61.2 + - + +
174C LYS* 3.7 29.8 + - - -
175C TYR* 3.9 2.9 - - - -
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TRP* 3.9 23.6 - - + +
124C THR* 3.6 33.4 - - + +
128C ARG* 4.3 7.2 - - - +
136C VAL* 4.9 0.7 - - + -
168C LEU* 2.8 39.0 + - + +
169C ALA* 5.4 0.2 - - - -
171C GLU* 1.3 79.7 - - + +
173C GLY* 1.3 67.4 + - - +
174C LYS 3.0 3.1 - - - -
175C TYR* 2.9 38.4 + - + +
177C ILE* 3.3 44.1 + - + +
179C ALA* 5.5 1.3 - - + -
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Residues in contact with GLY 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ALA* 3.3 26.6 - - - +
210A MSE 3.4 20.2 - - - +
211A LYS* 3.1 13.7 + - - -
169C ALA 3.0 15.9 + - - -
170C THR 3.6 3.6 + - - -
172C LEU* 1.3 78.0 - - - +
174C LYS* 1.3 56.0 + - - +
176C ASN 3.1 14.6 + - - -
177C ILE 4.1 1.6 - - - -
235C THR* 6.0 0.2 - - - -
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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