Contacts of the helix formed by residues 119 - 145 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.2 15.0 - - + +
59B ARG* 3.3 14.2 + - - -
63B ILE* 4.4 11.2 - - - +
114B ALA* 2.8 31.5 + - - +
115B GLN* 4.1 1.2 + - - +
117B SER 4.2 6.1 - - - +
118B ASP* 1.3 75.7 - - - +
120B GLU* 1.3 60.3 + - - +
121B MET* 3.3 8.0 - - - +
122B THR* 2.6 37.3 + - - -
123B SER 3.3 12.0 + - - -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN* 4.9 12.4 - - + +
118B ASP* 3.9 2.2 - - - +
119B ASP* 1.3 72.6 - - - +
121B MET* 1.3 74.1 + - + +
123B SER* 3.3 12.9 - - - -
124B ASP* 2.7 35.3 + - - +
111C MET* 3.9 17.9 - - - +
115C GLN* 3.7 31.9 + - - +
123C SER* 4.4 3.1 + - - -
127C LEU* 4.3 10.1 - - + +
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 3.0 24.0 - - - +
118B ASP 5.8 0.4 - - - +
119B ASP* 3.0 6.8 - - - +
120B GLU* 1.3 99.2 - - + +
122B THR* 1.3 65.3 + - - +
124B ASP* 2.9 15.2 + - - +
125B LEU* 3.0 11.3 + - - +
108C LYS* 6.1 2.5 - - - -
111C MET* 3.7 25.8 - - + -
127C LEU* 3.1 39.4 - - + +
130C TYR* 3.4 42.6 - - + -
131C THR* 3.8 12.8 + - - +
134C GLU* 4.2 0.4 - - - +
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.8 17.3 - - + +
9B LEU* 3.5 37.7 - - + +
59B ARG* 3.1 25.5 + - + +
63B ILE* 4.5 2.1 - - - +
114B ALA* 4.5 1.6 - - + -
119B ASP* 2.6 31.1 + - - -
121B MET* 1.3 78.2 - - - +
123B SER* 1.3 63.4 + - - +
125B LEU* 3.1 6.4 + - - +
126B LEU* 2.9 31.0 + - + +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B MET* 3.4 28.6 - - - +
114B ALA* 4.0 16.1 - - - +
115B GLN* 3.9 16.5 + - - +
119B ASP 3.3 5.5 + - - -
120B GLU* 3.2 21.5 + - - -
121B MET 3.0 0.2 - - - -
122B THR* 1.3 80.0 - - - +
124B ASP* 1.3 51.4 + - - +
126B LEU* 3.2 4.2 + - - +
127B LEU* 2.7 36.2 + - - +
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Residues in contact with ASP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU 2.7 16.5 + - - +
121B MET 3.2 9.4 - - - +
123B SER* 1.3 74.7 - - - +
125B LEU* 1.3 63.1 + - - +
127B LEU* 3.1 21.1 + - - +
128B GLY* 3.1 19.2 + - - -
124C ASP* 4.2 9.8 - - - +
127C LEU* 3.9 29.7 - - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 5.5 0.4 - - + -
55B GLU* 4.3 26.2 - - + +
56B ILE* 4.3 18.6 - - + +
59B ARG* 3.7 37.5 - - + -
121B MET 3.0 10.5 + - - +
122B THR* 3.3 10.1 - - - +
124B ASP* 1.3 77.8 + - - +
126B LEU* 1.3 75.3 + - + +
128B GLY* 3.2 10.9 + - - -
129B ILE* 3.5 20.8 + - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 6.1 0.4 - - + -
8B VAL* 4.4 12.3 - - + -
9B LEU* 3.7 23.8 - - + -
12B GLN* 5.4 4.5 - - + -
56B ILE* 5.7 1.3 - - + -
107B LEU* 3.7 24.8 - - + +
110B GLY* 3.8 36.8 - - - +
111B MET* 3.9 13.5 - - + +
122B THR* 2.9 27.6 + - + +
123B SER* 3.5 6.7 - - - +
125B LEU* 1.3 84.3 - - + +
127B LEU* 1.3 66.1 + - - +
129B ILE* 3.1 17.1 + - + +
130B TYR* 3.0 20.8 + - - +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B MET* 3.9 18.6 - - - -
123B SER* 2.7 18.7 + - - +
124B ASP* 3.3 23.6 - - - +
126B LEU* 1.3 71.7 - - - +
128B GLY* 1.3 64.4 + - - +
130B TYR* 3.2 9.6 - - + +
131B THR* 3.0 30.9 + - - +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP 3.1 12.7 + - - -
125B LEU 3.2 4.9 + - - -
126B LEU 3.1 0.2 - - - -
127B LEU* 1.3 78.2 - - - +
129B ILE* 1.3 62.7 + - - +
131B THR* 3.1 9.7 + - - -
132B GLU* 2.9 21.5 + - - +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLN* 3.9 16.4 - - - +
16B TRP* 3.6 30.1 - - + +
52B HIS* 4.0 26.5 - - + +
55B GLU* 5.5 0.9 - - - +
56B ILE* 4.0 23.1 - - + -
103B MET* 4.4 0.7 - - + -
107B LEU* 4.4 10.3 - - + -
125B LEU* 3.5 24.4 + - + +
126B LEU* 3.1 16.1 + - + +
128B GLY* 1.3 74.0 - - - +
130B TYR* 1.3 57.2 + - - +
132B GLU* 3.1 7.8 + - - +
133B LEU* 2.8 44.2 + - + +
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.3 41.7 - - + +
107B LEU* 3.9 10.0 - - + +
108B LYS* 3.2 46.0 + - + +
111B MET* 3.7 19.5 - - + -
126B LEU 3.0 11.3 + - - +
127B LEU* 3.2 18.4 - - + +
129B ILE* 1.3 78.1 - - - +
131B THR* 1.3 64.3 + - - +
134B GLU* 3.0 66.2 + - + +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.0 25.2 + - - +
128B GLY* 3.4 10.8 - - - -
130B TYR* 1.3 82.1 - - - +
132B GLU* 1.3 65.5 + - - +
134B GLU* 3.3 9.3 + - - +
135B LYS* 3.3 19.3 + - + +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 4.6 0.7 - - - -
48B GLU* 3.6 28.8 - - - +
52B HIS* 2.6 39.3 + - - -
128B GLY 2.9 12.7 + - - +
129B ILE* 3.2 9.0 - - - +
131B THR* 1.3 78.9 - - - +
133B LEU* 1.3 79.5 + - - +
135B LYS* 3.3 7.2 + - - +
136B HIS* 3.2 34.7 + - + +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 3.6 21.1 - - + -
100B TYR* 4.0 50.5 - - + +
103B MET* 4.1 30.7 - - + -
104B LEU* 4.0 10.1 - - + -
107B LEU* 4.3 9.0 - - + -
129B ILE* 2.8 23.9 + - + +
130B TYR 4.0 2.7 - - - +
132B GLU* 1.3 93.9 - - + +
134B GLU* 1.3 53.3 + - - +
136B HIS* 3.0 9.2 + - + +
137B ALA* 2.7 36.7 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 3.8 16.6 - - + +
130B TYR* 3.0 55.9 + - + +
131B THR* 3.6 8.8 - - - +
133B LEU* 1.3 75.3 - - - +
135B LYS* 1.3 62.2 + - - +
137B ALA* 3.6 8.1 + - - +
138B TRP* 3.2 20.4 + - - +
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B THR* 3.3 7.8 + - + +
132B GLU* 3.3 10.9 + - - +
133B LEU 3.2 0.4 - - - -
134B GLU* 1.3 75.3 - - - +
136B HIS* 1.3 69.5 + - + +
138B TRP* 3.1 42.7 + - + +
139B MET* 3.1 30.1 + - + +
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Residues in contact with HIS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 4.2 7.5 + - - -
44B GLU* 4.1 12.6 - - - -
45B LEU* 3.5 21.3 - - + +
48B GLU* 2.7 35.2 + - - -
100B TYR* 3.7 30.5 - + + -
132B GLU* 3.2 28.5 + - + +
133B LEU* 3.0 9.1 + - + +
135B LYS* 1.3 78.7 - - + +
137B ALA* 1.3 54.7 + - - +
139B MET* 3.0 22.2 + - + +
140B LEU* 2.7 43.1 + - + +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 4.2 7.1 - - + +
100B TYR* 4.7 7.8 - - + -
101B GLU* 4.5 14.8 - - + +
104B LEU* 5.5 4.3 - - + -
133B LEU 2.7 19.8 + - - +
134B GLU* 3.6 9.2 - - - +
136B HIS* 1.3 72.1 - - - +
138B TRP* 1.3 53.5 + - - +
140B LEU* 3.7 7.6 - - - +
141B ARG* 2.7 58.0 + - - +
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Residues in contact with TRP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLU 3.2 10.1 + - - +
135B LYS* 3.1 43.8 + - + +
137B ALA* 1.3 79.8 - - - +
139B MET* 1.3 75.6 + - + +
141B ARG* 3.3 14.8 + - - +
142B ALA* 2.7 44.6 + - + +
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Residues in contact with MET 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS* 3.2 34.1 - - - +
135B LYS* 3.4 22.9 - - + +
136B HIS* 3.0 27.9 + - + +
138B TRP* 1.3 102.3 - - + +
140B LEU* 1.3 69.9 + - + +
142B ALA* 3.3 5.7 + - - +
143B PHE* 2.9 23.6 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 6.0 3.4 - - + -
41B LYS* 5.1 21.1 - - + -
42B PHE* 6.3 1.3 - - + -
45B LEU* 5.1 6.7 - - + -
93B VAL* 3.6 29.5 - - + +
96B ILE* 4.1 25.1 - - + -
97B MET* 4.1 20.2 - - + -
100B TYR* 4.2 14.8 - - + -
136B HIS* 2.7 31.2 + - + +
137B ALA 3.7 3.1 - - - +
139B MET* 1.3 74.9 - - + +
141B ARG* 1.3 64.1 + - - +
143B PHE* 3.0 22.6 - - + +
144B LEU* 3.2 14.7 + - - +
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B MET* 3.8 17.4 - - + +
101B GLU* 2.4 34.6 + - - +
137B ALA* 2.7 49.4 + - - +
138B TRP* 3.5 12.8 - - - +
140B LEU* 1.3 73.7 - - - +
142B ALA* 1.3 57.4 + - - +
144B LEU* 2.9 19.9 + - - +
145B ASN* 2.9 45.5 + - + +
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B TRP* 2.7 37.0 + - + +
139B MET* 3.7 6.3 - - - +
141B ARG* 1.3 74.1 - - - +
143B PHE* 1.3 61.6 + - - +
144B LEU 3.4 0.3 + - - -
145B ASN* 3.5 17.8 - - - +
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Residues in contact with PHE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLN* 3.6 29.2 - - + -
37B THR* 5.2 2.7 - - - -
38B LEU* 3.5 28.7 - - + -
89B ALA* 5.9 0.9 - - + -
90B GLU* 4.9 12.6 - - - -
93B VAL* 3.8 29.6 - - + -
139B MET 2.9 13.0 + - - +
140B LEU* 3.0 16.8 + - + +
142B ALA* 1.3 79.1 - - - +
144B LEU* 1.3 76.6 + - + +
145B ASN* 4.7 0.2 - - - +
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU* 4.4 24.0 - - + +
93B VAL* 3.6 22.2 - - + -
94B GLU* 4.2 21.5 - - + +
97B MET* 4.3 14.4 - - + -
140B LEU 3.2 23.1 + - - +
141B ARG 2.9 4.4 + - - +
143B PHE* 1.3 103.9 - - + +
145B ASN* 1.3 78.7 + - - +
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Residues in contact with ASN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ARG* 2.9 42.8 + - + +
142B ALA* 3.5 16.3 - - - +
144B LEU* 1.3 86.1 - - - +
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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