Contacts of the helix formed by residues 164 - 185 (chain D) in PDB entry 1Z6Z
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 TRP 164 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.8 6.1 - - + -
104D VAL* 3.5 24.7 - - + +
156D CYS* 3.5 33.0 - - - -
161D PHE* 3.1 31.9 + + + +
162D LYS 3.6 10.8 + - - -
163D GLY* 1.3 86.3 - - - +
165D ALA* 1.3 57.0 + - - +
166D LEU 3.4 2.0 - - - -
167D TYR* 3.3 16.6 + + + -
168D CYS* 2.9 35.4 + - - -
203D GLN* 5.9 3.4 - - - -
206D ALA* 3.7 28.7 - - + -
210D SER* 3.1 25.2 + - - -
211D VAL 6.2 0.2 - - - -
215D MET* 4.0 23.8 - - - +
219D LEU* 4.1 12.1 - - + -
409D CL 4.6 10.1 - - + -
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Residues in contact with ALA 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.7 13.9 - - + +
180C VAL* 3.8 22.3 - - + +
184C GLU* 4.8 2.7 - - - +
108D PHE* 3.9 28.5 - - + -
111D LEU* 4.0 16.6 - - + +
163D GLY 3.5 3.6 + - - -
164D TRP* 1.3 75.2 - - - +
166D LEU* 1.3 63.1 + - - +
168D CYS* 4.0 0.9 - - - +
169D ALA* 3.0 26.7 + - - +
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Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C LEU* 3.8 25.4 - - + -
177C LEU* 5.0 0.2 - - + -
101D LEU 5.0 2.9 - - - +
102D GLY* 5.2 7.0 - - - -
103D ASP 5.3 4.5 - - - +
111D LEU* 4.1 25.1 - - + +
116D GLN* 5.0 7.2 - - + +
117D VAL* 4.1 16.6 - - + -
120D TYR* 3.3 47.9 - - + -
121D TRP* 3.7 29.3 - - + -
164D TRP 3.4 0.4 - - - -
165D ALA* 1.3 78.7 - - - +
167D TYR* 1.3 58.9 + - - +
169D ALA* 3.9 1.1 - - - +
170D GLY 2.9 24.6 + - - -
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Residues in contact with TYR 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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100D SER 3.6 12.6 - - - -
101D LEU* 3.7 32.4 + - + +
120D TYR* 3.3 18.6 + - - -
124D ASN* 5.9 0.2 - - - -
154D SER* 3.8 2.3 - - - -
156D CYS* 3.6 30.1 - - + -
164D TRP* 3.3 17.9 + + + +
166D LEU* 1.3 80.0 - - - +
168D CYS* 1.3 61.9 + - - +
170D GLY* 3.7 0.7 - - - -
171D LYS* 2.9 40.2 + - + +
202D MET* 4.1 13.6 - - - -
409D CL 3.0 32.2 - - + +
804D NAP 2.7 39.3 + - - -
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Residues in contact with CYS 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C MET* 3.5 18.6 - - + +
180C VAL* 4.1 5.2 - - + -
156D CYS* 3.5 32.3 - - - +
159D GLN 3.7 21.1 - - - -
160D PRO* 4.1 1.1 - - - -
161D PHE* 3.8 18.2 - - - -
164D TRP* 2.9 33.8 + - - +
165D ALA 4.0 2.0 - - - +
167D TYR* 1.3 72.2 - - - +
169D ALA* 1.3 57.9 + - - +
171D LYS 3.3 1.2 + - - -
172D ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA* 3.7 16.7 - - + +
176C MET* 3.7 12.0 - - - +
177C LEU* 3.7 29.6 - - + +
121D TRP* 3.9 15.0 - - + -
165D ALA 3.0 19.1 + - - +
168D CYS* 1.3 75.3 - - - +
170D GLY* 1.3 57.7 + - - +
172D ALA* 3.3 1.4 + - - +
173D ALA* 2.9 30.3 + - - +
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Residues in contact with GLY 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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120D TYR* 4.7 6.5 - - - -
121D TRP* 3.9 10.2 - - - -
124D ASN* 5.3 2.5 - - - -
125D LEU* 3.4 16.4 - - - +
166D LEU 2.9 17.6 + - - -
167D TYR 3.7 0.9 - - - -
169D ALA* 1.3 75.1 - - - +
171D LYS* 1.3 58.0 + - - +
173D ALA* 3.3 0.7 + - - -
174D ARG* 2.9 39.5 + - - +
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Residues in contact with LYS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D GLY* 5.3 2.8 - - - -
124D ASN* 5.6 2.3 + - - -
151D ASN* 5.0 0.2 + - - -
152D ILE 3.0 27.3 + - - +
153D SER* 4.2 14.1 - - - +
154D SER* 4.0 13.0 - - - -
156D CYS* 4.2 0.7 - - + -
157D ALA* 3.6 27.2 - - + +
167D TYR* 2.9 38.4 + - + +
168D CYS 3.8 1.3 - - - +
170D GLY* 1.3 73.0 - - - +
172D ALA* 1.3 67.2 + - - +
174D ARG* 3.4 26.7 + - + +
175D ASP* 3.0 26.5 + - - +
804D NAP 2.9 39.8 + - - -
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Residues in contact with ALA 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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172C ALA* 4.0 16.6 - - + +
176C MET* 3.9 21.3 - - + -
157D ALA* 3.6 23.7 - - - +
168D CYS 2.9 17.0 + - - +
169D ALA 3.7 3.8 - - - +
171D LYS* 1.3 77.2 - - - +
173D ALA* 1.3 61.9 + - - +
175D ASP* 3.5 3.9 + - - +
176D MET* 3.1 23.6 + - - +
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Residues in contact with ALA 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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169C ALA* 3.6 33.6 - - + +
173C ALA* 4.0 8.2 - - + +
125D LEU* 3.5 27.6 - - + -
169D ALA 2.9 17.4 + - - +
172D ALA* 1.3 73.4 - - - +
174D ARG* 1.3 58.8 + - - +
176D MET* 3.1 2.6 + - - +
177D LEU* 2.9 34.6 + - - +
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Residues in contact with ARG 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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96D ASN* 3.2 25.3 + - - +
98D ALA 3.8 18.5 + - - -
123D LEU 5.1 0.6 + - - -
124D ASN* 2.8 41.9 + - - +
125D LEU* 3.9 6.0 - - + +
128D MET* 3.6 32.7 - - + +
151D ASN* 2.9 40.9 + - - +
152D ILE 3.4 9.1 + - - -
170D GLY 2.9 26.5 + - - +
171D LYS* 3.6 28.2 - - - +
173D ALA* 1.3 75.1 - - - +
175D ASP* 1.3 62.9 + - - +
177D LEU* 3.3 9.7 + - - +
178D PHE* 3.1 26.0 + - - +
804D NAP 4.4 1.6 + - - -
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Residues in contact with ASP 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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151D ASN* 3.1 14.2 + - - -
153D SER* 2.5 25.8 + - - -
157D ALA* 3.7 12.2 - - + +
158D LEU* 4.7 4.9 - - + +
171D LYS 3.0 13.3 + - - +
172D ALA* 3.7 5.2 - - - +
174D ARG* 1.3 75.8 - - - +
176D MET* 1.3 57.8 + - - +
178D PHE 3.4 1.2 + - - -
179D GLN* 3.0 40.1 + - - +
192D ASN* 3.4 20.2 + - - +
252D HIS* 2.8 32.4 + - - +
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Residues in contact with MET 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C CYS 3.8 6.7 - - - +
157C ALA 3.5 25.8 - - - +
158C LEU 3.7 23.1 - - - +
159C GLN 3.8 1.8 - - - +
160C PRO* 4.0 21.1 - - + -
168C CYS* 3.5 41.7 - - + +
169C ALA* 3.6 2.2 - - - +
172C ALA* 3.9 9.6 - - + -
172D ALA 3.1 18.3 + - - +
173D ALA 3.1 3.6 + - - +
175D ASP* 1.3 73.8 - - - +
177D LEU* 1.3 65.7 + - - +
179D GLN* 3.1 18.9 + - - +
180D VAL* 2.9 22.6 + - - +
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Residues in contact with LEU 177 (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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108C PHE* 3.7 13.0 - - + -
121C TRP* 4.7 10.5 - - + -
165C ALA* 3.6 36.6 - - + +
166C LEU 4.5 0.7 - - - +
169C ALA* 3.6 12.1 - - + +
125D LEU* 4.7 9.0 - - + +
128D MET* 4.1 22.2 - - - -
129D LEU* 4.1 35.7 - - + -
173D ALA 2.9 19.0 + - - +
174D ARG* 3.5 9.9 - - - +
176D MET* 1.3 75.6 - - - +
178D PHE* 1.3 66.5 + - + +
180D VAL* 3.2 9.5 + - - +
181D LEU 3.0 23.0 + - - -
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Residues in contact with PHE 178 (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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108C PHE* 4.5 8.7 - + - -
96D ASN* 3.4 23.8 - - - -
128D MET* 3.6 21.5 - - + -
132D THR* 3.6 28.9 - - + -
149D VAL* 3.7 15.3 - - + -
150D VAL 3.7 5.2 - - - -
151D ASN* 3.5 33.7 - - + -
174D ARG 3.1 10.5 + - - +
175D ASP 3.8 0.4 - - - +
177D LEU* 1.3 83.4 - - + +
179D GLN* 1.3 60.2 + - - +
181D LEU* 3.4 4.3 + - + +
182D ALA* 2.9 24.9 + - - +
190D VAL* 3.4 31.8 - - + +
191D LEU 4.3 2.2 - - - -
192D ASN* 3.4 21.8 - - - +
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Residues in contact with GLN 179 (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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158C LEU 4.9 2.8 + - - +
160C PRO* 3.9 29.3 - - + +
175D ASP* 3.0 32.3 + - - +
176D MET* 3.1 25.0 + - - +
178D PHE* 1.3 75.2 - - - +
180D VAL* 1.3 61.8 + - - +
182D ALA* 3.4 8.8 + - - +
183D LEU* 3.3 24.1 + - - +
192D ASN* 4.4 1.9 - - - +
250D GLY* 3.6 22.9 - - - +
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Residues in contact with VAL 180 (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 PRO* 3.8 21.8 - - + -
161C PHE 3.4 22.7 - - - +
163C GLY 4.3 0.2 - - - +
165C ALA* 3.8 26.5 - - + +
168C CYS* 3.9 24.7 - - + -
176D MET* 2.9 18.8 + - - +
177D LEU 3.5 7.2 - - - +
179D GLN* 1.3 74.6 - - - +
181D LEU* 1.3 65.0 + - - +
183D LEU* 3.0 8.2 + - - +
184D GLU* 3.0 39.0 + - - +
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Residues in contact with LEU 181 (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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108C PHE* 3.6 48.9 - - + -
109C VAL* 5.4 0.4 - - + -
132D THR* 3.9 8.7 - - + -
136D LEU* 3.9 13.0 - - + -
149D VAL* 3.7 30.3 - - + -
177D LEU 3.0 12.1 + - - +
178D PHE* 3.6 13.2 - - + +
180D VAL* 1.3 76.5 - - - +
182D ALA* 1.3 58.2 + - - +
184D GLU* 4.4 4.0 - - - +
185D GLU* 2.8 56.7 + - + +
188D VAL* 4.9 0.9 - - + -
190D VAL* 4.0 9.0 - - + -
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Residues in contact with ALA 182 (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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178D PHE 2.9 17.8 + - - +
179D GLN 3.6 6.5 - - - +
180D VAL 3.3 0.2 - - - -
181D LEU* 1.3 77.1 - - - +
183D LEU* 1.3 62.9 + - + +
185D GLU 3.8 13.3 - - - +
186D PRO* 4.0 6.8 - - - +
190D VAL* 3.8 11.2 - - + +
249D SER* 3.7 23.4 + - - +
250D GLY* 3.7 25.8 - - - +
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C PRO* 3.4 44.0 - - + +
161C PHE* 4.2 7.6 - - + -
162C LYS* 3.6 39.3 + - + +
179D GLN 3.3 9.0 + - - +
180D VAL* 3.0 9.2 + - - +
182D ALA* 1.3 79.0 - - + +
184D GLU* 1.3 63.3 + - - +
186D PRO* 4.1 11.1 - - - +
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Residues in contact with GLU 184 (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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107C GLY* 3.5 9.2 - - - -
108C PHE* 3.0 36.1 + - + +
162C LYS* 3.6 19.8 - - + +
163C GLY* 2.7 40.8 + - - +
165C ALA* 4.8 1.2 + - - +
211C VAL* 6.0 0.3 - - - +
180D VAL* 3.0 26.2 + - - +
181D LEU* 3.8 5.4 - - - +
183D LEU* 1.3 78.5 - - - +
185D GLU* 1.3 75.6 + - + +
186D PRO* 3.2 9.4 - - - +
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Residues in contact with GLU 185 (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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108C PHE* 5.7 0.9 - - + -
109C VAL* 4.1 24.8 - - + +
136D LEU* 5.2 0.4 - - + -
147D ARG* 3.9 18.0 + - - -
181D LEU* 2.8 31.9 + - + +
182D ALA 3.8 7.0 - - - +
184D GLU* 1.3 92.1 - - + +
186D PRO* 1.3 61.2 - - - +
187D ASN* 3.1 5.0 - - - +
188D VAL* 2.9 42.4 + - + +
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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) + - + + + + + -
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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