Contacts of the helix formed by residues 141 - 164 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D VAL* 4.7 13.8 - - + +
25D GLU* 3.4 8.9 + - - +
29D THR* 3.8 17.6 + - - +
83D ARG* 2.7 35.2 + - - -
87D LEU* 4.2 6.7 - - - +
139D ALA* 3.5 1.3 - - - +
140D LYS* 1.3 76.4 - - - +
142D ASP* 1.3 67.9 + - - +
143D ASP* 3.9 3.3 + - - +
144D THR* 2.5 33.0 + - - +
145D ALA* 2.9 22.0 + - - +
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Residues in contact with ASP 142 (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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140D LYS 3.3 7.9 + - - +
141D ASP* 1.3 72.5 + - - +
143D ASP* 1.3 69.6 + - - +
145D ALA* 3.1 9.8 + - - +
146D ASP* 2.9 22.8 + - - +
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Residues in contact with ASP 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D ARG* 3.3 38.4 + - - +
141D ASP* 3.3 2.5 + - - -
142D ASP* 1.3 82.3 - - - +
144D THR* 1.3 62.6 + - - +
146D ASP* 3.2 9.8 + - - +
147D ILE* 3.0 29.5 + - + +
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Residues in contact with THR 144 (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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29D THR* 3.2 22.2 - - + +
32D LEU* 5.0 4.5 - - + -
33D LEU* 3.5 29.2 - - + -
83D ARG* 3.6 9.4 + - - +
139D ALA* 4.4 7.4 - - + -
141D ASP* 2.5 33.9 + - - -
143D ASP* 1.3 74.3 - - - +
145D ALA* 1.3 66.7 + - - +
147D ILE* 3.1 10.5 + - - +
148D LEU* 2.9 35.2 + - + +
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Residues in contact with ALA 145 (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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136D ILE* 4.0 24.6 - - + +
139D ALA* 3.9 16.5 - - + +
141D ASP 2.9 12.0 + - - +
142D ASP* 3.4 12.8 - - - +
144D THR* 1.3 76.4 - - - +
146D ASP* 1.3 54.5 + - - +
148D LEU* 3.3 5.1 + - - +
149D THR* 2.6 38.8 + - - +
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Residues in contact with ASP 146 (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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142D ASP 2.9 12.1 + - - +
143D ASP* 3.3 12.6 - - - +
145D ALA* 1.3 76.9 - - - +
147D ILE* 1.3 65.7 + - + +
149D THR* 3.0 8.1 + - - -
150D ALA* 3.0 23.1 + - - +
146F ASP* 4.3 2.9 - - - +
606F TRS 2.8 49.7 + - - -
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Residues in contact with ILE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D LEU* 5.2 2.5 - - + -
76D HIS* 4.7 3.5 + - - +
79D THR* 3.8 31.0 - - + +
80D MET* 3.6 30.3 - - + -
83D ARG* 3.6 40.8 - - + -
143D ASP* 3.0 16.3 + - + +
144D THR* 3.4 8.1 - - + +
146D ASP* 1.3 78.0 - - + +
148D LEU* 1.3 65.5 + - + +
150D ALA* 3.4 7.2 + - - +
151D ALA* 3.1 21.4 + - + +
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Residues in contact with LEU 148 (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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32D LEU* 4.3 7.4 - - + -
33D LEU* 4.6 8.3 - - + -
36D GLN* 4.0 11.2 - - + -
80D MET* 3.8 28.3 - - + -
132D VAL* 3.9 19.5 - - + +
135D ALA* 3.7 33.2 - - + +
136D ILE* 3.9 14.2 - - + +
139D ALA* 4.1 8.3 - - + -
144D THR* 2.9 36.5 + - + +
145D ALA 3.7 3.8 - - - +
147D ILE* 1.3 73.3 - - + +
149D THR* 1.3 56.2 + - - +
151D ALA* 3.3 4.1 + - - +
152D SER* 2.7 35.7 + - - -
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Residues in contact with THR 149 (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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136D ILE* 3.4 25.1 - - + +
145D ALA 2.6 23.5 + - - -
146D ASP* 3.4 8.8 - - - -
148D LEU* 1.3 73.9 - - - +
150D ALA* 1.3 58.9 + - - +
153D ARG* 2.8 32.8 + - - +
142F ASP* 4.2 4.6 - - + +
143F ASP* 3.4 21.4 - - - +
146F ASP* 3.6 37.9 - - + +
606F TRS 5.2 0.2 - - - -
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Residues in contact with ALA 150 (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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76D HIS* 3.4 19.2 - - + +
146D ASP 3.0 11.9 + - - +
147D ILE* 3.6 10.3 - - - +
149D THR* 1.3 76.7 - - - +
151D ALA* 1.3 62.5 + - - +
153D ARG* 3.4 8.9 - - - +
154D ASP* 3.4 17.3 + - - +
146F ASP* 5.2 0.9 - - - -
606F TRS 4.5 19.9 + - - +
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Residues in contact with ALA 151 (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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40D PHE* 3.9 22.2 - - + -
76D HIS* 3.4 31.3 - - + +
80D MET* 5.0 5.6 - - - -
132D VAL* 4.7 3.1 - - + -
147D ILE 3.1 16.6 + - - +
148D LEU* 3.7 7.2 - - - +
150D ALA* 1.3 74.9 - - - +
152D SER* 1.3 66.1 + - - +
154D ASP* 3.1 4.5 + - - +
155D LEU* 3.0 27.9 + - - +
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Residues in contact with SER 152 (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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132D VAL* 4.0 21.2 - - - +
133D ARG* 3.7 18.9 - - - +
136D ILE* 3.6 9.4 - - - -
148D LEU 2.7 22.7 + - - -
149D THR 3.2 0.2 + - - -
151D ALA* 1.3 72.9 - - - +
153D ARG* 1.3 63.4 + - - +
155D LEU* 3.1 1.9 + - - +
156D ASP* 2.9 29.1 + - - +
143F ASP* 2.4 33.9 + - - -
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Residues in contact with ARG 153 (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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149D THR 2.8 15.4 + - - +
150D ALA* 3.4 10.3 - - - +
151D ALA 3.2 0.2 - - - -
152D SER* 1.3 77.1 - - - +
154D ASP* 1.3 64.1 + - - +
156D ASP* 3.6 4.6 + - - +
157D LYS* 3.3 19.1 + - - +
79F THR* 3.5 19.0 - - - +
83F ARG* 5.2 3.6 - - - +
86F GLN* 4.3 4.0 - - - +
143F ASP* 3.8 25.8 - - + +
146F ASP* 3.1 26.8 + - - -
147F ILE* 3.5 44.4 - - + +
150F ALA* 4.9 10.7 - - - +
606F TRS 4.6 7.9 + - - -
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Residues in contact with ASP 154 (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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72D ALA* 4.2 9.4 - - - +
76D HIS* 2.7 31.8 + - + +
150D ALA 3.4 3.9 + - - -
151D ALA 3.1 8.8 + - - +
153D ARG* 1.3 80.9 - - - +
155D LEU* 1.3 61.7 + - + +
157D LYS* 3.0 12.2 + - - +
158D PHE* 2.8 56.8 + - + -
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Residues in contact with LEU 155 (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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40D PHE* 3.3 38.6 - - + -
43D LEU* 3.9 17.5 - - + -
73D LEU* 4.1 14.8 - - + -
76D HIS* 5.5 1.1 - - + -
125D TYR* 4.2 10.4 - - + +
128D VAL* 3.5 29.8 - - + -
129D ALA* 3.8 25.3 - - + +
132D VAL* 4.8 1.8 - - + -
151D ALA* 3.0 23.8 + - + +
152D SER* 3.8 5.6 - - - +
154D ASP* 1.3 77.2 - - + +
156D ASP* 1.3 58.5 + - - +
158D PHE* 3.2 8.1 + - + +
159D LEU* 2.8 31.0 + - - +
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Residues in contact with ASP 156 (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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129D ALA* 3.6 11.3 - - - +
133D ARG* 2.6 34.0 + - - -
152D SER* 2.9 19.4 + - - +
153D ARG 4.0 1.6 - - - +
155D LEU* 1.3 77.0 - - - +
157D LYS* 1.3 62.4 + - - +
159D LEU* 3.6 6.1 + - - +
160D TRP* 3.1 23.7 + - - +
19F ASN* 3.3 16.4 + - - +
83F ARG* 2.6 42.2 + - - +
86F GLN* 3.7 9.5 - - + +
143F ASP* 3.5 3.7 - - - +
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Residues in contact with LYS 157 (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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153D ARG 3.3 12.2 + - - +
154D ASP* 3.0 17.3 + - - +
156D ASP* 1.3 79.2 - - - +
158D PHE* 1.3 72.2 + - + +
160D TRP* 3.2 16.1 + - + +
161D PHE* 2.9 57.6 + - + +
82F GLU* 4.0 20.2 + - - +
86F GLN* 3.8 18.8 + - - +
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Residues in contact with PHE 158 (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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68D GLY 5.6 0.2 - - - -
69D PHE* 3.3 56.3 - + + -
72D ALA* 3.6 32.3 - - + -
73D LEU* 4.1 12.8 - - + -
76D HIS* 5.8 0.2 - + - -
125D TYR* 3.8 25.4 - + + -
154D ASP* 2.8 45.6 + - + +
155D LEU* 3.2 8.0 + - - +
157D LYS* 1.3 88.6 - - + +
159D LEU* 1.3 66.4 + - - +
161D PHE* 2.9 2.3 + - - +
162D ILE* 2.7 29.7 + - - +
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Residues in contact with LEU 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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122D ALA* 3.5 28.9 - - - +
125D TYR* 4.2 12.2 - - + -
126D ALA* 3.9 23.3 - - + +
129D ALA* 4.4 10.3 - - + -
155D LEU 2.8 20.7 + - - +
156D ASP* 3.7 5.4 - - - +
158D PHE* 1.3 71.9 - - - +
160D TRP* 1.3 58.2 + - - +
162D ILE* 3.5 4.1 - - - +
163D GLU* 2.8 57.4 + - + +
17F THR* 4.3 2.5 - - - +
18F ARG 4.2 1.3 - - - -
19F ASN* 3.7 40.6 - - + +
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Residues in contact with TRP 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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156D ASP 3.1 12.4 + - - +
157D LYS* 3.3 10.1 - - + +
159D LEU* 1.3 80.3 - - - +
161D PHE* 1.3 85.9 + + - +
163D GLU* 3.8 8.3 - - - +
164D SER* 2.7 63.7 + - - -
52E TRP* 3.9 20.2 + - - -
54E MET 5.2 2.0 + - - -
55E ARG* 4.2 13.7 - - - +
59E PHE* 4.2 15.3 - + - -
63E HIS* 3.9 15.0 - + - -
17F THR* 5.8 0.9 - - - -
82F GLU* 3.8 39.9 - - + -
85F VAL* 3.2 31.3 - - + +
86F GLN* 3.6 33.7 - - + +
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Residues in contact with PHE 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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65D MET* 4.0 7.2 - - + -
69D PHE* 3.7 29.6 - + + -
157D LYS* 2.9 37.6 + - + +
158D PHE 2.9 7.2 + - - +
160D TRP* 1.3 113.6 - + - +
162D ILE* 1.3 66.0 + - - +
164D SER* 3.5 2.3 + - - -
165D ASN* 2.8 29.9 + - - -
59E PHE* 3.8 13.4 - + - -
60E ILE* 3.5 29.4 - - + -
63E HIS* 3.9 20.9 - + - -
64E GLU* 4.9 4.5 - - - -
82F GLU* 5.7 0.9 - - - -
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Residues in contact with ILE 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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65D MET* 4.4 10.8 - - + -
66D LEU* 4.8 6.1 - - + -
69D PHE* 3.8 15.5 - - + -
118D LEU* 3.3 39.4 - - + +
121D LEU* 4.1 9.4 - - + -
122D ALA* 3.9 12.3 - - + +
125D TYR* 3.5 53.2 - - + -
158D PHE 2.7 19.2 + - - +
159D LEU* 3.5 4.3 - - - +
161D PHE* 1.3 72.9 - - - +
163D GLU* 1.3 64.4 + - - +
165D ASN* 3.0 18.6 + - - +
166D ILE* 3.6 6.8 + - + +
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Residues in contact with GLU 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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122D ALA* 4.3 4.3 - - + -
159D LEU* 2.8 34.4 + - + +
160D TRP* 3.8 7.6 - - - +
162D ILE* 1.3 74.1 - - - +
164D SER* 1.3 57.7 + - - +
166D ILE* 2.9 36.5 + - + +
55E ARG* 4.7 13.7 + - - +
16F TYR* 4.2 4.4 - - - +
17F THR* 2.9 31.7 + - - -
18F ARG* 2.7 59.7 + - - +
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Residues in contact with SER 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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160D TRP* 2.7 49.8 + - - -
161D PHE 3.8 0.7 - - - -
162D ILE 3.2 0.4 - - - -
163D GLU* 1.3 71.8 - - - +
165D ASN* 1.3 56.8 + - - +
166D ILE 3.4 0.2 - - - -
54E MET 4.4 3.1 - - - -
55E ARG* 3.9 19.7 + - - +
56E GLY 2.9 26.3 + - - -
59E PHE* 3.0 45.6 - - - +
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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