Contacts of the helix formed by residues 111 - 149 (chain D) in PDB entry 5C5B
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 MET 111 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C PHE* 5.9 0.7 - - - -
44D MET* 3.6 39.7 - - - +
47D VAL* 4.0 21.3 - - + -
48D TYR 5.0 0.2 - - - +
107D LEU* 3.2 40.7 + - + +
109D ASP 3.5 1.0 - - - -
110D THR* 1.3 80.9 + - - +
112D VAL* 1.3 75.8 + - + +
113D LEU 3.4 0.4 - - - -
114D PRO* 3.2 8.2 - - - +
115D ILE* 3.4 19.1 - - - +
199D PRO* 3.5 24.4 - - + +
203D PHE* 3.6 36.3 - - + +
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Residues in contact with VAL 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 4.2 4.4 - - + +
44D MET* 3.9 34.3 - - + +
45D GLN* 3.9 27.8 - - + +
48D TYR* 4.1 16.2 - - + -
107D LEU 3.0 18.8 + - - +
108D ALA* 3.9 7.9 - - - +
111D MET* 1.3 77.5 - - + +
113D LEU* 1.3 58.9 + - - +
115D ILE* 3.2 8.7 + - - +
116D ILE* 2.9 48.4 + - + +
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Residues in contact with LEU 113 (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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108D ALA 3.2 16.8 + - - +
109D ASP* 3.4 24.7 - - + +
112D VAL* 1.3 76.9 - - - +
114D PRO* 1.3 62.2 - - + +
116D ILE* 4.0 22.9 - - + -
117D GLN* 2.9 56.3 + - + +
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Residues in contact with PRO 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D ASP 3.3 17.9 - - - +
110D THR* 3.6 20.0 - - - +
111D MET 3.2 17.7 - - - +
113D LEU* 1.3 87.2 - - + +
115D ILE* 1.3 55.8 + - - +
117D GLN* 3.4 9.3 + - + +
118D PHE* 2.9 30.5 + - - +
195D ALA* 5.0 3.7 - - - +
198D GLU* 4.3 27.8 - - + +
199D PRO* 4.4 5.4 - - + -
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Residues in contact with ILE 115 (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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37D THR* 4.1 20.2 - - + +
40D LEU* 4.0 19.3 - - + +
41D LEU* 4.1 23.3 - - + +
44D MET* 3.5 43.3 - - + -
111D MET 3.4 14.4 - - - +
112D VAL 3.2 6.2 + - - +
114D PRO* 1.3 72.7 - - - +
116D ILE* 1.3 66.4 + - - +
118D PHE* 3.2 9.4 + - + +
119D ARG* 2.9 26.0 + - + +
195D ALA 4.7 5.2 - - - +
196D MET* 6.1 1.3 - - + -
199D PRO* 3.6 15.3 - - + -
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Residues in contact with ILE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 3.6 20.9 - - + -
45D GLN* 4.4 11.7 - - - +
112D VAL* 2.9 35.5 + - + +
113D LEU* 3.6 25.1 - - + +
115D ILE* 1.3 76.5 - - - +
117D GLN* 1.3 58.6 + - + +
119D ARG* 3.9 4.3 - - - +
120D GLU* 2.9 37.6 + - + +
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Residues in contact with GLN 117 (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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113D LEU* 2.9 51.9 + - + +
114D PRO* 3.8 7.4 - - + +
116D ILE* 1.3 76.4 - - + +
118D PHE* 1.3 59.3 + - - +
120D GLU* 4.3 4.5 - - - -
121D LYS* 2.9 36.9 + - + +
122D ASP* 4.9 0.2 - - - +
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Residues in contact with PHE 118 (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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33D LEU* 3.9 16.4 - - + -
37D THR* 3.5 32.8 - - + -
114D PRO 2.9 18.4 + - - +
115D ILE* 3.5 10.3 - - + +
117D GLN* 1.3 75.2 - - - +
119D ARG* 1.3 73.6 + - - +
122D ASP* 2.9 57.6 + - + +
123D LEU* 3.2 33.0 + - + -
188D LEU* 4.1 10.5 - - + -
191D ARG* 4.0 13.7 - - + -
192D LYS* 4.8 2.5 - - - -
195D ALA* 3.5 34.3 - - + -
196D MET* 5.7 1.1 - - + -
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Residues in contact with ARG 119 (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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34D THR* 5.4 2.2 - - + +
37D THR* 4.7 7.6 - - - +
38D ASN* 2.7 42.8 + - - +
41D LEU* 3.7 31.0 - - + +
115D ILE* 2.9 18.4 + - + +
116D ILE* 3.9 4.0 - - - +
118D PHE* 1.3 81.3 - - + +
120D GLU* 1.3 63.6 + - - +
123D LEU* 3.4 36.2 - - + +
124D THR* 3.5 10.3 + - + +
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Residues in contact with GLU 120 (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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116D ILE* 2.9 25.4 + - + +
117D GLN* 3.8 6.1 - - - +
119D ARG* 1.3 78.6 - - - +
121D LYS* 1.3 53.3 + - + +
124D THR* 2.2 34.0 + - - +
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Residues in contact with LYS 121 (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 GLN* 2.9 22.0 + - + +
120D GLU* 1.3 75.9 - - + +
122D ASP* 1.3 66.2 + - - +
124D THR* 3.1 2.5 + - - -
125D GLU* 2.9 31.5 + - - +
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Residues in contact with ASP 122 (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 GLN 5.3 0.2 - - - -
118D PHE* 2.9 49.1 + - + +
121D LYS* 1.3 74.8 - - - +
123D LEU* 1.3 60.5 + - - +
125D GLU* 3.2 14.3 + - - +
126D VAL* 3.0 33.0 + - + +
188D LEU* 5.0 3.8 - - + -
191D ARG* 4.0 37.7 + - - +
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Residues in contact with LEU 123 (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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30D ALA* 5.3 0.7 - - + +
33D LEU* 3.6 26.7 - - + -
34D THR* 3.7 31.0 - - + +
37D THR* 3.6 24.5 - - + +
118D PHE* 3.2 23.6 + - + -
119D ARG* 3.4 24.7 - - + +
122D ASP* 1.3 79.6 - - - +
124D THR* 1.3 59.5 + - + +
126D VAL* 3.2 8.5 + - + +
127D SER* 2.9 25.8 + - - -
188D LEU* 3.6 20.0 - - + -
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Residues in contact with THR 124 (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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119D ARG 3.5 10.3 + - - +
120D GLU* 2.2 37.2 + - - +
121D LYS* 3.1 7.6 + - - -
123D LEU* 1.3 74.8 - - + +
125D GLU* 1.3 59.6 + - - +
127D SER* 3.5 8.9 - - - -
128D THR* 2.9 37.9 + - - +
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Residues in contact with GLU 125 (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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121D LYS 2.9 20.3 + - - +
122D ASP* 3.2 20.5 - - - +
124D THR* 1.3 76.9 + - - +
126D VAL* 1.3 62.1 + - + +
128D THR* 2.7 22.3 + - - +
129D LEU* 3.0 33.4 + - + +
184D ALA* 5.7 3.4 - - - +
191D ARG* 4.2 13.2 + - - -
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Residues in contact with VAL 126 (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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30D ALA* 5.0 7.2 - - + -
122D ASP 3.0 18.3 + - - +
123D LEU* 3.3 10.5 - - + +
125D GLU* 1.3 77.6 - - + +
127D SER* 1.3 58.1 + - - +
129D LEU* 3.4 5.8 + - - +
130D LYS* 2.9 30.4 + - + +
181D TYR* 3.8 7.9 - - + +
184D ALA* 4.3 24.9 - - + +
185D LEU* 3.6 26.2 - - + -
188D LEU* 4.1 29.4 - - + -
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Residues in contact with SER 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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123D LEU 2.9 13.8 + - - -
124D THR* 3.3 13.2 + - - -
126D VAL* 1.3 77.6 - - - +
128D THR* 1.3 60.2 + - - +
130D LYS* 3.1 13.9 + - - +
131D ASP* 2.9 30.0 + - - +
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Residues in contact with THR 128 (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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124D THR* 2.9 19.7 + - - +
125D GLU* 2.7 25.8 + - - +
127D SER* 1.3 74.8 - - - +
129D LEU* 1.3 68.3 + - - +
131D ASP* 2.6 36.4 + - - +
132D LEU* 3.0 15.1 + - - +
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Residues in contact with LEU 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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125D GLU* 3.0 33.7 + - + +
126D VAL 3.8 4.0 - - - +
128D THR* 1.3 82.2 + - - +
130D LYS* 1.3 58.1 + - - +
132D LEU* 3.4 18.8 + - + +
133D PHE* 2.9 30.0 + - - +
177D SER* 4.6 3.9 - - - +
180D GLN* 3.8 35.7 - - + +
181D TYR* 4.2 18.1 - - + +
184D ALA* 3.6 27.6 - - + -
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Residues in contact with LYS 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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27D GLU* 3.8 28.6 + - + +
126D VAL* 2.9 16.3 + - + +
127D SER* 3.2 14.1 - - - +
129D LEU* 1.3 76.8 - - - +
131D ASP* 1.3 58.1 + - + +
133D PHE* 3.4 5.0 + - + +
134D GLY* 2.9 23.9 + - - -
181D TYR* 3.2 36.7 - - + +
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Residues in contact with ASP 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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127D SER* 2.9 13.1 + - - +
128D THR* 2.6 30.3 + - - +
130D LYS* 1.3 75.2 - - - +
132D LEU* 1.3 95.2 + - - +
134D GLY* 3.3 2.7 + - - +
135D LEU* 2.9 40.3 + - + +
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Residues in contact with LEU 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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128D THR* 3.0 20.9 + - - +
129D LEU* 3.9 24.0 - - + +
131D ASP* 1.3 91.6 + - - +
133D PHE* 1.3 59.3 + - - +
135D LEU* 3.9 9.8 - - + +
136D ALA* 3.0 31.9 + - - +
177D SER* 4.0 10.3 - - - -
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Residues in contact with PHE 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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15D ASP* 4.7 1.1 - - - -
20D ARG* 3.3 43.3 - - - -
23D LEU* 3.5 24.7 - - + -
27D GLU* 4.9 3.8 - - - -
129D LEU 2.9 17.5 + - - +
130D LYS* 3.6 4.5 - - + +
132D LEU* 1.3 77.1 - - - +
134D GLY* 1.3 60.0 + - - +
136D ALA* 3.8 0.7 - - - +
137D SER* 2.9 29.9 + - - -
174D GLN* 4.3 12.1 - - + -
177D SER* 3.5 19.4 - - - +
178D SER* 3.6 36.8 - - - -
181D TYR* 3.7 26.0 - + + -
182D TYR* 4.4 4.3 - + - -
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Residues in contact with GLY 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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130D LYS 2.9 15.2 + - - -
131D ASP* 3.3 4.0 + - - -
132D LEU 3.2 0.2 - - - -
133D PHE* 1.3 81.4 - - - +
135D LEU* 1.3 56.8 + - - +
137D SER* 3.2 7.6 + - - -
138D ASN* 3.0 35.4 + - - -
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Residues in contact with LEU 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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131D ASP* 2.9 28.1 + - + +
132D LEU* 4.1 9.2 - - + +
134D GLY* 1.3 72.8 - - - +
136D ALA* 1.3 60.1 + - - +
138D ASN* 3.2 18.0 + - + +
139D GLU* 2.9 44.2 + - - +
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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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132D LEU 3.0 19.3 + - - +
133D PHE 3.8 0.7 - - - +
135D LEU* 1.3 75.6 - - - +
137D SER* 1.3 57.8 + - - +
139D GLU* 3.4 13.6 + - - +
140D HIS* 2.9 30.1 + - - +
170D ALA 4.5 1.9 - - - +
173D LYS* 4.1 17.3 - - + +
174D GLN* 3.7 21.2 - - - +
177D SER* 3.5 20.2 - - - +
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Residues in contact with SER 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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314C ARG* 3.9 5.0 + - - -
20D ARG* 3.5 29.5 + - - -
133D PHE* 2.9 20.9 + - - -
134D GLY* 3.3 8.3 - - - -
136D ALA* 1.3 77.6 - - - +
138D ASN* 1.3 64.7 + - - +
140D HIS* 3.3 2.9 + - - +
141D ASP* 2.9 37.5 + - - +
174D GLN* 3.8 15.7 + - - +
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Residues in contact with ASN 138 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D GLY 3.0 22.6 + - - +
135D LEU* 3.2 21.5 + - + +
137D SER* 1.3 77.2 + - - +
139D GLU* 1.3 63.4 + - + +
141D ASP* 3.1 13.3 + - - +
142D LEU* 3.0 30.9 + - + +
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Residues in contact with GLU 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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135D LEU* 2.9 32.0 + - - +
136D ALA* 3.6 7.5 + - - +
137D SER 3.3 0.2 - - - -
138D ASN* 1.3 76.0 - - + +
140D HIS* 1.3 63.6 + - - +
142D LEU* 3.4 9.4 + - + +
143D SER* 3.0 24.4 + - - -
170D ALA* 4.3 12.1 - - + +
173D LYS* 3.1 34.5 + - - +
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Residues in contact with HIS 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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299C ARG* 5.3 2.5 - - - -
314C ARG* 5.6 1.0 + - - -
136D ALA 2.9 12.7 + - - +
137D SER 3.6 1.6 - - - +
139D GLU* 1.3 74.9 - - - +
141D ASP* 1.3 57.8 + - - +
143D SER* 3.4 2.8 + - - -
144D MET* 2.9 63.0 + - + +
167D VAL* 4.3 6.2 + - + +
170D ALA* 3.8 16.3 - - + +
171D ARG* 3.1 56.7 + - + -
174D GLN* 2.7 33.5 + - - +
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Residues in contact with ASP 141 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ARG* 4.2 1.7 + - - -
314C ARG* 3.4 33.0 + - - -
137D SER* 2.9 30.1 + - - +
138D ASN* 3.1 13.3 + - - +
140D HIS* 1.3 78.5 + - - +
142D LEU* 1.3 58.7 + - + +
144D MET* 3.6 14.1 - - - +
145D ALA* 2.9 28.1 + - - +
174D GLN* 5.2 0.7 - - - +
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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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138D ASN* 3.0 22.7 + - + +
139D GLU* 3.9 7.4 - - + +
141D ASP* 1.3 76.5 - - + +
143D SER* 1.3 62.5 + - - +
145D ALA* 3.0 11.1 + - + +
146D LYS* 3.0 27.9 + - - +
149D ARG* 4.8 3.1 + - - +
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Residues in contact with SER 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D GLU 3.0 18.8 + - - -
140D HIS* 3.5 5.7 + - - -
142D LEU* 1.3 77.3 - - - +
144D MET* 1.3 57.5 + - - +
146D LYS* 3.3 9.8 + - - +
147D TYR* 2.9 28.1 + - - +
163D VAL* 4.8 0.5 - - - +
166D GLU* 4.8 5.6 - - - -
167D VAL* 3.1 38.4 + - - +
170D ALA* 4.2 12.8 - - - +
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Residues in contact with MET 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ARG* 3.6 49.6 - - - +
314C ARG* 4.6 1.1 - - - +
358C GLU* 3.9 15.7 - - - +
140D HIS* 2.9 61.1 + - + +
141D ASP* 3.6 19.7 - - - +
143D SER* 1.3 73.2 + - - +
145D ALA* 1.3 59.8 + - - +
147D TYR* 3.6 7.8 - - - +
148D SER* 2.9 30.5 + - - -
167D VAL* 4.6 5.2 - - + -
171D ARG* 3.7 10.1 - - - +
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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
----------------------------------------------------------
141D ASP 2.9 15.2 + - - +
142D LEU* 3.0 16.6 + - + +
144D MET* 1.3 77.1 - - - +
146D LYS* 1.3 60.4 + - - +
148D SER* 3.3 20.5 - - - -
149D ARG* 3.4 29.5 + - - +
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D LEU* 3.0 16.4 + - - +
143D SER* 4.1 9.0 - - - +
145D ALA* 1.3 73.7 - - - +
147D TYR* 1.3 65.9 + - - +
149D ARG* 3.3 32.3 + - - +
150D LEU* 4.0 12.6 + - - +
163D VAL* 4.4 20.0 - - + -
166D GLU* 5.0 9.5 + - - +
401D GOL 3.7 39.3 + - - +
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Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C PRO* 3.9 19.5 - - + -
265C ASP* 3.6 21.1 - - - +
339C ARG* 3.4 28.1 + - - -
340C TYR* 5.9 0.2 - + - -
358C GLU* 3.5 44.6 + - + -
143D SER 2.9 17.8 + - - +
144D MET* 3.6 7.4 - - - +
146D LYS* 1.3 76.6 - - - +
148D SER* 1.3 69.3 + - - +
149D ARG 3.1 0.2 - - - -
150D LEU* 3.1 34.4 + - + +
160D LYS 4.7 2.2 - - - -
163D VAL* 3.6 22.4 - - + -
164D GLY* 4.1 8.5 - - - -
167D VAL* 3.7 20.4 - - + -
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ASN* 3.7 13.2 + - - -
297C TRP* 5.7 0.2 - - - +
338C ARG* 2.4 34.1 + - - -
339C ARG* 4.7 1.6 + - - +
356C GLN* 2.8 45.9 + - - +
144D MET 2.9 13.4 + - - -
145D ALA* 3.3 14.6 + - - -
147D TYR* 1.3 81.8 - - - +
149D ARG* 1.3 56.3 + - - +
150D LEU 3.2 9.1 + - - +
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Residues in contact with ARG 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C ASP* 5.3 5.7 - - - +
338C ARG* 3.4 25.4 - - - +
142D LEU* 4.8 3.2 + - - +
145D ALA* 3.4 21.0 + - - +
146D LYS* 3.3 36.0 - - - +
147D TYR 3.1 1.4 - - - -
148D SER* 1.3 74.2 - - - +
150D LEU* 1.3 64.6 + - - +
151D PRO* 3.5 3.5 - - - +
401D GOL 2.8 54.9 + - - +
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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
------------------------------------------------------------
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