Contacts of the helix formed by residues 164 - 185 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E VAL* 4.4 0.2 - - - -
101F LEU* 4.8 6.3 - - + -
104F VAL* 3.6 22.7 - - + +
156F CYS* 3.5 31.6 - - - -
161F PHE* 3.0 31.2 + + + +
162F LYS 3.5 11.7 + - - -
163F GLY* 1.3 85.7 - - - +
165F ALA* 1.3 58.5 + - - +
166F LEU 3.4 2.2 - - - -
167F TYR* 3.3 16.9 + + + -
168F CYS* 2.9 35.0 + - - +
203F GLN* 5.9 3.4 - - - -
206F ALA* 3.7 28.7 - - + -
210F SER* 3.1 24.3 + - - -
211F VAL 6.2 0.2 - - - -
215F MET* 5.5 7.4 - - + +
219F LEU* 4.1 19.3 - - + -
411F CL 4.4 10.3 - - + -
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Residues in contact with ALA 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E LEU* 3.7 16.0 - - + +
180E VAL* 3.9 22.7 - - + +
184E GLU* 4.9 2.9 - - - +
108F PHE* 3.9 29.2 - - + -
111F LEU* 4.0 14.6 - - + -
163F GLY 3.5 4.4 + - - -
164F TRP* 1.3 76.2 - - - +
166F LEU* 1.3 63.4 + - - +
168F CYS* 3.5 1.0 + - - +
169F ALA* 3.0 26.9 + - - +
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Residues in contact with LEU 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E LEU* 3.7 25.1 - - + -
177E LEU* 5.0 0.2 - - + -
101F LEU 4.9 3.1 - - - +
102F GLY* 5.2 6.7 - - - -
103F ASP 5.3 4.0 - - - +
111F LEU* 4.1 26.6 - - + +
116F GLN* 4.9 7.2 - - - +
117F VAL* 4.2 16.8 - - + -
120F TYR* 3.3 47.3 - - + -
121F TRP* 3.7 29.7 - - + -
164F TRP 3.4 0.2 - - - -
165F ALA* 1.3 78.2 - - - +
167F TYR* 1.3 57.7 + - - +
169F ALA* 3.9 1.0 - - - +
170F GLY 2.9 24.6 + - - -
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Residues in contact with TYR 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100F SER 3.5 23.1 - - - -
101F LEU* 3.7 33.4 + - + +
104F VAL* 5.6 0.2 - - + -
120F TYR* 3.3 9.1 + - - -
124F ASN* 5.8 0.2 - - - -
154F SER* 3.8 2.9 - - - -
156F CYS* 3.5 37.7 - - + -
164F TRP* 3.3 16.4 + + + +
166F LEU* 1.3 79.1 - - - +
168F CYS* 1.3 61.6 + - - +
170F GLY* 3.3 1.6 + - - -
171F LYS* 3.0 40.6 + - + +
202F MET* 4.1 12.2 - - - -
411F CL 3.2 25.0 - - + +
806F NAP 2.7 41.2 + - - -
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Residues in contact with CYS 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E MET* 3.6 17.7 - - + -
180E VAL* 4.0 6.1 - - + -
156F CYS* 3.5 33.5 - - - +
159F GLN 3.6 22.4 - - - -
160F PRO* 4.1 0.9 - - - -
161F PHE* 3.8 18.2 - - - -
164F TRP* 2.9 32.4 + - - +
165F ALA 4.0 2.5 - - - +
167F TYR* 1.3 72.4 - - - +
169F ALA* 1.3 57.8 + - - +
171F LYS 3.3 1.2 + - - -
172F ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E ALA* 3.5 18.4 - - + +
176E MET* 3.7 12.6 - - - +
177E LEU* 3.7 28.3 - - + +
121F TRP* 3.9 12.3 - - + -
165F ALA 3.0 18.9 + - - +
166F LEU 3.9 2.7 - - - +
168F CYS* 1.3 76.0 - - - +
170F GLY* 1.3 57.6 + - - +
172F ALA* 3.8 0.7 - - - +
173F ALA* 3.0 29.8 + - - +
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Residues in contact with GLY 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F TYR* 4.8 6.5 - - - -
121F TRP* 4.0 10.2 - - - -
124F ASN* 5.3 2.9 - - - -
125F LEU* 3.5 15.5 - - - +
166F LEU 2.9 17.8 + - - -
167F TYR 3.8 1.1 - - - -
169F ALA* 1.3 73.1 - - - +
171F LYS* 1.3 61.0 + - - +
173F ALA* 3.3 0.9 + - - -
174F ARG* 2.9 39.5 + - - +
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Residues in contact with LYS 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F GLY* 5.4 2.6 - - - -
124F ASN* 5.6 2.5 + - - -
151F ASN* 5.9 0.2 - - - +
152F ILE 2.9 26.8 + - - +
153F SER* 4.2 13.2 - - - -
154F SER* 4.0 12.1 - - - -
156F CYS* 4.2 0.9 - - + -
157F ALA* 3.6 26.8 - - + +
167F TYR* 3.0 41.1 + - + +
168F CYS 3.8 1.6 - - - +
170F GLY* 1.3 74.2 - - - +
172F ALA* 1.3 65.3 + - - +
174F ARG* 3.3 25.5 + - + +
175F ASP* 3.0 26.2 + - - +
806F NAP 3.0 39.1 + - - -
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Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E ALA* 4.2 17.0 - - + +
176E MET* 4.0 20.9 - - + -
157F ALA* 3.6 24.6 - - - +
168F CYS 2.9 17.8 + - - +
169F ALA 3.8 4.3 - - - +
171F LYS* 1.3 75.6 - - - +
173F ALA* 1.3 63.1 + - - +
175F ASP* 3.5 3.5 + - - +
176F MET* 3.1 23.4 + - - +
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Residues in contact with ALA 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E TRP* 5.5 0.2 - - + -
169E ALA* 3.7 33.0 - - + +
173E ALA* 4.1 6.7 - - + +
125F LEU* 3.5 27.8 - - + -
169F ALA 3.0 18.1 + - - +
172F ALA* 1.3 75.2 - - - +
174F ARG* 1.3 60.1 + - - +
176F MET* 3.1 2.3 + - - +
177F LEU* 2.8 34.5 + - - +
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Residues in contact with ARG 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ASN* 3.2 24.9 + - - +
98F ALA 3.8 22.1 + - - -
123F LEU 5.1 0.6 + - - -
124F ASN* 2.8 40.8 + - - +
125F LEU* 3.9 5.4 - - + -
128F MET* 3.6 32.1 - - + +
151F ASN* 2.9 39.0 + - - +
152F ILE 3.5 7.7 + - - -
170F GLY 2.9 25.4 + - - +
171F LYS* 3.3 28.0 + - + +
173F ALA* 1.3 75.5 - - - +
175F ASP* 1.3 63.6 + - - +
177F LEU* 3.4 10.1 + - - +
178F PHE* 3.1 26.3 + - - +
806F NAP 4.5 1.4 + - - -
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Residues in contact with ASP 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F ASN* 3.0 15.4 + - - -
153F SER* 2.7 23.2 + - - -
157F ALA* 3.8 10.4 - - + +
158F LEU* 4.7 4.8 - - + +
171F LYS 3.0 13.6 + - - +
172F ALA* 3.8 4.9 - - - +
174F ARG* 1.3 77.0 - - - +
176F MET* 1.3 56.6 + - - +
178F PHE 3.4 0.3 + - - -
179F GLN* 2.9 39.9 + - - +
192F ASN* 3.3 21.8 + - - +
252F HIS* 2.7 33.3 + - - +
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Residues in contact with MET 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E CYS 3.9 5.8 - - - +
157E ALA 3.7 23.3 - - - +
158E LEU 3.8 22.7 - - - +
159E GLN 4.0 1.3 - - - +
160E PRO* 3.9 31.2 - - + -
168E CYS* 3.6 35.2 - - + +
169E ALA* 3.7 2.9 - - - +
172E ALA* 4.0 9.6 - - + -
172F ALA 3.1 17.9 + - - +
173F ALA 3.1 3.5 + - - +
175F ASP* 1.3 73.9 - - - +
177F LEU* 1.3 63.9 + - - +
179F GLN* 3.2 17.4 + - - +
180F VAL* 3.0 23.4 + - + +
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Residues in contact with LEU 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E PHE* 3.6 15.1 - - + -
121E TRP* 4.8 7.4 - - + -
165E ALA* 3.8 35.0 - - + +
166E LEU 4.7 0.2 - - - +
169E ALA* 3.8 12.5 - - + +
125F LEU* 4.6 12.3 - - + +
128F MET* 4.1 22.9 - - - -
129F LEU* 4.1 37.0 - - + -
173F ALA 2.8 20.9 + - - +
174F ARG* 3.6 8.1 - - - +
176F MET* 1.3 74.4 - - - +
178F PHE* 1.3 64.6 + - + +
180F VAL* 3.1 9.1 + - - +
181F LEU 2.9 23.2 + - - -
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Residues in contact with PHE 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E PHE* 4.7 4.9 - + - -
96F ASN* 3.4 24.0 - - - -
128F MET* 3.7 21.8 - - + -
132F THR* 3.6 28.3 - - + -
149F VAL* 3.7 15.5 - - + -
150F VAL 3.7 5.8 - - - -
151F ASN* 3.6 34.1 - - + -
174F ARG 3.1 11.5 + - - +
175F ASP 3.9 0.2 - - - +
177F LEU* 1.3 82.2 - - + +
179F GLN* 1.3 61.2 + - - +
181F LEU* 3.7 8.6 - - + +
182F ALA* 3.0 24.3 + - - +
190F VAL* 3.3 31.9 - - + +
191F LEU 4.1 1.8 - - - -
192F ASN* 3.4 21.8 - - - +
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Residues in contact with GLN 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E LEU 5.1 2.5 + - - +
160E PRO* 4.0 28.2 - - + +
175F ASP* 2.9 31.9 + - - +
176F MET* 3.2 25.2 + - - +
178F PHE* 1.3 76.1 - - - +
180F VAL* 1.3 62.0 + - - +
182F ALA* 3.5 8.2 + - - +
183F LEU* 3.4 23.7 + - - +
192F ASN* 4.4 1.7 - - - +
250F GLY* 3.6 22.7 - - - +
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Residues in contact with VAL 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E PHE* 4.9 0.4 - - + -
160E PRO* 3.8 24.7 - - + -
161E PHE 3.7 20.4 - - - +
163E GLY 4.4 0.4 - - - +
165E ALA* 3.9 32.3 - - + +
168E CYS* 4.2 13.9 - - + -
176F MET* 3.0 18.8 + - - +
177F LEU* 3.1 7.4 + - - +
179F GLN* 1.3 74.1 - - - +
181F LEU* 1.3 65.6 + - - +
183F LEU* 3.0 8.2 + - - +
184F GLU* 3.0 41.5 + - + +
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Residues in contact with LEU 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E PHE* 3.7 37.2 - - + -
109E VAL* 5.4 1.1 - - + -
132F THR* 3.9 20.4 - - + -
136F LEU* 3.9 15.0 - - + -
149F VAL* 3.7 29.6 - - + -
177F LEU 2.9 14.0 + - - +
178F PHE* 3.7 13.2 - - + +
179F GLN 3.4 0.2 - - - -
180F VAL* 1.3 76.6 - - - +
182F ALA* 1.3 57.6 + - - +
184F GLU* 3.1 4.3 + - + -
185F GLU* 2.8 53.6 + - + +
188F VAL* 4.9 0.9 - - + -
190F VAL* 4.0 8.7 - - + -
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Residues in contact with ALA 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F PHE 3.0 17.4 + - - +
179F GLN 3.7 5.2 - - - +
180F VAL 3.3 0.2 - - - -
181F LEU* 1.3 75.4 - - - +
183F LEU* 1.3 62.2 - - + +
185F GLU 3.9 14.6 - - - +
186F PRO* 4.0 6.9 - - - +
190F VAL* 3.8 11.4 - - + +
249F SER* 3.7 22.8 + - - +
250F GLY* 3.7 26.2 - - - +
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Residues in contact with LEU 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160E PRO* 3.8 41.7 - - + +
161E PHE* 4.5 7.6 - - + +
162E LYS* 3.9 37.5 - - + +
179F GLN 3.4 8.4 + - - +
180F VAL* 3.0 9.4 + - - +
182F ALA* 1.3 79.2 - - + +
184F GLU* 1.3 61.9 + - - +
186F PRO* 4.1 11.4 - - - +
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Residues in contact with GLU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E GLY* 3.5 8.5 - - - -
108E PHE* 2.9 40.7 + - + +
109E VAL 4.8 0.3 + - - -
162E LYS* 4.0 17.4 - - + -
163E GLY* 3.1 36.8 + - - +
165E ALA* 4.9 1.0 - - - +
180F VAL* 3.0 25.9 + - - +
181F LEU* 3.1 5.8 + - - +
183F LEU* 1.3 77.5 - - - +
185F GLU* 1.3 75.6 + - + +
186F PRO* 3.3 8.2 - - - +
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Residues in contact with GLU 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E PHE* 5.9 0.4 - - + -
109E VAL* 4.0 24.3 - - + +
136F LEU* 5.3 0.7 - - + -
147F ARG* 3.9 18.2 + - - -
181F LEU* 2.8 31.7 + - + +
182F ALA* 3.9 5.9 - - - +
184F GLU* 1.3 90.6 - - + +
186F PRO* 1.3 60.7 - - - +
187F ASN* 3.1 5.1 - - - +
188F VAL* 2.8 43.7 + - + +
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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