Contacts of the helix formed by residues 141 - 164 (chain F) in PDB entry 1F33
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 141 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133D ARG* 4.2 12.5 - - - +
21F VAL* 4.7 9.5 - - + +
25F GLU* 3.4 9.8 + - - +
29F THR* 3.8 17.5 + - - +
83F ARG* 2.7 34.5 + - - -
87F LEU* 4.2 6.5 - - + +
139F ALA* 3.6 1.5 - - - +
140F LYS* 1.3 76.8 - - - +
142F ASP* 1.3 67.8 + - - +
143F ASP 3.9 2.6 + - - -
144F THR* 2.6 33.5 + - - +
145F ALA* 2.9 21.6 + - - +
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Residues in contact with ASP 142 (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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133D ARG* 4.3 7.5 - - + +
136D ILE* 3.7 43.3 - - + +
137D GLY* 4.1 10.5 + - - -
149D THR* 4.2 4.5 - - + +
140F LYS 3.3 8.5 + - - +
141F ASP* 1.3 71.2 + - - +
143F ASP* 1.3 64.0 + - - +
145F ALA* 3.0 10.5 + - - +
146F ASP* 2.9 22.0 + - - +
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Residues in contact with ASP 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ARG* 3.9 4.6 - - - -
136D ILE* 3.3 17.9 - - - +
149D THR* 3.4 14.8 - - - +
152D SER* 2.4 38.0 + - - -
153D ARG* 3.8 15.4 - - - +
156D ASP* 3.5 6.4 - - - +
83F ARG* 3.2 35.2 + - - +
141F ASP* 3.3 1.4 + - - -
142F ASP* 1.3 78.9 - - - +
144F THR* 1.3 62.7 + - - +
146F ASP* 3.1 5.0 + - - +
147F ILE* 3.0 27.5 + - - +
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Residues in contact with THR 144 (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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29F THR* 3.1 21.9 - - + +
32F LEU* 5.0 4.3 - - + -
33F LEU* 3.5 28.5 - - + -
83F ARG* 3.6 10.3 - - - +
139F ALA* 4.3 8.1 - - + -
141F ASP* 2.6 32.8 + - - -
143F ASP* 1.3 74.1 - - - +
145F ALA* 1.3 67.1 + - - +
147F ILE* 3.2 10.1 + - - +
148F LEU* 2.9 35.7 + - + +
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Residues in contact with ALA 145 (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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136F ILE* 4.0 24.3 - - + +
139F ALA* 4.0 16.4 - - + +
141F ASP 2.9 11.4 + - - +
142F ASP* 3.0 12.8 + - - +
144F THR* 1.3 76.8 - - - +
146F ASP* 1.3 54.2 + - - +
148F LEU* 3.3 5.1 + - - +
149F THR* 2.7 37.7 + - - -
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Residues in contact with ASP 146 (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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146D ASP* 4.3 3.1 - - - +
149D THR* 3.6 27.3 - - + +
150D ALA 5.1 0.5 + - - -
153D ARG* 3.1 23.6 + - - +
142F ASP 2.9 5.7 + - - +
143F ASP 3.2 9.6 - - - +
145F ALA* 1.3 75.3 - - - +
147F ILE* 1.3 66.2 + - - +
149F THR* 3.0 10.5 + - - +
150F ALA* 2.9 23.4 + - - +
606F TRS 2.4 44.4 + - - -
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Residues in contact with ILE 147 (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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153D ARG* 3.5 37.5 - - + +
33F LEU* 5.2 1.8 - - + -
76F HIS* 4.7 3.2 + - - +
79F THR* 3.8 25.1 - - + +
80F MET* 3.6 30.5 - - + -
83F ARG* 3.7 39.5 - - + -
143F ASP 3.0 17.5 + - - +
144F THR* 3.5 8.7 - - - +
146F ASP* 1.3 75.6 - - - +
148F LEU* 1.3 60.4 + - + +
150F ALA* 3.4 4.2 + - - +
151F ALA* 3.1 26.8 + - + +
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Residues in contact with LEU 148 (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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32F LEU* 4.2 7.9 - - + -
33F LEU* 4.5 8.3 - - + -
36F GLN* 4.0 10.5 - - + -
80F MET* 3.8 28.3 - - + -
132F VAL* 3.9 20.1 - - + +
135F ALA* 3.8 34.3 - - + +
136F ILE* 4.0 13.1 - - + +
139F ALA* 4.1 7.4 - - + -
144F THR* 2.9 35.2 + - + +
145F ALA 3.7 4.0 - - - +
147F ILE* 1.3 73.7 - - + +
149F THR* 1.3 55.9 + - - +
151F ALA* 3.3 3.7 + - - +
152F SER* 2.7 35.9 + - - -
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Residues in contact with THR 149 (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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136F ILE* 3.4 29.6 - - + +
145F ALA* 2.7 24.2 + - - +
146F ASP* 3.0 13.2 + - - +
148F LEU* 1.3 76.7 - - - +
150F ALA* 1.3 58.2 + - - +
152F SER* 3.2 1.6 + - - -
153F ARG* 2.8 42.5 + - - +
606F TRS 5.7 4.3 - - - +
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Residues in contact with ALA 150 (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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153D ARG* 4.9 9.6 - - - +
76F HIS* 3.4 18.9 + - + +
146F ASP 2.9 11.6 + - - +
147F ILE* 3.7 10.3 - - - +
149F THR* 1.3 79.9 - - - +
151F ALA* 1.3 61.4 + - - +
153F ARG* 3.4 9.5 + - - +
154F ASP* 3.3 16.3 + - - +
606F TRS 4.4 17.9 + - - +
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Residues in contact with ALA 151 (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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40F PHE* 3.9 22.2 - - + -
76F HIS* 3.4 32.7 - - + +
80F MET* 5.0 6.3 - - - -
132F VAL* 4.7 3.1 - - + -
147F ILE* 3.1 16.9 + - + +
148F LEU* 3.8 6.7 - - - +
150F ALA* 1.3 73.6 - - - +
152F SER* 1.3 66.5 + - - +
154F ASP* 3.1 4.2 + - - +
155F LEU* 3.0 28.1 + - - +
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Residues in contact with SER 152 (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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132F VAL* 3.9 21.4 - - - +
133F ARG* 3.6 30.4 + - - +
136F ILE* 3.7 16.1 - - - +
148F LEU 2.7 23.0 + - - -
149F THR* 3.5 4.3 - - - -
151F ALA* 1.3 72.9 - - - +
153F ARG* 1.3 65.0 + - - +
155F LEU* 3.1 2.6 + - - +
156F ASP* 2.9 30.9 + - - +
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Residues in contact with ARG 153 (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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149F THR* 2.8 30.3 + - - +
150F ALA* 3.4 10.9 - - - +
152F SER* 1.3 74.1 + - - +
154F ASP* 1.3 62.6 + - - +
156F ASP* 3.8 4.9 + - - +
157F LYS* 3.4 18.9 + - - +
606F TRS 4.4 23.0 + - - -
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Residues in contact with ASP 154 (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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72F ALA* 4.2 8.5 - - - +
76F HIS* 2.7 32.2 + - + +
150F ALA 3.3 4.1 + - - -
151F ALA 3.1 9.2 + - - +
153F ARG* 1.3 80.5 - - - +
155F LEU* 1.3 62.3 + - + +
157F LYS* 3.1 11.2 + - - +
158F PHE* 2.8 57.3 + - + -
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Residues in contact with LEU 155 (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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40F PHE* 3.2 37.7 - - + -
43F LEU* 3.8 16.8 - - + -
73F LEU* 4.2 15.3 - - + -
76F HIS* 5.5 1.1 - - + -
125F TYR* 4.2 9.8 - - + +
128F VAL* 3.4 33.7 - - + -
129F ALA* 3.8 23.1 - - + +
132F VAL* 4.8 1.8 - - + -
151F ALA* 3.0 24.5 + - - +
152F SER* 3.8 5.6 - - - +
154F ASP* 1.3 78.0 - - + +
156F ASP* 1.3 59.3 + - - +
158F PHE* 3.8 7.1 - - + +
159F LEU* 2.8 30.7 + - - +
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Residues in contact with ASP 156 (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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129F ALA* 3.7 11.1 - - - +
133F ARG* 2.6 47.5 + - - -
152F SER* 2.9 20.6 + - - +
153F ARG* 4.1 6.2 - - - +
155F LEU* 1.3 76.7 - - - +
157F LYS* 1.3 60.8 - - - +
159F LEU* 3.6 9.2 + - - +
160F TRP* 3.2 22.7 + - - +
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Residues in contact with LYS 157 (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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153F ARG 3.4 12.7 + - - +
154F ASP* 3.1 17.3 + - - +
156F ASP* 1.3 78.2 - - - +
158F PHE* 1.3 73.2 + - + +
160F TRP* 3.2 26.6 + - + +
161F PHE* 2.8 56.2 + - + +
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Residues in contact with PHE 158 (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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68F GLY 5.4 0.2 - - - -
69F PHE* 3.4 61.7 - + + -
72F ALA* 3.6 32.8 - - + -
73F LEU* 4.1 14.1 - - + -
76F HIS* 5.8 0.2 - + - -
125F TYR* 3.8 19.5 - + + -
154F ASP* 2.8 43.7 + - + +
155F LEU* 3.8 4.9 - - - +
157F LYS* 1.3 90.0 - - + +
159F LEU* 1.3 67.9 + - - +
161F PHE* 2.9 2.3 + + - +
162F ILE* 2.7 29.7 + - - +
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Residues in contact with LEU 159 (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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122F ALA* 3.5 31.2 - - - +
125F TYR* 4.2 10.5 - - + -
126F ALA* 4.0 25.1 - - + +
129F ALA* 4.4 9.4 - - + -
130F ASN* 5.3 6.1 - - - +
133F ARG* 6.2 0.4 - - - +
155F LEU 2.8 18.4 + - - +
156F ASP* 3.8 8.5 - - - +
158F PHE* 1.3 75.4 - - - +
160F TRP* 1.3 59.3 + - - +
162F ILE* 3.1 4.1 + - - +
163F GLU* 2.8 62.8 + - + +
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Residues in contact with TRP 160 (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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156F ASP 3.2 11.5 + - - +
157F LYS* 3.3 24.0 - - + +
158F PHE 3.1 0.2 - - - -
159F LEU* 1.3 80.5 - - - +
161F PHE* 1.3 89.8 + + - +
163F GLU* 3.8 9.3 - - + +
164F SER* 2.7 65.9 + - - -
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Residues in contact with PHE 161 (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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65F MET* 3.9 15.7 - - + -
69F PHE* 3.7 28.9 - + + -
157F LYS* 2.8 42.1 + - + +
158F PHE 2.9 8.2 + - - +
160F TRP* 1.3 115.4 - + - +
162F ILE* 1.3 57.6 + - - +
164F SER* 3.6 6.1 + - - -
165F ASN* 2.7 35.4 + - - -
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Residues in contact with ILE 162 (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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65F MET* 4.5 10.5 - - + -
66F LEU* 4.8 5.4 - - + -
69F PHE* 3.7 16.2 - - + -
118F LEU* 3.3 39.8 - - + +
121F LEU* 4.1 10.3 - - + -
122F ALA* 3.9 12.8 - - + +
125F TYR* 3.6 52.7 - - + -
158F PHE 2.7 17.9 + - - +
159F LEU* 3.5 6.3 - - - +
161F PHE* 1.3 72.3 - - - +
163F GLU* 1.3 64.5 + - - +
165F ASN* 3.0 19.5 + - - +
166F ILE* 3.6 7.3 + - + +
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Residues in contact with GLU 163 (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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122F ALA* 4.3 13.9 - - + +
126F ALA* 5.7 1.6 - - - +
159F LEU* 2.8 49.7 + - + +
160F TRP* 3.8 8.1 - - + +
162F ILE* 1.3 72.7 - - - +
164F SER* 1.3 57.4 + - - +
166F ILE* 2.8 41.4 + - + +
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Residues in contact with SER 164 (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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160F TRP* 2.7 52.8 + - - -
161F PHE* 3.9 8.7 - - - -
162F ILE 3.2 0.2 - - - -
163F GLU* 1.3 72.0 - - - +
165F ASN* 1.3 60.8 + - - +
166F ILE 3.4 3.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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