Contacts of the helix formed by residues 154 - 176 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D LEU* 1.3 75.1 - - - +
155D GLU* 1.3 69.0 + - - +
156D THR* 2.6 42.9 + - - -
157D LEU* 3.0 25.2 + - + +
158D LEU* 3.1 12.4 + - - +
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Residues in contact with GLU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ARG* 3.8 18.8 - - + +
140D MET* 3.6 37.1 - - + +
141D ARG* 3.8 32.4 + - + +
144D LYS* 4.2 21.5 + - - -
151D TYR* 4.7 14.5 + - + +
153D LEU 3.5 8.1 + - - +
154D ASP* 1.3 78.3 + - - +
156D THR* 1.3 56.0 + - - +
158D LEU* 4.4 3.1 - - - +
159D ALA* 2.7 34.5 + - - +
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Residues in contact with THR 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D GLU* 4.4 4.0 - - - +
137D ARG* 3.8 30.1 + - - +
141D ARG* 4.8 5.0 + - - -
154D ASP* 2.6 25.7 + - - -
155D GLU* 1.3 73.1 - - - +
157D LEU* 1.3 60.1 + - - +
159D ALA* 4.3 0.5 - - - +
160D SER* 3.1 24.9 + - - -
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Residues in contact with LEU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ASP* 4.2 12.1 - - + +
188C ALA* 3.9 36.3 - - + +
189C ARG* 3.6 41.9 + - + +
192C LEU* 4.1 18.2 - - + -
153D LEU* 4.3 23.1 - - + -
154D ASP* 3.0 17.7 + - + +
156D THR* 1.3 79.2 - - - +
158D LEU* 1.3 54.9 - - - +
160D SER* 3.0 7.9 + - - -
161D GLN* 3.0 29.4 + - - +
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C LEU* 3.9 17.7 - - + -
140D MET* 3.6 17.7 - - - +
151D TYR* 3.6 46.0 - - + -
153D LEU* 4.0 18.6 - - + +
154D ASP 3.1 11.2 + - - +
155D GLU* 3.9 4.0 - - - +
157D LEU* 1.3 76.6 - - + +
159D ALA* 1.3 61.3 + - - +
161D GLN* 3.3 6.8 - - + +
162D LEU* 3.0 25.8 + - - +
196D GLN* 3.3 26.5 - - + +
197D LEU* 4.2 11.4 - - + +
198D GLN 3.7 10.1 - - - +
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Residues in contact with ALA 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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133D GLU* 3.9 30.6 - - + +
136D LEU* 3.9 9.2 - - + +
137D ARG* 4.1 12.1 - - - +
140D MET* 3.4 20.8 - - + +
155D GLU 2.7 20.9 + - - +
156D THR 4.3 0.7 - - - +
158D LEU* 1.3 72.3 - - - +
160D SER* 1.3 57.6 + - - +
162D LEU* 3.2 4.8 + - - +
163D LEU* 2.9 26.9 + - - +
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Residues in contact with SER 160 (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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169C MET* 6.4 0.4 - - - -
172C ARG* 3.1 34.4 + - - +
189C ARG* 2.9 39.0 + - - -
133D GLU* 3.4 16.2 + - - -
156D THR* 3.1 14.5 + - - -
157D LEU 3.0 6.6 + - - -
159D ALA* 1.3 73.6 - - - +
161D GLN* 1.3 55.2 + - - +
163D LEU 3.3 0.6 + - - +
164D ALA* 2.8 34.1 + - - +
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Residues in contact with GLN 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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165C PHE* 3.5 15.4 - - - -
189C ARG* 2.9 43.4 + - - +
192C LEU* 4.3 15.6 - - + +
193C VAL* 3.3 23.6 - - - +
157D LEU* 3.0 12.8 + - - +
158D LEU* 3.3 14.6 - - - +
160D SER* 1.3 76.9 + - - +
162D LEU* 1.3 65.1 + - + +
164D ALA* 3.4 5.7 + - - +
165D PHE* 3.2 21.0 + - - +
196D GLN* 2.7 44.7 + - + +
197D LEU* 6.2 0.4 - - + -
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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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88D LEU* 4.3 23.1 - - + -
92D VAL* 4.2 16.4 - - + -
136D LEU* 4.1 13.9 - - + -
140D MET* 3.4 30.1 - - + -
158D LEU 3.0 7.8 + - - +
159D ALA 3.2 8.3 + - - +
161D GLN* 1.3 77.9 - - + +
163D LEU* 1.3 66.1 + - - +
165D PHE* 3.2 9.1 + - + +
166D CYS* 3.1 24.5 + - - -
190D TRP* 4.8 2.2 - - + -
193D VAL* 3.5 29.6 - - + +
196D GLN* 5.0 2.5 - - + +
197D LEU* 3.9 27.1 - - + -
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Residues in contact with LEU 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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172C ARG* 4.1 6.1 - - - +
175C ARG* 4.4 2.2 - - - +
95D ILE* 5.1 4.3 - - + -
129D PHE* 3.7 49.6 - - + +
132D ILE* 4.4 15.5 - - + -
133D GLU* 3.1 31.4 - - + +
136D LEU* 4.5 10.0 - - + +
159D ALA 2.9 13.7 + - - +
160D SER 3.8 3.4 - - - +
162D LEU* 1.3 76.7 - - - +
164D ALA* 1.3 53.4 + - - +
166D CYS* 3.0 15.9 + - + +
167D GLU* 2.8 52.8 + - + +
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Residues in contact with ALA 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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164C ALA 3.9 2.1 - - - +
165C PHE* 4.5 10.8 - - + -
168C GLY* 3.2 22.3 - - - -
169C MET* 3.9 30.1 - - + +
172C ARG* 4.5 5.6 - - - +
160D SER 2.8 22.0 + - - +
161D GLN* 3.6 8.5 - - - +
162D LEU 3.2 0.2 - - - -
163D LEU* 1.3 72.0 - - - +
165D PHE* 1.3 57.5 + - - +
167D GLU* 4.5 2.0 - - - +
168D GLY* 2.9 25.6 + - - -
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Residues in contact with PHE 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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161C GLN* 3.8 29.6 - - - -
164C ALA* 4.6 14.3 - - + +
165C PHE* 5.3 3.3 - - - +
92D VAL* 3.8 30.7 - - + -
96D LEU* 3.9 14.6 - - + -
161D GLN 3.2 9.8 + - - +
162D LEU* 3.2 11.5 + - - +
164D ALA* 1.3 80.2 - - - +
166D CYS* 1.3 59.6 + - - +
168D GLY* 3.4 0.9 + - - -
169D MET* 3.0 59.9 + - + +
186D PHE* 4.9 6.1 - + - -
189D ARG* 4.2 17.3 - - + -
190D TRP* 5.5 0.2 - + - -
193D VAL* 3.9 32.5 - - + -
196D GLN* 5.5 2.7 - - - +
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Residues in contact with CYS 166 (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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92D VAL* 3.9 42.6 - - - -
95D ILE* 4.2 31.2 - - + -
96D LEU* 4.3 9.4 - - + -
129D PHE* 6.1 1.1 - - + -
136D LEU* 6.2 0.9 - - - -
162D LEU 3.1 16.9 + - - -
163D LEU* 3.0 18.2 + - + +
165D PHE* 1.3 75.1 - - - +
167D GLU* 1.3 65.4 + - + +
169D MET* 3.2 3.8 + - - +
170D LEU* 3.0 29.7 + - + +
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Residues in contact with GLU 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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168C GLY* 4.2 11.0 - - - +
171C SER* 4.3 12.0 + - - -
172C ARG* 3.1 21.7 - - - +
175C ARG* 2.7 53.1 + - - +
110D THR* 5.3 0.5 - - - +
129D PHE* 4.0 25.9 - - + -
163D LEU* 2.8 33.2 + - + +
164D ALA 4.0 2.5 - - - +
166D CYS* 1.3 71.4 - - - +
168D GLY* 1.3 57.1 + - - +
170D LEU* 3.3 8.3 + - - +
171D SER* 2.8 32.1 + - - -
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Residues in contact with GLY 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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164C ALA* 3.2 27.1 - - - -
167C GLU* 4.1 5.6 - - - +
168C GLY* 3.5 11.4 - - - -
164D ALA 2.9 12.3 + - - -
165D PHE 3.8 0.9 - - - -
167D GLU* 1.3 76.8 - - - +
169D MET* 1.3 61.2 + - - +
171D SER* 3.5 1.8 + - - -
172D ARG* 3.1 33.2 + - - +
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Residues in contact with MET 169 (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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160C SER* 5.4 0.4 - - - +
164C ALA* 4.0 15.7 - - + -
96D LEU* 3.8 16.4 - - + -
165D PHE* 3.0 51.5 + - + +
166D CYS 3.2 4.9 + - - +
168D GLY* 1.3 76.7 - - - +
170D LEU* 1.3 57.8 + - - +
172D ARG* 3.5 13.3 + - - +
173D PHE* 3.1 25.8 + - - +
180D TYR 4.6 1.9 - - - +
181D ARG 4.6 4.3 - - - +
182D PRO* 3.2 36.1 - - + +
184D ASP 4.7 1.3 - - - +
189D ARG* 3.7 35.7 - - - +
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Residues in contact with LEU 170 (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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95D ILE* 4.2 21.1 - - + +
96D LEU* 4.2 11.0 - - + -
99D GLY* 4.3 13.9 - - - -
106D THR* 4.1 15.2 - - + +
109D LEU* 4.1 27.4 - - + -
110D THR* 3.9 15.3 - - + -
129D PHE* 5.3 9.9 - - + -
166D CYS* 3.0 23.9 + - + +
167D GLU* 3.8 6.5 - - - +
169D MET* 1.3 73.8 - - - +
171D SER* 1.3 65.7 + - - +
173D PHE* 3.1 7.0 + - - +
174D VAL* 3.0 25.3 + - - +
182D PRO* 3.9 22.2 - - + -
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Residues in contact with SER 171 (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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110C THR* 4.8 11.1 + - - +
167C GLU* 3.4 18.1 + - - +
171C SER* 3.7 20.7 + - - -
110D THR* 4.0 12.9 - - - +
112D HIS* 5.2 6.5 - - - -
167D GLU 2.8 18.4 + - - -
168D GLY* 3.6 7.4 - - - -
170D LEU* 1.3 76.5 - - - +
172D ARG* 1.3 56.8 + - - +
174D VAL* 3.2 5.9 + - - +
175D ARG* 2.9 33.5 + - - +
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Residues in contact with ARG 172 (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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133C GLU* 2.9 29.9 + - - -
160C SER* 3.5 22.0 + - - -
163C LEU* 3.1 29.5 - - - +
164C ALA* 4.1 18.2 - - - +
167C GLU* 3.0 41.0 + - - +
168D GLY 3.1 22.5 + - - +
169D MET* 3.7 14.3 - - - +
171D SER* 1.3 73.3 - - - +
173D PHE* 1.3 66.9 + - - +
175D ARG* 3.4 19.5 - - - +
176D SER* 2.8 29.2 + - - -
180D TYR* 4.2 30.9 - - + +
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Residues in contact with PHE 173 (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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99D GLY 3.4 22.9 - - - -
100D GLU* 3.8 24.5 - - + -
103D PRO* 4.1 12.3 - - + -
106D THR* 4.0 18.2 - - + -
169D MET 3.1 13.6 + - - +
170D LEU 3.1 8.3 + - - +
172D ARG* 1.3 73.8 - - - +
174D VAL* 1.3 56.7 + - - +
176D SER* 3.1 7.5 + - - -
178D PHE* 2.8 84.7 + + + -
180D TYR 3.2 25.9 + - - +
181D ARG* 4.0 9.2 - - + -
182D PRO* 3.5 23.3 - - + -
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Residues in contact with VAL 174 (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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106D THR* 3.8 15.5 - - + +
107D ARG* 4.4 24.2 + - + +
110D THR* 3.6 25.1 - - + +
112D HIS* 3.9 30.7 - - + +
170D LEU 3.0 13.4 + - - +
171D SER 3.5 7.2 - - - +
172D ARG 3.2 0.2 - - - -
173D PHE* 1.3 74.2 - - - +
175D ARG* 1.3 66.8 + - - +
177D GLU* 3.0 14.9 + - - -
178D PHE* 4.2 16.3 - - + -
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Residues in contact with ARG 175 (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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109C LEU 5.3 2.0 - - - -
110C THR 5.5 6.5 - - - +
122C GLN* 4.3 20.6 - - - +
126C ASN* 2.9 58.4 + - - +
129C PHE* 3.6 43.9 - - - +
130C GLU* 4.8 7.7 + - - -
133C GLU* 4.8 1.4 + - - -
163C LEU* 4.3 1.0 - - - +
167C GLU* 2.6 43.1 + - - +
112D HIS* 6.0 1.8 + - - +
171D SER* 2.9 33.1 + - - +
172D ARG* 3.4 27.6 - - - +
174D VAL* 1.3 75.1 - - - +
176D SER* 1.3 58.7 + - - +
177D GLU* 3.2 9.2 + - - +
180D TYR* 4.9 10.5 - - - -
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Residues in contact with SER 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C ASN* 4.6 4.7 - - - +
172D ARG 2.8 19.3 + - - -
173D PHE 3.1 5.5 + - - -
175D ARG* 1.3 78.0 - - - +
177D GLU* 1.3 73.2 + - - +
179D LYS* 3.1 28.7 + - - +
180D TYR* 3.0 49.1 + - - +
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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