Contacts of the helix formed by residues 126 - 155 (chain D) in PDB entry 2NS8
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 SER 126 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLY 3.9 2.0 + - - -
125D PHE* 1.3 73.7 - - - +
127D LEU* 1.3 53.7 + - - +
128D GLU* 3.7 7.9 + - - +
129D ASN* 2.9 37.6 + - - +
130D ALA 2.7 31.5 + - - -
201D LEU* 5.3 0.6 - - - +
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Residues in contact with LEU 127 (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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169C LEU* 4.4 19.1 - - + +
172C GLN* 4.4 17.5 - - + +
173C ALA* 4.2 17.7 - - - +
176C LEU* 5.3 4.7 - - + -
117D LEU* 4.1 35.9 - - + -
121D THR* 3.9 23.1 - - + +
125D PHE 3.7 1.4 + - - -
126D SER* 1.3 70.5 - - - +
128D GLU* 1.3 65.5 + - - +
130D ALA* 3.1 4.2 + - + +
131D LEU* 2.9 43.0 + - + +
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C LEU* 3.7 33.9 - - + +
180C GLN* 4.0 5.9 - - - +
126D SER* 3.2 8.6 - - - +
127D LEU* 1.3 81.0 - - - +
129D ASN* 1.3 65.6 + - - +
131D LEU* 3.3 5.6 - - - +
132D TYR* 3.2 59.8 + - + +
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Residues in contact with ASN 129 (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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188C HIS* 3.3 33.4 + - - +
125D PHE* 3.8 17.8 - - + -
126D SER* 2.9 31.3 + - - +
128D GLU* 1.3 78.8 - - - +
130D ALA* 1.3 66.0 + - - +
132D TYR* 3.3 9.0 + - - +
133D ALA* 3.0 24.6 + - - +
200D GLN* 5.7 4.6 + - - +
201D LEU* 5.6 6.0 - - + +
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Residues in contact with ALA 130 (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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117D LEU* 4.5 11.4 - - + +
120D LEU* 4.0 21.5 - - + +
121D THR* 4.3 7.9 - - + -
125D PHE* 3.8 20.7 - - + +
126D SER 2.7 17.0 + - - +
127D LEU* 3.3 13.9 - - + +
129D ASN* 1.3 71.0 - - - +
131D LEU* 1.3 63.1 + - - +
133D ALA* 3.3 2.3 + - - +
134D LEU* 3.1 29.7 + - - +
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Residues in contact with LEU 131 (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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173C ALA* 3.7 32.1 - - + +
176C LEU* 4.0 20.6 - - + -
177C PHE* 3.4 31.4 - - + -
117D LEU* 4.6 5.8 - - + -
127D LEU* 2.9 28.1 + - + +
128D GLU 3.3 8.1 - - - +
130D ALA* 1.3 77.1 - - - +
132D TYR* 1.3 59.4 + - + +
134D LEU* 3.3 7.5 + - - +
135D SER* 2.7 37.9 + - - -
3G TRP* 3.5 29.1 - - + +
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Residues in contact with TYR 132 (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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176C LEU* 4.9 2.0 - - + -
177C PHE* 4.9 5.4 - + - -
180C GLN* 2.5 40.2 + - - -
184C PRO* 3.5 20.8 - - + +
185C ALA* 3.6 32.6 - - + +
188C HIS* 3.3 48.9 - + + -
189C GLY* 5.0 3.0 - - - +
128D GLU* 3.2 45.6 + - + +
129D ASN* 3.3 6.9 + - - +
131D LEU* 1.3 87.3 - - + +
133D ALA* 1.3 57.9 + - - +
135D SER* 4.0 4.0 - - - -
136D ALA* 3.0 28.9 + - - +
197D PHE* 4.7 1.4 - - - -
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Residues in contact with ALA 133 (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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188C HIS* 5.4 0.6 - - - -
79D LEU* 4.4 9.0 - - + -
120D LEU* 5.3 2.5 - - + -
125D PHE* 4.2 13.0 - - + -
129D ASN 3.0 16.5 + - - +
130D ALA* 3.7 4.3 - - - +
132D TYR* 1.3 73.7 - - - +
134D LEU* 1.3 67.4 + - + +
136D ALA* 3.2 1.6 + - - +
137D VAL* 3.0 30.5 + - - +
197D PHE* 3.6 38.8 - - + -
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Residues in contact with LEU 134 (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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78D PHE* 4.5 9.9 - - + -
79D LEU* 4.6 7.0 - - + -
82D ASN* 5.5 5.4 - - - +
116D GLN* 3.9 28.7 - - + +
117D LEU* 3.5 31.6 - - + -
120D LEU* 3.5 26.0 - - + -
130D ALA 3.1 16.7 + - - +
131D LEU* 3.6 3.8 - - - +
133D ALA* 1.3 78.4 - - - +
135D SER* 1.3 63.7 + - - +
137D VAL* 3.4 5.4 + - - +
138D GLY* 3.1 19.9 + - - -
1G TRP 4.5 0.9 - - - +
3G TRP* 3.6 31.8 - - + +
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Residues in contact with SER 135 (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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140C PHE* 6.0 0.3 - - - -
177C PHE* 5.3 1.8 - - - -
185C ALA* 4.2 19.2 - - - +
131D LEU 2.7 23.7 + - - -
132D TYR* 4.0 5.4 - - - -
134D LEU* 1.3 75.1 - - - +
136D ALA* 1.3 63.2 + - - +
138D GLY 3.3 0.2 + - - -
139D HIS* 2.8 47.5 + - - -
2G THR 3.2 16.3 - - - +
3G TRP* 3.9 15.4 + - - +
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Residues in contact with ALA 136 (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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140C PHE* 4.0 22.1 - - + -
189C GLY* 4.2 11.9 - - - -
132D TYR 3.0 20.8 + - - +
133D ALA 3.2 4.0 + - - +
135D SER* 1.3 76.9 + - - +
137D VAL* 1.3 63.0 + - - +
140D PHE* 3.1 27.0 + - - +
193D LEU* 3.8 15.8 - - + +
197D PHE* 4.1 14.4 - - + -
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Residues in contact with VAL 137 (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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79D LEU* 4.2 24.5 - - + +
82D ASN* 5.3 5.6 - - - +
83D ALA* 3.5 32.8 - - + +
86D PHE* 6.3 0.4 - - + -
133D ALA 3.0 21.7 + - - +
134D LEU* 3.8 6.1 - - - +
136D ALA* 1.3 76.7 - - - +
138D GLY* 1.3 54.9 + - - +
140D PHE* 3.8 1.8 - - - +
141D THR* 2.6 37.2 + - - +
190D LEU* 4.2 9.4 - - + -
193D LEU* 4.1 11.9 - - + -
194D ILE* 5.2 0.4 - - + -
197D PHE* 3.8 23.1 - - + -
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Residues in contact with GLY 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D PHE* 3.8 21.4 - - - -
134D LEU 3.1 14.1 + - - -
135D SER 3.8 1.8 - - - -
137D VAL* 1.3 77.6 - - - +
139D HIS* 1.3 56.5 + - - +
141D THR* 4.4 0.7 - - - -
142D LEU* 2.8 31.9 + - - +
1G TRP 4.4 3.8 - - - -
2G THR* 4.1 16.8 - - - -
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Residues in contact with HIS 139 (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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139C HIS 4.1 0.5 - - - +
140C PHE* 4.5 7.1 - + + -
143C GLY* 3.6 27.7 - - - -
144C SER* 3.7 27.1 + - - +
147C GLU* 3.6 16.3 - - + +
148C ASP* 4.7 0.4 + - - -
135D SER* 2.8 39.9 + - - +
136D ALA 4.3 2.0 - - - +
138D GLY* 1.3 72.6 - - - +
140D PHE* 1.3 58.4 + - - +
142D LEU* 4.4 3.1 - - - +
143D GLY* 2.7 31.9 + - - -
2G THR* 2.9 29.7 + - - -
4G ASN* 3.4 33.1 + - - -
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Residues in contact with PHE 140 (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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135C SER* 5.2 1.1 - - - -
136C ALA* 4.3 31.9 - - + -
139C HIS* 4.4 9.3 - + + +
140C PHE* 4.2 17.8 - - + +
193C LEU* 6.0 2.2 - - + -
136D ALA 3.1 19.6 + - - +
137D VAL 3.8 4.3 - - - +
139D HIS* 1.3 77.4 - - - +
141D THR* 1.3 60.4 + - - +
143D GLY* 3.8 0.3 - - - -
144D SER* 2.9 51.4 + - - -
185D ALA 4.3 1.6 - - - -
186D PHE* 3.4 38.6 - + - -
189D GLY* 3.6 13.5 - - - -
190D LEU* 3.3 26.2 - - + -
193D LEU* 3.9 21.8 - - + -
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Residues in contact with THR 141 (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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83D ALA* 3.7 37.8 - - - +
86D PHE* 3.7 21.0 - - + -
87D ARG* 3.9 20.0 - - + +
90D LEU* 4.9 1.6 - - + -
137D VAL* 2.6 25.4 + - - +
138D GLY 3.8 3.6 - - - -
140D PHE* 1.3 77.5 - - - +
142D LEU* 1.3 63.5 + - - +
144D SER* 3.2 3.5 + - - -
145D VAL* 3.2 27.3 + - + +
186D PHE* 3.9 18.6 - - + -
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Residues in contact with LEU 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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143C GLY 5.1 2.7 - - - +
147C GLU* 3.4 39.7 - - + +
86D PHE* 4.5 4.0 - - + -
90D LEU* 3.6 26.2 - - + -
97D ALA* 3.5 26.0 - - + +
100D HIS* 4.4 9.9 - - + -
101D LEU* 4.1 10.8 - - + +
138D GLY 2.8 22.9 + - - +
139D HIS* 4.0 3.1 - - - +
141D THR* 1.3 74.2 - - - +
143D GLY* 1.3 61.1 + - - +
145D VAL* 3.3 2.3 + - - +
146D LEU* 3.0 38.6 + - + +
2G THR* 3.6 14.6 - - + -
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Residues in contact with GLY 143 (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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139C HIS* 3.6 20.5 - - - -
142C LEU* 5.3 2.0 - - - +
143C GLY* 3.6 13.4 - - - -
146C LEU* 5.5 1.3 - - - -
139D HIS 2.7 23.3 + - - -
142D LEU* 1.3 72.0 - - - +
144D SER* 1.3 65.3 + - - +
146D LEU* 3.9 5.5 - - - +
147D GLU* 3.2 25.5 + - - +
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Residues in contact with SER 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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139C HIS* 3.7 17.8 - - - +
87D ARG* 5.4 1.3 - - - -
140D PHE* 2.9 41.9 + - - -
141D THR 3.2 5.6 + - - -
143D GLY* 1.3 75.2 - - - +
145D VAL* 1.3 61.8 + - - +
147D GLU* 3.4 1.9 + - - +
148D ASP* 3.0 39.5 + - - +
186D PHE* 3.9 20.8 - - - +
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Residues in contact with VAL 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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87D ARG* 3.7 35.7 - - + +
90D LEU* 3.7 30.3 - - + -
91D LEU* 3.7 16.2 - - + -
97D ALA* 3.8 3.4 - - + -
141D THR 3.2 17.3 + - - +
142D LEU 4.0 2.7 - - - +
144D SER* 1.3 77.6 - - - +
146D LEU* 1.3 55.9 + - - +
148D ASP* 3.7 6.5 - - - +
149D GLN* 2.7 58.7 + - - +
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Residues in contact with LEU 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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101C LEU* 3.8 18.7 - - + +
143C GLY* 5.4 0.9 - - - -
146C LEU* 3.7 26.7 - - + -
97D ALA* 3.2 25.3 - - + +
98D LYS* 3.3 33.8 - - + +
101D LEU* 4.1 12.3 - - + -
142D LEU* 3.0 48.5 + - + +
143D GLY* 3.9 4.9 - - - +
144D SER 3.5 0.2 - - - -
145D VAL* 1.3 75.0 - - - +
147D GLU* 1.3 54.1 + - - +
149D GLN* 3.6 3.9 - - - +
150D GLU* 2.7 37.6 + - - +
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Residues in contact with GLU 147 (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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100C HIS 5.0 1.9 - - - +
101C LEU* 3.2 17.4 - - - +
102C GLY 3.0 25.0 + - - -
103C THR* 6.0 0.2 - - - -
139C HIS* 3.6 18.4 - - + -
142C LEU* 3.6 24.2 - - + -
143D GLY 3.2 10.8 + - - +
144D SER 3.7 0.2 - - - +
145D VAL 3.2 0.4 - - - -
146D LEU* 1.3 77.1 - - - +
148D ASP* 1.3 61.9 + - - +
150D GLU* 4.4 0.4 - - - +
151D HIS* 2.9 58.8 + - - +
1F TRP* 5.2 0.5 + - - -
2F THR* 2.6 25.3 + - + +
4F ASN* 3.3 17.0 - - - +
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Residues in contact with ASP 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C HIS* 4.7 0.5 + - - -
87D ARG* 4.6 10.9 + - - -
91D LEU* 5.2 11.6 - - + +
144D SER* 3.0 26.2 + - - +
145D VAL* 3.7 8.0 - - - +
147D GLU* 1.3 75.2 - - - +
149D GLN* 1.3 64.4 + - - +
151D HIS* 3.9 1.2 - - - +
152D GLN* 3.0 31.2 + - + +
182D ALA* 3.2 24.6 - - - +
186D PHE* 6.1 0.7 - - - +
4F ASN* 2.6 34.3 + - - +
6F TYR* 3.7 21.8 - - + -
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Residues in contact with GLN 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LEU 2.9 26.9 + - - -
91D LEU* 3.7 17.7 + - + +
93D HIS 3.6 12.2 + - - -
94D ARG* 5.4 0.2 - - - +
95D ASP* 3.6 15.2 - - - +
96D GLY 3.3 8.5 + - - -
97D ALA* 3.1 27.4 + - - +
98D LYS 4.4 0.5 + - - -
145D VAL* 2.7 34.1 + - + +
146D LEU* 3.7 3.4 - - - +
148D ASP* 1.3 73.6 - - - +
150D GLU* 1.3 62.5 + - - +
152D GLN* 3.1 19.2 + - + +
153D VAL* 3.2 17.4 + - + +
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 4.0 16.3 + - - +
101C LEU* 3.9 37.9 - - + +
102C GLY* 4.1 7.4 - - - +
95D ASP* 5.4 2.6 - - - +
98D LYS* 2.6 38.7 + - - +
146D LEU 2.7 20.9 + - - +
147D GLU 4.3 0.9 - - - +
149D GLN* 1.3 73.3 - - - +
151D HIS* 1.3 59.0 + - - +
153D VAL* 3.3 15.5 + - - +
154D ALA* 2.7 31.3 + - - +
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Residues in contact with HIS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLY* 3.1 28.4 + - - -
103C THR 3.0 25.2 + - - -
147D GLU* 2.9 55.3 + - - +
148D ASP 4.0 0.4 - - - +
150D GLU* 1.3 73.6 - - - +
152D GLN* 1.3 66.6 + - - +
154D ALA* 3.8 3.8 - - - -
155D LYS* 3.1 29.2 + - + +
158D ARG* 4.8 4.5 - - - -
1F TRP* 5.1 0.4 - - - -
2F THR* 4.7 0.7 - - - -
4F ASN* 3.8 15.2 + - + +
6F TYR* 3.7 24.0 - - + +
7F ALA* 3.4 28.5 - - + +
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Residues in contact with GLN 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D ASP* 3.0 24.5 + - + +
149D GLN* 3.1 12.7 + - + +
151D HIS* 1.3 78.0 - - - +
153D VAL* 1.3 63.1 + - + +
155D LYS* 3.1 48.3 - - - +
156D GLU* 3.7 10.7 - - - +
6F TYR* 3.0 45.6 - - + -
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Residues in contact with VAL 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 6.3 0.4 - - - +
94D ARG* 6.1 4.7 - - + -
95D ASP* 4.8 13.2 - - - +
149D GLN* 3.2 14.5 + - + +
150D GLU* 3.7 17.7 - - - +
152D GLN* 1.3 79.0 - - + +
154D ALA* 1.3 64.6 + - - +
156D GLU* 3.3 16.9 + - - +
157D GLU* 3.8 24.3 - - - +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ARG* 3.8 35.1 - - - +
102C GLY* 4.4 4.9 - - - +
150D GLU 2.7 23.6 + - - +
151D HIS* 4.2 4.5 - - - -
153D VAL* 1.3 71.5 - - - +
155D LYS* 1.3 59.5 + - - +
156D GLU 3.0 2.5 - - - -
157D GLU* 2.9 30.3 + - - +
158D ARG* 3.8 24.5 - - - +
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Residues in contact with LYS 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ARG* 4.0 14.2 + - - +
151D HIS* 3.1 15.9 + - + +
152D GLN* 3.1 39.8 - - - +
154D ALA* 1.3 75.9 - - - +
156D GLU* 1.3 84.0 + - - +
157D GLU 3.1 0.7 - - - -
158D ARG* 2.8 27.8 - - - +
6F TYR* 4.7 6.7 - - + +
7F ALA 6.0 0.2 - - - +
9F ALA* 3.4 36.8 - - + +
10F ALA 3.7 15.9 + - - +
11F PRO* 3.7 11.3 - - + +
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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