Contacts of the helix formed by residues 154 - 176 (chain C) in PDB entry 4GCK
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 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C THR 4.1 0.2 + - - -
153C LEU* 1.3 73.5 - - - +
155C GLU* 1.3 62.4 + - - +
156C THR* 2.4 51.1 + - - -
157C LEU* 3.2 16.3 + - + +
158C LEU* 3.0 28.2 + - - +
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Residues in contact with GLU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG* 3.8 18.2 - - + -
140C MET* 3.6 30.7 - - + +
141C ARG* 3.5 37.1 - - + +
144C LYS* 3.7 23.1 + - - +
151C TYR* 4.3 8.4 + - + +
153C LEU 4.1 9.2 - - - +
154C ASP* 1.3 76.0 + - - +
156C THR* 1.3 58.7 + - - +
158C LEU* 3.7 7.4 - - - -
159C ALA* 2.8 33.4 + - - +
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Residues in contact with THR 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLU* 4.4 4.0 - - - +
137C ARG* 3.6 31.6 - - - +
154C ASP* 2.4 34.7 + - - -
155C GLU* 1.3 69.5 - - - +
157C LEU* 1.3 57.8 + - - -
159C ALA* 4.0 0.7 - - - +
160C SER* 2.8 29.5 + - - +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C LEU* 4.6 19.7 - - + -
154C ASP* 3.2 18.8 + - + +
156C THR* 1.3 80.1 - - - +
158C LEU* 1.3 62.3 + - - +
160C SER* 3.1 5.8 + - - -
161C GLN* 3.0 25.8 + - - +
185D ASP* 4.4 13.7 - - + -
188D ALA* 4.0 28.5 - - + +
189D ARG* 3.5 46.1 + - + +
192D LEU* 4.1 16.6 - - + -
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Residues in contact with LEU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C MET* 3.5 18.4 - - + -
151C TYR* 3.7 33.2 - - + -
153C LEU* 4.1 16.8 - - + +
154C ASP 3.0 15.6 + - - +
155C GLU* 3.8 1.6 - - - +
157C LEU* 1.3 77.3 - - + +
159C ALA* 1.3 56.8 + - - +
161C GLN* 3.3 6.3 - - + +
162C LEU* 3.0 30.1 + - - +
196C GLN* 3.7 22.2 - - + +
197C LEU* 4.2 10.7 - - + +
198C GLN 3.5 22.7 - - - +
192D LEU* 3.8 20.2 - - + -
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Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLU* 3.8 31.4 - - + +
136C LEU* 4.0 16.1 - - + +
137C ARG* 4.0 10.8 - - + +
140C MET* 3.6 10.7 - - - -
155C GLU 2.8 21.8 + - - +
156C THR 4.2 2.0 - - - +
158C LEU* 1.3 71.7 - - - +
160C SER* 1.3 60.3 + - - +
162C LEU* 3.2 4.3 + - - +
163C LEU* 2.9 28.6 + - - +
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Residues in contact with SER 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLU* 3.3 22.4 + - - -
156C THR* 2.8 23.0 + - - +
157C LEU* 3.1 3.3 + - - -
159C ALA* 1.3 77.6 - - - +
161C GLN* 1.3 53.1 + - - +
163C LEU* 3.7 1.3 - - - +
164C ALA* 2.8 35.7 + - - +
169D MET* 5.4 0.2 - - - +
172D ARG* 3.5 19.0 + - - +
189D ARG* 3.0 38.1 + - - -
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Residues in contact with GLN 161 (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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157C LEU 3.0 17.1 + - - +
158C LEU* 3.3 10.3 - - + +
160C SER* 1.3 78.6 + - - +
162C LEU* 1.3 62.3 + - + +
164C ALA* 3.4 5.2 + - - +
165C PHE* 3.3 19.9 + - - +
196C GLN* 2.3 50.6 - - + +
165D PHE* 3.8 15.0 - - - -
169D MET* 5.4 0.2 - - - +
189D ARG* 2.9 43.7 + - - +
192D LEU* 4.4 11.9 - - + -
193D VAL* 3.4 23.8 - - - +
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 3.9 24.9 - - + -
92C VAL* 4.3 13.7 - - + -
136C LEU* 4.4 15.3 - - + -
140C MET* 3.3 27.8 - - + -
158C LEU 3.0 15.4 + - - +
159C ALA 3.2 6.7 + - - +
161C GLN* 1.3 73.6 - - + +
163C LEU* 1.3 63.2 + - - +
165C PHE* 3.2 7.5 + - - +
166C CYS* 3.1 25.5 + - - -
190C TRP* 4.2 11.9 - - + -
193C VAL* 3.3 33.4 - - + +
196C GLN* 5.9 1.8 - - + +
197C LEU* 4.3 13.9 - - + -
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE* 4.8 6.5 - - + -
129C PHE* 3.7 33.0 - - + +
132C ILE* 4.3 19.3 - - + -
133C GLU* 3.1 31.6 - - + +
136C LEU* 4.7 6.0 - - + +
159C ALA 2.9 17.0 + - - +
160C SER* 3.8 1.8 - - - +
162C LEU* 1.3 77.1 - - - +
164C ALA* 1.3 58.6 + - - +
166C CYS* 3.2 13.5 + - + +
167C GLU* 2.9 37.0 + - + +
172D ARG* 3.1 28.0 - - - +
175D ARG* 4.3 2.7 - - - +
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Residues in contact with ALA 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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160C SER 2.8 22.9 + - - +
161C GLN* 3.7 7.6 - - - +
162C LEU 3.2 0.2 - - - -
163C LEU* 1.3 73.6 - - - +
165C PHE* 1.3 57.3 + - - +
167C GLU* 4.6 0.4 - - - -
168C GLY* 2.8 25.5 + - - -
164D ALA 3.9 2.4 - - - +
165D PHE* 4.6 11.0 - - + +
168D GLY* 3.2 16.6 - - - -
169D MET* 4.0 28.7 - - + +
172D ARG* 4.1 14.3 - - - +
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Residues in contact with PHE 165 (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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92C VAL* 4.0 28.7 - - + -
96C LEU* 4.0 14.1 - - + -
161C GLN 3.3 8.7 + - - +
162C LEU* 3.2 11.6 + - - +
163C LEU 3.2 0.2 - - - -
164C ALA* 1.3 76.8 - - - +
166C CYS* 1.3 67.3 + - - +
168C GLY* 3.2 1.2 + - - -
169C MET* 2.9 57.0 + - + +
186C PHE* 5.3 4.5 - + - -
189C ARG* 4.2 15.5 - - + -
190C TRP* 5.7 0.9 - + - -
193C VAL* 3.9 29.4 - - + -
196C GLN* 5.7 3.6 - - - +
161D GLN* 3.5 36.1 - - - -
164D ALA* 4.5 16.1 - - + +
165D PHE* 5.3 3.5 - - + +
196D GLN* 5.3 1.3 - - - -
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Residues in contact with CYS 166 (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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92C VAL* 3.9 40.6 - - - -
95C ILE* 4.1 23.6 - - + -
96C LEU* 3.9 19.9 - - + +
129C PHE* 6.3 0.4 - - + -
136C LEU* 6.4 0.9 - - - -
162C LEU 3.1 16.9 + - - -
163C LEU* 3.2 16.6 + - + +
165C PHE* 1.3 80.4 - - - +
167C GLU* 1.3 63.0 + - + +
169C MET* 3.2 2.9 + - - +
170C LEU* 3.0 31.5 + - + +
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Residues in contact with GLU 167 (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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110C THR* 5.1 1.1 - - - +
129C PHE* 3.9 25.4 - - + -
163C LEU* 2.9 21.0 + - + +
164C ALA 3.9 3.6 - - - +
166C CYS* 1.3 76.8 - - + +
168C GLY* 1.3 56.2 + - - +
170C LEU* 3.8 6.7 - - + +
171C SER* 2.9 34.6 + - - -
168D GLY* 4.1 10.1 - - - +
171D SER* 3.4 16.2 + - - +
172D ARG* 3.0 29.4 + - - +
175D ARG* 2.6 50.7 + - - -
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Residues in contact with GLY 168 (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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164C ALA 2.8 11.2 + - - -
165C PHE 3.6 1.6 - - - -
166C CYS 3.1 0.2 - - - -
167C GLU* 1.3 75.5 - - - +
169C MET* 1.3 63.3 + - - +
171C SER* 3.5 2.8 + - - -
172C ARG* 3.2 26.3 + - - +
164D ALA* 3.2 31.4 - - - -
167D GLU* 4.2 6.0 - - - +
168D GLY* 3.5 10.5 - - - -
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Residues in contact with MET 169 (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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96C LEU* 4.4 14.1 - - + -
165C PHE* 2.9 47.6 + - + +
166C CYS* 3.8 4.0 - - - +
168C GLY* 1.3 72.5 - - - +
170C LEU* 1.3 62.2 + - - +
172C ARG* 3.3 13.5 + - - +
173C PHE* 3.0 27.3 + - - +
180C TYR 4.6 2.6 - - - +
181C ARG 4.7 4.0 - - - +
182C PRO* 3.4 33.1 - - + +
184C ASP 4.9 0.7 - - - +
189C ARG* 3.6 37.0 - - - +
160D SER 5.5 0.7 - - - +
164D ALA* 3.9 16.2 - - - -
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ILE* 4.2 24.0 - - + +
96C LEU* 4.7 4.5 - - + -
99C GLY* 4.2 15.0 - - - -
106C THR* 3.8 17.4 - - + +
109C LEU* 4.0 28.3 - - + -
110C THR* 3.8 15.7 - - + -
129C PHE* 5.3 7.6 - - + -
166C CYS* 3.0 23.7 + - + +
167C GLU* 3.9 6.3 - - - +
169C MET* 1.3 73.6 - - - +
171C SER* 1.3 67.1 + - - +
173C PHE* 3.2 4.1 + - - +
174C VAL* 2.9 27.2 + - - +
182C PRO* 4.2 24.0 - - + -
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C THR* 3.9 15.3 - - - +
112C HIS* 5.1 8.2 - - - -
167C GLU 2.9 22.4 + - - -
168C GLY* 3.7 7.4 - - - -
169C MET 3.3 0.2 - - - -
170C LEU* 1.3 75.6 - - - +
172C ARG* 1.3 57.8 + - - +
174C VAL* 3.3 4.1 + - - +
175C ARG* 2.9 34.2 + - - +
110D THR 6.0 1.8 - - - -
112D HIS* 6.1 0.5 - - - -
167D GLU* 4.3 16.6 + - - -
171D SER* 3.7 22.9 + - - -
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Residues in contact with ARG 172 (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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168C GLY 3.2 10.6 + - - +
169C MET* 3.6 15.8 - - - +
170C LEU 3.2 0.4 - - - -
171C SER* 1.3 76.2 - - - +
173C PHE* 1.3 57.6 + - - +
175C ARG* 3.3 15.8 - - - +
176C SER* 2.7 37.9 + - - -
180C TYR* 3.3 41.4 - - + +
189C ARG* 6.0 0.4 - - - -
130D GLU* 5.0 0.4 + - - -
133D GLU* 3.2 31.9 + - - -
160D SER* 3.1 44.9 + - - +
163D LEU* 4.1 4.9 - - - +
164D ALA* 4.9 9.1 - - - +
167D GLU* 3.1 28.7 - - - +
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Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C GLY 3.4 23.6 - - - -
100C GLU* 3.7 25.6 - - + -
103C PRO* 4.1 9.4 - - + -
106C THR* 4.1 17.9 - - + -
169C MET 3.0 12.9 + - - +
170C LEU 3.3 8.5 - - - +
172C ARG* 1.3 77.2 - - - +
174C VAL* 1.3 56.1 + - - +
176C SER* 3.1 5.0 + - - -
178C PHE* 2.7 87.0 + + + -
180C TYR 3.2 25.0 + - - +
181C ARG* 3.9 12.6 - - - -
182C PRO* 3.6 22.7 - - + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C THR* 3.7 20.2 - - + -
107C ARG* 4.1 29.2 + - + +
110C THR* 3.5 20.4 - - + +
112C HIS* 3.8 30.5 - - + +
170C LEU 2.9 15.7 + - - +
171C SER* 3.6 7.6 - - - +
173C PHE* 1.3 77.1 - - - +
175C ARG* 1.3 57.9 + - - +
177C GLU* 2.8 34.5 + - - +
178C PHE* 4.1 12.6 - - + -
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Residues in contact with ARG 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C HIS* 6.5 0.4 - - + -
171C SER* 2.9 32.1 + - - +
172C ARG* 3.3 26.7 + - - +
174C VAL* 1.3 74.7 - - - +
176C SER* 1.3 60.5 + - - +
177C GLU* 3.3 9.7 + - - +
180C TYR* 4.3 11.9 - - - -
109D LEU 5.3 1.8 - - - -
110D THR 5.7 6.3 - - - +
122D GLN* 4.0 24.4 - - - +
126D ASN* 2.8 61.5 + - - +
129D PHE* 3.6 38.9 - - - +
130D GLU* 4.7 7.5 + - - -
163D LEU* 4.4 4.9 - - - +
167D GLU* 2.7 40.1 + - - +
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Residues in contact with SER 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ARG 2.7 20.5 + - - -
173C PHE 3.1 6.1 + - - -
175C ARG* 1.3 79.6 - - - +
177C GLU* 1.3 68.9 + - - +
179C LYS* 3.3 19.7 + - - +
180C TYR* 3.1 49.6 + - - +
126D ASN* 4.5 6.7 - - - +
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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