Contacts of the helix formed by residues 129 - 162 (chain N) in PDB entry 3Q84
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 PHE 129 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N ASP* 3.3 27.8 + - + -
36N HIS* 3.4 52.9 - + + -
121N TYR* 3.7 28.5 - + + -
122N HIS 3.3 17.5 - - - +
123N LYS* 4.1 17.7 - - + -
124N GLN* 4.2 1.8 - - - -
128N GLY* 1.3 76.9 - - - -
130N LYS* 1.3 67.7 + - - +
131N GLU* 3.9 9.6 - - - +
132N THR* 2.9 27.0 + - - +
133N LYS* 3.0 12.6 + - - +
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Residues in contact with LYS 130 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122N HIS* 2.7 36.0 + - + +
124N GLN* 4.1 22.6 - - + +
128N GLY 3.7 1.6 + - - -
129N PHE* 1.3 70.1 - - - +
131N GLU* 1.3 68.6 + - - +
133N LYS* 3.2 2.3 + - - +
134N GLU* 2.8 66.8 + - + +
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Residues in contact with GLU 131 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ILE* 4.0 18.9 - - + +
120N ALA 3.1 23.8 - - - +
121N TYR* 3.7 3.2 - - + -
122N HIS* 3.0 45.5 + - - -
129N PHE* 3.9 5.1 - - + +
130N LYS* 1.3 85.4 + - - +
132N THR* 1.3 63.7 + - - +
134N GLU* 3.4 8.8 + - - +
135N ALA* 3.0 24.3 + - - +
237N PHE* 4.0 19.7 - - + -
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Residues in contact with THR 132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 3.5 29.8 - - + +
32N ILE* 3.6 17.1 - - + +
33N ASP* 2.8 38.6 + - - +
128N GLY* 5.6 1.3 - - - -
129N PHE* 2.9 25.9 + - - +
131N GLU* 1.3 73.5 - - - +
133N LYS* 1.3 58.6 + - - +
135N ALA* 3.3 4.7 + - - +
136N GLU* 2.9 29.9 + - + +
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Residues in contact with LYS 133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124N GLN* 4.0 24.5 - - - +
129N PHE 3.0 10.5 + - - +
130N LYS 3.5 7.4 - - - +
132N THR* 1.3 74.2 - - - +
134N GLU* 1.3 59.0 + - + +
136N GLU* 2.9 12.8 + - + +
137N ASP* 2.7 46.8 + - - +
140N ARG* 3.3 27.2 - - - +
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Residues in contact with GLU 134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130N LYS* 2.8 51.1 + - + +
131N GLU* 3.7 8.9 - - - +
133N LYS* 1.3 77.3 - - + +
135N ALA* 1.3 59.0 + - - +
137N ASP* 3.8 10.8 + - - +
138N GLY* 3.2 17.5 + - - -
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Residues in contact with ALA 135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29N VAL* 4.7 11.2 - - + -
32N ILE* 4.7 10.1 - - + -
131N GLU 3.0 13.8 + - - +
132N THR 3.6 7.2 - - - +
134N GLU* 1.3 74.6 - - - +
136N GLU* 1.3 66.5 - - - +
138N GLY* 2.8 14.0 + - - -
139N PHE* 3.0 21.5 + - + -
230N VAL* 4.4 4.4 - - - +
234N CYS* 4.2 25.4 - - - -
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Residues in contact with GLU 136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25N TYR* 3.6 24.3 + - - -
26N LYS* 5.6 2.1 - - - +
29N VAL* 3.7 30.5 - - + +
132N THR* 2.9 14.6 + - + +
133N LYS* 2.9 22.5 + - + +
135N ALA* 1.3 71.0 - - - +
137N ASP* 1.3 59.3 + - - +
139N PHE* 3.6 3.6 + - - +
140N ARG* 3.2 47.4 + - - +
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Residues in contact with ASP 137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133N LYS* 2.7 33.1 + - - +
134N GLU* 3.8 10.3 - - - +
136N GLU* 1.3 69.1 - - - +
138N GLY* 1.3 67.0 + - - +
140N ARG* 3.1 50.7 + - - +
141N LYS* 3.1 13.0 + - - +
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Residues in contact with GLY 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134N GLU 3.2 8.6 + - - -
135N ALA* 2.8 11.8 + - - -
137N ASP* 1.3 76.0 - - - +
139N PHE* 1.3 64.6 + - - +
141N LYS* 3.5 6.5 - - - +
142N ALA* 3.2 21.1 + - - +
230N VAL* 4.2 21.6 - - - +
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Residues in contact with PHE 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N PHE* 3.9 18.6 - + - -
25N TYR* 3.1 53.6 - + + -
28N THR* 4.2 17.9 - - + -
29N VAL* 4.5 6.7 - - + -
135N ALA* 3.0 20.7 + - + -
136N GLU 4.0 2.5 - - - +
138N GLY* 1.3 75.7 - - - +
140N ARG* 1.3 55.9 + - - +
142N ALA 2.8 22.7 + - - -
143N GLN* 2.9 12.1 + - - +
227N MSE 3.3 36.2 - - + +
230N VAL* 3.4 26.7 - - + -
231N PHE* 3.9 18.4 - - + -
234N CYS* 4.2 16.2 - - - -
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Residues in contact with ARG 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N TYR* 4.2 14.5 + - - +
133N LYS* 3.3 28.7 - - - +
136N GLU* 3.2 28.5 + - - +
137N ASP* 3.1 44.9 + - - +
139N PHE* 1.3 76.7 - - - +
141N LYS* 1.3 76.4 + - + +
143N GLN* 2.9 15.3 + - - +
144N LYS* 2.9 17.1 + - - +
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Residues in contact with LYS 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137N ASP 3.3 14.4 - - - +
138N GLY* 3.5 7.0 - - - +
140N ARG* 1.3 81.2 - - + +
142N ALA* 1.3 65.4 + - + +
143N GLN 2.9 5.9 + - - -
144N LYS* 2.9 23.4 + - + +
145N PRO* 3.5 6.2 - - - +
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Residues in contact with ALA 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138N GLY 3.2 10.1 + - - +
139N PHE 2.8 6.7 + - - -
141N LYS* 1.3 80.3 - - + +
143N GLN* 1.3 56.8 + - - +
144N LYS 3.6 0.4 - - - -
145N PRO* 4.6 9.2 - - - +
223N TYR* 3.9 15.8 - - - -
226N ASN* 3.6 34.9 - - + +
227N MSE 3.3 26.6 - - + +
230N VAL* 5.1 3.8 - - + -
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Residues in contact with GLN 143 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19N PHE 5.4 2.4 + - - -
20N TRP 4.7 0.4 + - - -
21N GLU 5.2 0.8 + - - -
22N VAL* 2.9 37.3 - - + +
23N GLY 3.1 15.1 + - - +
25N TYR* 3.8 17.5 - - + +
139N PHE 2.9 13.2 + - - +
140N ARG* 2.9 10.0 + - - +
141N LYS 2.9 1.0 - - - -
142N ALA* 1.3 82.2 - - - +
144N LYS* 1.3 53.6 + - - +
145N PRO 3.5 1.1 - - - -
146N TRP* 4.1 4.3 - - + -
147N ALA* 2.7 39.3 + - + +
223N TYR* 3.2 32.4 + - + -
227N MSE 3.5 18.1 - - - -
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Residues in contact with LYS 144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N ARG 2.9 8.5 + - - +
141N LYS* 2.9 15.3 + - - +
143N GLN* 1.3 73.5 - - - +
145N PRO* 1.4 77.9 - - + +
147N ALA* 2.8 17.9 + - + +
148N LYS* 2.9 41.3 + - + +
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Residues in contact with PRO 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141N LYS 3.5 9.2 - - - +
142N ALA* 4.7 9.0 - - - +
143N GLN 4.5 0.2 - - - +
144N LYS* 1.4 96.1 - - + +
146N TRP* 1.3 61.9 + - + +
148N LYS* 3.1 21.7 + - + +
149N LYS* 3.1 32.7 + - + +
219N THR* 5.4 3.4 - - - +
222N GLN* 6.5 0.9 - - + -
223N TYR* 6.6 0.7 - - - -
226N ASN* 5.7 4.0 - - - +
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Residues in contact with TRP 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297M MSE 4.9 5.4 - - + -
299M TRP* 3.4 35.7 - + - -
300M PRO* 4.5 13.9 - - + -
20N TRP 4.2 4.9 + - - -
22N VAL* 4.3 15.4 - - + +
143N GLN* 3.7 8.7 + - + +
144N LYS 3.3 0.6 - - - -
145N PRO* 1.3 81.6 - - + +
147N ALA* 1.3 63.2 + - - +
149N LYS* 3.5 6.6 + - - +
150N MSE 3.0 64.7 + - + +
216N VAL* 4.2 12.3 - - + -
219N THR* 4.2 13.0 - - + +
220N THR* 3.4 22.9 - - - -
223N TYR* 3.4 66.4 + + + -
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Residues in contact with ALA 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N VAL* 4.7 13.0 - - + -
143N GLN* 2.7 32.9 + - + +
144N LYS* 2.8 11.5 + - + +
146N TRP* 1.3 74.3 - - - +
148N LYS* 1.3 65.2 + - + +
150N MSE 3.1 20.1 - - - +
151N LYS* 3.2 22.2 + - - +
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Residues in contact with LYS 148 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144N LYS* 2.9 51.9 + - + +
145N PRO* 3.3 13.5 - - + +
147N ALA* 1.3 71.2 - - + +
149N LYS* 1.3 58.4 + - + +
150N MSE 2.7 15.1 + - - -
151N LYS* 2.8 29.6 + - + +
152N GLU* 3.0 25.9 + - + +
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Residues in contact with LYS 149 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145N PRO* 3.1 34.8 + - + +
146N TRP* 3.8 8.7 - - - +
148N LYS* 1.3 80.3 - - + +
150N MSE 1.3 67.5 + - + +
152N GLU* 3.5 20.2 + - - +
153N LEU* 2.8 29.6 + - - +
212N VAL* 4.7 5.5 - - + +
215N ASP* 3.0 35.0 + - + +
216N VAL* 4.1 19.0 - - + +
219N THR* 3.5 34.7 + - + -
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Residues in contact with MSE 150 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300M PRO* 5.0 10.5 - - - -
22N VAL* 3.9 26.0 - - + -
146N TRP* 3.0 73.9 + - + +
147N ALA* 3.1 16.4 - - - +
148N LYS 2.7 5.3 + - - -
149N LYS* 1.3 84.0 - - + +
151N LYS* 1.3 60.8 + - - +
153N LEU* 3.6 20.4 + - - +
154N GLU* 3.3 19.2 + - - +
216N VAL* 4.2 9.0 - - + -
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Residues in contact with LYS 151 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147N ALA* 3.2 22.3 + - - +
148N LYS* 2.8 26.2 + - + +
150N MSE 1.3 75.5 - - - +
152N GLU* 1.3 55.4 + - + +
154N GLU* 2.8 10.1 + - - +
155N ALA* 2.8 34.3 + - - +
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Residues in contact with GLU 152 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N LYS* 3.0 22.4 + - + +
149N LYS* 3.5 29.7 + - - +
151N LYS* 1.3 78.3 - - + +
153N LEU* 1.3 61.9 + - - +
155N ALA* 3.4 6.8 - - - +
156N ALA* 2.9 26.3 + - - +
212N VAL* 4.2 23.4 - - + +
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Residues in contact with LEU 153 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300M PRO* 4.4 17.5 - - + -
301M GLN 5.5 1.6 - - - +
149N LYS 2.8 20.9 + - - +
150N MSE 3.7 18.8 - - - +
151N LYS 3.2 0.2 - - - -
152N GLU* 1.3 73.9 - - - +
154N GLU* 1.3 74.4 + - - +
156N ALA* 3.6 1.8 - - - +
157N LYS* 2.6 49.6 + - - +
209N TYR* 4.7 12.8 - - + +
212N VAL* 4.1 16.1 - - + +
213N LEU* 3.7 30.3 - - + -
216N VAL* 5.1 6.7 - - + -
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Residues in contact with GLU 154 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 6.5 1.1 - - + -
150N MSE 3.3 9.2 + - - +
151N LYS* 2.8 13.4 + - - +
153N LEU* 1.3 91.1 - - - +
155N ALA* 1.3 68.4 + - - +
157N LYS* 3.7 26.1 - - - +
158N LYS* 3.6 25.6 + - + +
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Residues in contact with ALA 155 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151N LYS 2.8 12.4 + - - +
152N GLU* 3.4 13.0 - - - +
154N GLU* 1.3 80.1 - - - +
156N ALA* 1.3 59.4 + - - +
158N LYS* 3.2 1.7 + - - +
159N ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 156 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152N GLU 2.9 15.3 + - - +
153N LEU* 4.1 2.2 - - - +
155N ALA* 1.3 74.9 - - - +
157N LYS* 1.3 66.1 + - - +
159N ALA* 3.8 9.7 - - - +
160N TYR* 3.2 25.3 + - - +
208N LYS* 3.5 31.6 - - + +
209N TYR* 4.2 20.0 - - + +
212N VAL* 5.5 5.6 - - + -
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Residues in contact with LYS 157 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301M GLN 5.5 1.6 + - - -
303M GLU* 3.4 28.9 - - - +
153N LEU* 2.6 34.1 + - + +
154N GLU* 3.7 32.8 - - - +
155N ALA 3.2 0.2 - - - -
156N ALA* 1.3 73.1 - - - +
158N LYS* 1.3 59.5 - - + +
160N TYR* 4.3 1.7 - - - +
161N HIS* 2.6 53.3 + - + +
209N TYR* 3.8 28.4 + - + +
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Residues in contact with LYS 158 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154N GLU* 3.6 14.8 + - + +
155N ALA 3.2 6.0 + - - +
157N LYS* 1.3 83.0 - - + +
159N ALA* 1.3 65.9 + - - +
160N TYR 2.8 6.9 + - - -
161N HIS* 3.7 12.1 - - + +
162N LEU* 2.9 26.6 + - - +
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Residues in contact with ALA 159 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155N ALA 2.9 19.4 + - - +
156N ALA* 3.8 12.6 - - - +
158N LYS* 1.3 74.8 - - - +
160N TYR* 1.3 56.6 + - - +
162N LEU* 3.4 26.9 - - - +
205N THR* 3.6 14.7 - - + +
208N LYS* 4.5 16.4 - - + +
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Residues in contact with TYR 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156N ALA 3.2 15.1 + - - +
157N LYS 4.3 1.3 - - - +
158N LYS 2.8 0.6 - - - -
159N ALA* 1.3 78.6 - - + +
161N HIS* 1.3 63.3 + - - +
162N LEU* 3.2 3.2 + - - -
163N ALA* 3.5 16.5 + - - +
202N VAL* 5.3 3.8 - - - +
205N THR* 3.6 36.2 + - - +
206N GLN* 4.4 7.2 - - + +
208N LYS* 6.0 0.2 - - - -
209N TYR* 4.5 12.1 - - + -
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Residues in contact with HIS 161 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303M GLU* 2.9 31.5 + - + +
304M GLU 4.0 13.9 + - - -
157N LYS* 2.6 56.8 + - + +
158N LYS* 3.0 14.6 + - + +
160N TYR* 1.3 75.1 - - - +
162N LEU* 1.3 65.0 + - - +
163N ALA* 3.1 2.2 + - - -
164N CYS* 3.3 32.8 + - - +
209N TYR* 4.8 4.5 - + - -
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Residues in contact with LEU 162 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158N LYS 2.9 13.1 + - - +
159N ALA* 3.4 28.3 - - - +
160N TYR 5.0 0.7 - - - +
161N HIS* 1.3 77.2 - - - +
163N ALA* 1.3 75.2 + - + +
164N CYS* 2.8 16.1 + - - -
166N GLU* 3.5 20.0 + - + +
201N ASP* 6.4 2.5 - - + -
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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).
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