Contacts of the helix formed by residues 164 - 185 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 4.9 6.3 - - + -
104B VAL* 3.6 23.2 - - + +
156B CYS* 3.5 33.2 - - - -
161B PHE* 3.1 30.7 + + + +
162B LYS 3.5 11.0 + - - -
163B GLY* 1.3 86.2 - - - +
165B ALA* 1.3 63.6 + - - +
166B LEU 3.4 2.7 - - - -
167B TYR* 3.3 16.3 + + + -
168B CYS* 2.9 30.7 + - - -
203B GLN* 5.9 3.4 - - - -
206B ALA* 3.7 28.0 - - + -
210B SER* 3.1 25.6 + - - -
215B MET* 4.1 23.8 - - + +
219B LEU* 4.1 11.7 - - + -
408B CL 4.5 10.1 - - + -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 3.7 13.4 - - + +
180A VAL* 3.8 29.4 - - + +
184A GLU* 4.9 2.0 - - - +
108B PHE* 3.9 23.8 - - + -
111B LEU* 3.9 17.0 - - + +
163B GLY 3.5 4.0 + - - -
164B TRP* 1.3 75.2 - - - +
166B LEU* 1.3 62.4 + - - +
168B CYS* 4.0 1.0 - - - +
169B ALA* 3.0 27.2 + - - +
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.8 22.4 - - + -
177A LEU* 4.8 0.4 - - + -
101B LEU 5.0 2.5 - - - +
102B GLY* 5.2 6.5 - - - -
103B ASP 5.4 4.5 - - - +
111B LEU* 4.1 27.1 - - + +
116B GLN* 4.9 7.0 - - - +
117B VAL* 4.1 16.6 - - + -
120B TYR* 3.3 46.1 - - + -
121B TRP* 3.7 32.8 - - + -
164B TRP 3.4 0.4 - - - -
165B ALA* 1.3 79.7 - - - +
167B TYR* 1.3 58.1 + - - +
169B ALA* 3.9 0.9 - - - +
170B GLY 2.9 24.9 + - - -
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B SER 3.5 22.9 - - - -
101B LEU* 3.7 33.9 + - + +
104B VAL* 5.5 0.2 - - + -
120B TYR* 3.3 8.1 + - - -
124B ASN* 5.9 0.2 - - - -
154B SER* 3.8 3.3 - - - -
156B CYS* 3.6 37.7 - - + -
164B TRP* 3.3 17.8 + + + +
166B LEU* 1.3 78.8 - - - +
168B CYS* 1.3 61.4 + - - +
170B GLY* 3.3 1.9 + - - -
171B LYS* 3.0 44.0 + - + +
202B MET* 4.0 12.7 - - - -
408B CL 3.4 21.8 - - + +
802B NAP 2.7 42.5 + - - -
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Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A MET* 3.5 22.4 - - + +
180A VAL* 4.1 4.0 - - + -
156B CYS* 3.5 30.2 - - - +
159B GLN 3.7 20.4 - - - -
160B PRO* 4.1 0.7 - - - -
161B PHE* 3.8 19.1 - - - -
164B TRP* 2.9 34.0 + - - +
165B ALA 4.1 2.0 - - - +
167B TYR* 1.3 72.9 - - - +
169B ALA* 1.3 57.5 + - - +
171B LYS 3.3 0.5 + - - -
172B ALA* 2.9 30.8 + - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA* 3.6 27.8 - - + +
176A MET* 3.7 11.3 - - - +
177A LEU* 3.7 18.8 - - + +
121B TRP* 3.8 14.6 - - + -
165B ALA 3.0 19.1 + - - +
168B CYS* 1.3 77.1 - - - +
170B GLY* 1.3 58.8 + - - +
172B ALA* 3.3 1.9 + - - +
173B ALA* 3.0 30.0 + - - +
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 4.7 6.5 - - - -
121B TRP* 3.9 10.0 - - - -
124B ASN* 5.3 2.7 - - - -
125B LEU* 3.4 16.6 - - - +
166B LEU 2.9 17.4 + - - -
167B TYR 3.7 1.1 - - - -
169B ALA* 1.3 78.4 - - - +
171B LYS* 1.3 56.4 + - - +
174B ARG* 2.9 38.5 + - - +
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Residues in contact with LYS 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 5.3 3.0 - - - -
124B ASN* 5.5 2.7 + - - -
152B ILE 3.0 21.8 + - - +
153B SER* 4.2 12.3 - - - -
154B SER* 4.0 12.8 - - - -
156B CYS 4.2 0.7 - - - -
157B ALA* 3.5 31.8 - - + +
167B TYR* 3.0 41.0 + - + +
168B CYS 3.9 1.3 - - - +
170B GLY* 1.3 73.3 - - - +
172B ALA* 1.3 66.8 + - - +
174B ARG* 3.4 27.3 + - + +
175B ASP* 3.0 20.4 + - - +
802B NAP 2.9 44.6 + - - -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA* 4.0 25.3 - - + +
176A MET* 4.1 10.8 - - + -
157B ALA* 3.6 24.8 - - - +
168B CYS 2.9 17.8 + - - +
169B ALA 3.8 4.5 - - - +
171B LYS* 1.3 76.8 - - - +
173B ALA* 1.3 62.2 + - - +
175B ASP* 3.5 4.3 + - - +
176B MET* 3.1 22.7 + - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ALA* 3.5 36.7 - - + +
172A ALA* 4.7 0.2 - - - +
173A ALA* 4.0 6.5 - - + +
125B LEU* 3.6 25.6 - - + -
169B ALA 3.0 17.5 + - - +
172B ALA* 1.3 74.7 - - - +
174B ARG* 1.3 58.9 + - - +
176B MET* 3.1 2.4 + - - -
177B LEU* 2.8 34.6 + - - +
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASN* 3.3 28.1 + - - +
98B ALA 3.8 18.5 + - - -
99B GLY* 5.8 0.2 - - - -
123B LEU 5.1 0.6 + - - -
124B ASN* 2.8 41.0 + - - +
125B LEU* 3.9 5.6 - - + -
128B MET* 3.5 29.4 - - + +
151B ASN* 2.9 39.7 + - - +
152B ILE 3.4 8.9 + - - -
170B GLY 2.9 24.2 + - - +
171B LYS* 3.7 32.4 - - + +
172B ALA 3.4 0.2 - - - -
173B ALA* 1.3 76.2 - - - +
175B ASP* 1.3 62.6 + - - +
177B LEU* 3.4 9.8 + - - +
178B PHE* 3.2 26.3 + - - +
802B NAP 4.5 1.2 + - - -
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Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ASN* 3.1 14.7 + - - -
153B SER* 2.7 25.0 + - - -
157B ALA* 3.8 11.8 - - + +
158B LEU* 4.7 5.1 - - + +
171B LYS 3.0 14.0 + - - +
172B ALA* 3.7 5.4 - - - +
173B ALA 3.3 0.2 - - - -
174B ARG* 1.3 75.8 - - - +
176B MET* 1.3 57.1 + - - +
178B PHE 3.4 1.4 + - - -
179B GLN* 2.9 41.4 + - - +
192B ASN* 3.4 19.6 + - - +
252B HIS* 2.8 32.3 + - - +
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Residues in contact with MET 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A CYS 3.6 16.8 - - - +
157A ALA 3.6 18.2 - - - +
158A LEU 3.7 21.1 - - - +
159A GLN 3.8 2.7 - - - +
160A PRO* 3.7 24.5 - - + -
168A CYS* 3.4 40.4 - - + +
169A ALA* 3.6 2.5 - - - +
172A ALA* 4.0 10.1 - - + -
172B ALA 3.1 15.8 + - - +
173B ALA 3.1 5.8 + - - +
175B ASP* 1.3 74.4 - - - +
177B LEU* 1.3 66.1 + - - +
179B GLN* 3.2 14.6 + - - +
180B VAL* 3.0 22.6 + - - +
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.6 15.1 - - + -
121A TRP* 4.7 9.6 - - + -
165A ALA* 3.6 36.1 - - + +
166A LEU 4.4 0.7 - - - +
169A ALA* 3.6 12.3 - - + +
125B LEU* 4.6 8.7 - - + +
128B MET* 4.1 22.4 - - - -
129B LEU* 4.1 35.9 - - + -
173B ALA 2.8 18.7 + - - +
174B ARG* 3.4 10.1 + - - +
176B MET* 1.3 74.6 - - - +
178B PHE* 1.3 63.8 + - + +
180B VAL* 3.1 9.4 + - - +
181B LEU 2.9 23.4 + - - -
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Residues in contact with PHE 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 4.3 9.4 - + - -
96B ASN* 3.5 22.9 - - - -
128B MET* 3.7 21.3 - - + -
132B THR* 3.6 28.5 - - + -
149B VAL* 3.6 18.4 - - + -
150B VAL 3.7 4.0 - - - -
151B ASN* 3.5 33.7 - - + -
174B ARG 3.2 10.8 + - - +
175B ASP 3.9 0.7 - - - +
177B LEU* 1.3 83.1 - - + +
179B GLN* 1.3 61.1 + - - +
181B LEU* 3.4 5.0 + - + +
182B ALA* 2.9 24.6 + - - +
190B VAL* 3.4 32.2 - - + +
191B LEU 4.1 2.0 - - - -
192B ASN* 3.4 22.9 - - - +
250B GLY* 5.1 0.4 - - - -
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Residues in contact with GLN 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU 4.9 2.8 + - - +
160A PRO* 3.6 39.7 - - + +
175B ASP* 2.9 34.3 + - - +
176B MET* 3.2 19.1 + - - +
178B PHE* 1.3 76.9 - - - +
180B VAL* 1.3 60.4 - - - +
182B ALA* 3.5 8.2 + - - +
183B LEU* 3.4 19.6 + - - +
192B ASN* 4.4 1.1 - - - +
250B GLY* 3.6 23.1 - - - +
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Residues in contact with VAL 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PRO* 3.9 18.4 - - + -
161A PHE 3.3 25.1 - - - +
163A GLY 4.1 0.4 - - - +
165A ALA* 3.7 32.3 - - + +
168A CYS* 4.0 18.2 - - + -
176B MET 3.0 18.3 + - - +
177B LEU 3.4 7.6 - - - +
179B GLN* 1.3 73.9 - - - +
181B LEU* 1.3 65.6 + - - +
183B LEU* 3.1 8.3 + - - +
184B GLU* 3.0 39.8 + - - +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 3.5 49.1 - - + -
109A VAL* 5.2 0.7 - - + -
132B THR* 4.0 8.5 - - + -
136B LEU* 3.9 13.0 - - + -
149B VAL* 3.7 30.5 - - + -
177B LEU 2.9 12.7 + - - +
178B PHE* 3.7 12.3 - - + +
179B GLN 3.4 0.2 - - - -
180B VAL* 1.3 77.6 - - - +
182B ALA* 1.3 57.3 + - - +
184B GLU* 3.1 4.2 + - - -
185B GLU* 2.8 56.4 + - + +
188B VAL* 4.9 0.9 - - + -
190B VAL* 4.0 9.4 - - + -
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B PHE 2.9 17.5 + - - +
179B GLN 3.7 5.8 - - - +
180B VAL 3.2 0.2 - - - -
181B LEU* 1.3 76.1 - - - +
183B LEU* 1.3 63.2 + - + +
185B GLU 3.9 13.7 - - - +
186B PRO* 4.0 6.9 - - - +
190B VAL* 3.8 10.7 - - + +
249B SER* 3.7 23.3 + - - +
250B GLY* 3.6 26.2 - - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PRO* 3.5 43.7 - - + +
161A PHE* 4.1 9.4 - - + -
162A LYS* 3.4 44.0 + - + +
179B GLN 3.4 8.2 + - - +
180B VAL 3.1 9.9 + - - +
182B ALA* 1.3 82.2 - - + +
184B GLU* 1.3 61.6 + - - +
186B PRO* 4.1 10.6 - - - +
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Residues in contact with GLU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLY* 3.2 10.7 - - - -
108A PHE* 3.0 36.1 + - + +
162A LYS* 3.7 18.3 - - + +
163A GLY* 2.8 39.8 + - - +
165A ALA* 4.9 1.4 + - - +
211A VAL* 5.6 1.0 - - - +
180B VAL* 3.0 24.0 + - - +
181B LEU* 3.1 6.5 + - - +
183B LEU* 1.3 77.5 - - - +
185B GLU* 1.3 77.4 + - + +
186B PRO* 3.2 9.5 - - - +
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Residues in contact with GLU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A PHE* 5.7 0.7 - - + -
109A VAL* 4.0 24.3 - - + +
136B LEU* 5.3 0.2 - - + -
147B ARG* 3.9 17.5 + - - -
181B LEU* 2.8 32.6 + - + +
182B ALA* 3.9 6.4 - - - +
184B GLU* 1.3 92.7 - - + +
186B PRO* 1.3 61.0 - - - +
187B ASN* 3.1 5.0 - - - +
188B VAL* 2.8 42.2 + - + +
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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