Contacts of the helix formed by residues 119 - 145 (chain D) in PDB entry 1JI5
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 119 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D VAL* 4.2 14.6 - - + +
59D ARG* 3.1 14.4 + - - -
63D ILE* 4.4 10.8 - - - +
114D ALA* 2.8 30.3 + - - +
115D GLN 4.2 1.0 + - - -
117D SER 4.2 5.4 - - - +
118D ASP* 1.3 77.2 - - - +
120D GLU* 1.3 60.4 + - - +
121D MET* 3.1 8.9 + - - +
122D THR* 2.4 39.5 + - - -
123D SER 3.3 11.3 + - - -
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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
----------------------------------------------------------
115D GLN* 4.9 12.2 - - + +
118D ASP* 3.9 2.6 - - - +
119D ASP* 1.3 72.6 - - - +
121D MET* 1.3 77.2 + - + +
123D SER* 3.3 13.0 - - - -
124D ASP* 2.7 34.5 + - - +
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Residues in contact with MET 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ARG* 2.9 31.9 - - - +
118D ASP 5.8 0.4 - - - +
119D ASP* 3.0 7.2 - - - +
120D GLU* 1.3 102.1 - - + +
122D THR* 1.3 61.3 + - - +
124D ASP* 2.9 18.8 + - - +
125D LEU* 3.0 11.3 + - - +
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Residues in contact with THR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 3.7 16.5 - - + +
9D LEU* 3.6 37.3 - - + +
59D ARG* 3.1 25.0 + - + +
63D ILE* 4.5 1.6 - - - +
114D ALA* 4.5 2.5 - - + -
119D ASP* 2.4 32.3 + - - -
121D MET* 1.3 77.7 - - - +
123D SER* 1.3 62.5 + - - +
125D LEU* 3.1 7.6 + - + +
126D LEU* 2.9 29.1 + - + +
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Residues in contact with SER 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D MET* 3.5 27.5 - - - +
114D ALA* 4.0 16.0 - - - +
115D GLN* 3.9 16.1 - - - +
119D ASP 3.3 5.7 + - - -
120D GLU* 3.3 22.0 - - - -
121D MET 3.0 0.8 - - - -
122D THR* 1.3 80.2 - - - +
124D ASP* 1.3 51.8 + - - +
126D LEU* 3.2 3.7 + - - +
127D LEU* 2.7 35.8 + - - +
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Residues in contact with ASP 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D GLU 2.7 17.6 + - - +
121D MET* 2.9 11.0 + - - +
123D SER* 1.3 69.9 - - - +
125D LEU* 1.3 68.3 + - - +
127D LEU* 3.2 21.4 + - - +
128D GLY* 3.1 18.5 + - - -
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU* 5.7 0.7 - - + -
55D GLU* 4.2 27.8 - - + +
56D ILE* 4.3 19.1 - - + +
59D ARG* 3.7 37.2 - - + -
121D MET 3.0 10.3 + - - +
122D THR* 3.1 11.0 + - - +
124D ASP* 1.3 81.0 + - - +
126D LEU* 1.3 71.8 + - + +
128D GLY* 3.2 8.8 + - - -
129D ILE* 3.4 21.6 + - + +
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Residues in contact with LEU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 6.1 0.4 - - + -
8D VAL* 4.3 12.6 - - + -
9D LEU* 3.8 25.1 - - + -
12D GLN* 5.3 5.2 - - + -
56D ILE* 5.7 1.8 - - + -
107D LEU* 3.6 25.3 - - + +
110D GLY* 3.8 36.1 - - - +
111D MET* 3.8 12.6 - - + +
122D THR* 2.9 23.5 + - + +
123D SER* 3.5 7.4 - - - +
125D LEU* 1.3 86.5 - - + +
127D LEU* 1.3 65.1 + - - +
129D ILE* 3.2 15.8 + - + +
130D TYR* 3.0 21.3 + - - +
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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
----------------------------------------------------------
111D MET* 3.8 18.8 - - + -
123D SER* 2.7 21.1 + - - +
124D ASP* 3.4 22.4 - - - +
126D LEU* 1.3 72.1 - - - +
128D GLY* 1.3 66.0 + - - +
130D TYR* 3.1 9.6 - - + +
131D THR* 3.0 30.3 + - - +
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Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ASP 3.1 11.9 + - - -
125D LEU 3.2 5.1 + - - -
126D LEU 3.1 0.6 - - - -
127D LEU* 1.3 79.1 - - - +
129D ILE* 1.3 61.8 + - - +
131D THR* 3.1 8.9 + - - -
132D GLU* 2.9 22.3 + - - +
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Residues in contact with ILE 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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12D GLN* 3.9 16.4 - - - +
16D TRP* 3.6 29.8 - - + +
52D HIS* 3.9 26.9 - - + +
55D GLU* 5.4 0.9 - - - +
56D ILE* 4.1 22.0 - - + -
103D MET* 4.4 0.4 - - + -
107D LEU* 4.4 9.2 - - + -
125D LEU* 3.4 24.5 - - + +
126D LEU* 3.2 17.2 + - + +
128D GLY* 1.3 73.2 - - - +
130D TYR* 1.3 57.5 + - - +
132D GLU* 3.1 7.3 + - - +
133D LEU* 2.8 43.6 + - + +
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Residues in contact with TYR 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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104D LEU* 3.3 41.9 - - + +
107D LEU* 3.9 9.1 - - + +
108D LYS* 3.2 45.8 + - + +
111D MET* 3.7 20.2 - - + -
126D LEU 3.0 12.2 + - - +
127D LEU* 3.1 17.0 - - + +
129D ILE* 1.3 77.5 - - - +
131D THR* 1.3 65.8 + - - +
133D LEU 3.4 0.2 + - - -
134D GLU* 2.9 66.4 + - + +
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Residues in contact with THR 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 LEU* 3.0 24.2 + - - +
128D GLY* 3.1 10.2 + - - -
130D TYR* 1.3 82.2 - - - +
132D GLU* 1.3 65.0 + - - +
134D GLU* 3.4 7.4 + - - +
135D LYS* 3.3 20.9 + - + +
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Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D TRP* 4.6 0.5 - - - -
48D GLU* 3.6 30.2 - - - +
52D HIS* 2.7 40.3 + - - -
128D GLY 2.9 13.6 + - - +
129D ILE* 3.3 9.2 - - - +
131D THR* 1.3 80.5 - - - +
133D LEU* 1.3 75.7 + - - +
135D LYS* 3.3 6.9 + - - +
136D HIS* 3.3 31.5 + - + +
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Residues in contact with LEU 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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16D TRP* 3.6 21.5 - - + -
100D TYR* 4.1 48.4 - - + +
103D MET* 4.0 30.7 - - + -
104D LEU* 4.0 9.4 - - + -
107D LEU* 4.3 9.2 - - + -
129D ILE* 2.8 24.1 + - + +
130D TYR 4.0 2.7 - - - +
132D GLU* 1.3 90.7 - - + +
134D GLU* 1.3 60.4 + - - +
136D HIS* 3.0 9.3 + - + +
137D ALA* 2.7 32.1 + - - +
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Residues in contact with GLU 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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104D LEU* 3.8 16.5 - - + +
130D TYR* 2.9 56.2 + - + +
131D THR* 3.6 8.7 - - - +
133D LEU* 1.3 76.8 - - - +
135D LYS* 1.3 62.8 + - - +
137D ALA* 3.5 7.3 + - - +
138D TRP* 3.2 20.6 + - - +
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Residues in contact with LYS 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 THR* 3.3 9.7 + - + +
132D GLU* 3.6 9.4 - - - +
133D LEU 3.2 0.6 - - - -
134D GLU* 1.3 75.3 - - - +
136D HIS* 1.3 69.0 + - + +
138D TRP* 3.1 42.5 + - + +
139D MET* 3.1 30.3 + - + +
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Residues in contact with HIS 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LYS* 4.3 7.0 + - - -
44D GLU* 4.1 13.2 - - - -
45D LEU* 3.5 20.9 - - + +
48D GLU* 2.8 34.6 + - - -
100D TYR* 3.8 30.1 - + + -
132D GLU* 3.3 29.8 + - + +
133D LEU* 3.0 8.9 + - + +
135D LYS* 1.3 78.6 - - + +
137D ALA* 1.3 55.3 + - - +
139D MET* 3.0 20.7 + - + +
140D LEU* 2.7 43.0 + - + +
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Residues in contact with ALA 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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97D MET* 4.2 7.5 - - + +
100D TYR* 4.7 7.7 - - + -
101D GLU* 4.5 15.5 - - + +
104D LEU* 5.4 4.5 - - + -
133D LEU 2.7 19.5 + - - +
134D GLU* 3.6 9.4 - - - +
136D HIS* 1.3 73.1 - - - +
138D TRP* 1.3 53.7 + - - +
140D LEU* 3.8 7.2 - - - +
141D ARG* 2.7 58.1 + - - +
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Residues in contact with TRP 138 (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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134D GLU 3.2 8.7 + - - +
135D LYS* 3.1 44.5 + - + +
137D ALA* 1.3 78.9 - - - +
139D MET* 1.3 75.7 + - + +
141D ARG* 3.3 14.6 + - - +
142D ALA* 2.7 45.4 + - + +
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Residues in contact with MET 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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41D LYS* 3.3 33.4 - - - +
135D LYS* 3.4 21.5 - - + +
136D HIS* 3.0 29.2 + - + +
138D TRP* 1.3 104.4 - - + +
140D LEU* 1.3 70.3 + - + +
142D ALA* 3.3 5.7 + - - +
143D PHE* 3.0 22.7 + - - +
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Residues in contact with LEU 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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38D LEU* 5.9 3.1 - - + -
41D LYS* 5.1 22.2 - - + -
42D PHE* 6.3 1.6 - - + -
45D LEU* 5.1 7.0 - - + -
93D VAL* 3.6 30.4 - - + +
96D ILE* 4.1 24.2 - - + -
97D MET* 4.1 15.3 - - + -
100D TYR* 4.2 18.4 - - + -
136D HIS* 2.7 32.0 + - + +
137D ALA 3.8 2.7 - - - +
139D MET* 1.3 75.4 - - + +
141D ARG* 1.3 63.8 + - - +
143D PHE* 3.0 22.0 - - + +
144D LEU* 3.2 15.2 + - - +
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Residues in contact with ARG 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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97D MET* 3.8 18.1 - - + +
101D GLU* 2.4 35.0 + - - +
137D ALA* 2.7 47.7 + - - +
138D TRP* 3.5 12.8 - - + +
140D LEU* 1.3 73.0 - - - +
142D ALA* 1.3 56.5 + - - +
144D LEU* 2.9 20.3 + - - +
145D ASN* 2.9 42.9 + - + +
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Residues in contact with ALA 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 TRP* 2.7 37.0 + - + +
139D MET* 3.8 6.1 - - - +
141D ARG* 1.3 73.5 - - - +
143D PHE* 1.3 62.7 + - - +
144D LEU 3.4 0.2 + - - -
145D ASN* 3.5 18.5 - - - +
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Residues in contact with PHE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D GLN* 3.5 30.3 - - + -
37D THR* 5.1 2.7 - - - -
38D LEU* 3.6 28.9 - - + -
89D ALA* 5.9 1.3 - - + -
90D GLU* 5.0 11.2 - - - -
93D VAL* 3.9 28.0 - - + -
139D MET 3.0 13.5 + - - +
140D LEU* 3.0 17.3 - - + +
142D ALA* 1.3 78.4 - - - +
144D LEU* 1.3 78.7 + - + +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLU* 4.4 23.1 - - + +
93D VAL* 3.7 22.9 - - + -
94D GLU* 4.2 24.0 - - + +
97D MET* 4.2 15.3 - - + -
140D LEU 3.2 21.3 + - - +
141D ARG* 2.9 5.8 + - - +
143D PHE* 1.3 101.9 - - + +
145D ASN* 1.3 78.3 + - - +
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Residues in contact with ASN 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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97D MET* 6.3 0.4 - - - +
141D ARG* 2.9 42.1 + - + +
142D ALA* 3.5 16.0 - - - +
143D PHE 4.7 0.2 - - - +
144D LEU* 1.3 87.0 - - - +
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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