Contacts of the helix formed by residues 109 - 137 (chain B) in PDB entry 1JT0
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 THR 109 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU* 6.1 0.4 - - - +
106B TYR* 2.8 39.8 + - + +
108B LYS* 1.3 71.7 - - - +
110B ASN* 1.3 66.6 + - - +
111B SER* 3.3 4.5 - - - -
112B ILE* 3.2 17.1 + - + +
113B ASN* 3.0 18.7 + - - +
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B TYR 5.6 0.2 - - - +
108B LYS 2.9 16.0 + - - +
109B THR* 1.3 67.9 - - - +
111B SER* 1.3 68.6 + - - +
113B ASN* 3.0 12.1 + - - +
114B GLU* 2.8 46.1 + - + +
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B THR* 3.3 4.0 + - - -
110B ASN* 1.3 79.2 - - - +
112B ILE* 1.3 74.2 + - - +
114B GLU* 3.7 5.4 + - - +
115B LYS* 3.3 43.3 + - - +
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLU* 4.2 20.2 - - + +
51B LEU* 3.8 23.6 - - + -
102B PHE* 3.2 34.5 - - + -
103B TYR* 6.1 0.9 - - - -
106B TYR* 4.1 14.6 - - + +
109B THR* 3.5 30.7 - - + +
110B ASN 3.1 0.2 - - - -
111B SER* 1.3 83.7 - - - +
113B ASN* 1.3 68.5 + - - +
115B LYS* 3.2 7.1 + - - +
116B MET* 2.7 35.7 + - + +
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Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.5 27.0 + - - -
106B TYR 4.8 1.5 + - - -
107B TYR* 3.5 32.2 + - - +
109B THR 3.0 9.6 + - - +
110B ASN* 3.0 18.7 + - - +
112B ILE* 1.3 79.4 - - - +
114B GLU* 1.3 72.0 + - - +
116B MET* 3.2 4.8 + - - +
117B ASN* 2.9 40.8 + - - +
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Residues in contact with GLU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 2.8 42.7 + - + +
111B SER* 3.8 5.8 - - - +
113B ASN* 1.3 83.1 + - - +
115B LYS* 1.3 66.5 + - + +
117B ASN* 3.0 5.8 + - - +
118B LYS* 2.8 38.4 + - + +
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Residues in contact with LYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASN* 6.1 1.2 - - - +
51B LEU* 3.6 39.2 - - + +
55B ASN* 5.8 2.2 + - - -
111B SER* 3.3 32.3 + - - +
112B ILE* 3.2 6.9 + - - +
114B GLU* 1.3 80.1 - - + +
116B MET* 1.3 63.9 + - - +
118B LYS* 3.5 7.3 + - - +
119B LEU* 3.1 28.3 + - + +
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Residues in contact with MET 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.4 5.4 - - + +
54B LEU* 3.7 28.9 - - + -
92B TYR* 5.0 2.7 - - - +
99B ILE* 3.8 25.4 - - + -
102B PHE* 3.6 29.2 - - - -
103B TYR* 3.9 28.0 - - + -
112B ILE* 2.7 38.5 + - + +
113B ASN* 3.5 4.3 - - - +
115B LYS* 1.3 72.8 - - - +
117B ASN* 1.3 63.6 + - - +
119B LEU* 3.4 13.2 - - + +
120B GLU* 3.2 27.1 + - - +
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.5 26.8 + - - -
113B ASN* 2.9 42.9 + - - +
114B GLU* 3.6 5.5 + - - +
116B MET* 1.3 67.8 - - - +
118B LYS* 1.3 57.6 + - + +
119B LEU 3.0 1.8 - - - -
120B GLU* 2.8 18.5 + - - +
121B ASN* 2.7 47.0 + - - +
165D GLU* 5.3 10.2 + - - +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 2.8 32.3 + - + +
115B LYS* 3.6 7.9 - - - +
117B ASN* 1.3 72.4 - - + +
119B LEU* 1.3 63.3 + - + +
121B ASN* 3.3 14.0 + - + +
122B LYS* 3.2 27.4 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 5.4 3.4 - - + +
54B LEU* 3.8 34.8 - - + -
55B ASN* 4.3 20.6 - - - +
58B GLU* 3.7 31.2 - - + -
92B TYR* 4.1 20.2 - - + +
115B LYS* 3.1 17.7 + - + +
116B MET* 3.4 17.7 - - + +
117B ASN 3.0 0.4 - - - -
118B LYS* 1.3 79.4 - - + +
120B GLU* 1.3 61.9 + - - +
122B LYS* 3.4 24.0 + - + +
123B TYR* 3.4 13.9 - - - -
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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
----------------------------------------------------------
92B TYR* 4.1 13.2 - - - +
96B GLN* 4.7 9.7 - - - +
99B ILE* 4.8 9.4 - - - +
100B ILE* 6.0 1.9 - - - +
103B TYR* 4.7 15.0 - - - +
116B MET* 3.2 15.4 + - + +
117B ASN* 2.8 24.8 + - - +
119B LEU* 1.3 74.4 - - - +
121B ASN* 1.3 69.3 + - - +
123B TYR* 2.8 23.0 + - - +
124B ILE* 3.1 17.8 + - + +
162D PHE* 4.8 17.8 - - - +
165D GLU* 5.1 3.1 - - - +
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Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASN* 2.7 33.1 + - - +
118B LYS* 3.3 15.6 + - + +
120B GLU* 1.3 74.6 - - - +
122B LYS* 1.3 63.8 + - - +
124B ILE* 2.9 22.6 + - - +
125B ASP* 2.8 35.5 + - - +
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.5 45.5 - - + +
62B GLN* 4.0 13.1 + - - +
118B LYS 3.2 17.4 + - - +
119B LEU* 3.4 16.6 - - + +
120B GLU 3.1 0.4 - - - -
121B ASN* 1.3 74.8 - - - +
123B TYR* 1.3 62.5 + - - +
125B ASP* 3.4 11.5 + - - +
126B ALA* 3.2 20.6 + - - +
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Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.6 18.0 - - + -
61B TRP* 3.3 43.3 - + - +
82B TYR* 3.3 21.7 + - - +
92B TYR* 2.9 60.9 - + - +
93B TYR* 3.7 29.4 - + - +
119B LEU 3.4 15.7 - - - -
120B GLU* 2.8 10.3 + - - +
122B LYS* 1.3 76.3 - - - +
124B ILE* 1.3 67.6 + - + +
126B ALA* 3.3 12.5 + - - +
127B TYR* 3.4 20.0 - - + -
153B ALA* 5.1 3.4 - - + -
157B ASN* 6.0 4.0 - - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 3.1 14.4 + - + +
121B ASN* 2.9 27.0 + - - +
123B TYR* 1.3 77.4 - - + +
125B ASP* 1.3 65.0 + - - +
127B TYR* 3.1 7.8 + - - +
128B HIS* 3.0 18.6 + - + +
146B ASN* 5.1 0.9 - - - +
149B SER* 3.9 20.0 - - - -
150B LYS* 4.0 31.4 - - + +
153B ALA* 4.0 22.7 - - + -
154B ASN* 5.4 7.0 - - - +
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ASN* 2.8 32.3 + - - +
122B LYS* 3.7 9.7 + - - +
124B ILE* 1.3 76.8 - - - +
126B ALA* 1.3 67.4 + - - +
128B HIS* 2.8 15.0 + - + +
129B VAL* 2.7 31.1 + - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN* 5.5 4.7 - - - +
65B TRP* 4.8 9.2 + - + +
82B TYR* 3.3 39.9 - - + +
122B LYS 3.2 9.8 + - - +
123B TYR* 3.4 4.0 - - - +
124B ILE 3.2 0.2 - - - -
125B ASP* 1.3 78.4 - - - +
127B TYR* 1.3 61.7 + - - +
129B VAL* 3.3 9.3 + - - +
130B ILE* 3.1 28.4 + - - +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.6 31.9 - + - -
82B TYR* 3.3 35.6 - + + -
83B ASN* 2.6 29.4 + - - -
93B TYR* 4.4 5.5 + - - -
123B TYR* 3.4 20.6 + - + -
124B ILE 3.1 7.3 + - - +
125B ASP 3.0 0.2 - - - -
126B ALA* 1.3 75.1 - - - +
128B HIS* 1.3 68.6 + - - +
129B VAL 3.1 0.2 - - - -
130B ILE* 3.0 9.2 + - + +
131B PHE* 2.8 34.9 + + + -
149B SER* 3.7 13.2 - - - +
152B ALA* 4.0 17.0 - - + -
153B ALA* 3.7 28.5 - - + -
156B VAL* 3.5 15.1 - - - +
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.0 9.3 + - + +
125B ASP* 3.2 18.9 + - - +
127B TYR* 1.3 80.3 - - - +
129B VAL* 1.3 59.5 + - + +
131B PHE* 3.4 2.3 + - - +
132B LYS* 2.8 49.2 + - + +
145B VAL* 3.1 29.1 - - + +
146B ASN* 3.8 29.8 + - - -
149B SER* 3.0 17.3 + - - +
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Residues in contact with VAL 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLN* 6.3 0.9 - - - +
125B ASP* 2.7 19.5 + - + +
126B ALA* 3.4 11.9 - - - +
127B TYR 3.1 0.2 - - - -
128B HIS* 1.3 79.1 - - + +
130B ILE* 1.3 69.3 + - + +
131B PHE 3.1 0.2 + - - -
132B LYS* 4.6 4.9 - - - -
133B GLU* 2.8 49.0 + - + +
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 4.0 28.3 - - + +
75B ASN* 3.6 36.8 - - + +
78B LYS* 4.3 15.9 - - + +
79B PHE* 4.2 16.8 - - + +
82B TYR* 4.2 20.4 - - + -
126B ALA 3.1 15.2 + - - +
127B TYR* 3.0 18.7 + - + +
129B VAL* 1.3 78.3 - - + +
131B PHE* 1.3 60.5 + - + +
133B GLU* 4.5 0.2 - - - -
134B GLY 2.9 23.6 + - - -
140B TRP* 3.4 12.1 - - + -
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.6 33.2 - + - -
127B TYR* 2.8 34.4 + + + +
128B HIS 3.8 2.9 - - - +
130B ILE* 1.3 71.6 - - + +
132B LYS* 1.3 61.1 + - - +
134B GLY 3.2 0.2 + - - -
135B ASN* 2.8 29.6 + - - +
140B TRP* 3.0 25.6 + + - -
142B ILE* 3.5 23.1 - - + -
145B VAL* 4.2 13.0 - - + -
148B VAL* 3.9 24.2 - - + -
149B SER* 3.7 15.5 - - - -
152B ALA* 3.9 18.8 - - + -
182B PHE* 4.3 3.1 - + - -
183B LEU* 4.9 2.5 - - + -
186B LEU* 3.9 20.0 - - + -
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B HIS* 2.8 44.1 + - + +
129B VAL* 3.8 4.7 - - - +
131B PHE* 1.3 68.8 - - - +
133B GLU* 1.3 73.9 + - + +
135B ASN* 3.0 21.7 + - + +
136B LEU* 3.1 14.9 + - + +
145B VAL* 4.8 5.7 - - + +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 3.1 23.8 - - - +
78B LYS* 5.2 6.9 + - - -
129B VAL* 2.8 48.6 + - + +
130B ILE 4.5 0.2 - - - +
132B LYS* 1.3 77.1 - - + +
134B GLY* 1.3 64.8 + - - +
135B ASN 3.0 0.5 + - - -
136B LEU* 3.1 9.7 + - - +
137B ASN* 2.9 23.7 + - - +
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Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 3.5 17.2 - - - +
130B ILE 2.9 11.1 + - - -
131B PHE 3.5 3.6 - - - -
133B GLU* 1.3 76.3 - - - +
135B ASN* 1.3 58.8 + - - +
137B ASN 3.4 0.3 + - - -
138B GLY 3.1 2.4 + - - -
139B GLU* 2.8 33.9 + - - +
140B TRP* 3.4 26.7 + - - -
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Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE 2.8 12.3 + - - +
132B LYS* 3.1 14.4 - - + +
133B GLU 3.0 0.4 - - - -
134B GLY* 1.3 72.4 - - - +
136B LEU* 1.3 56.0 + - - +
137B ASN 2.9 3.4 - - - -
138B GLY* 2.7 27.5 + - - -
140B TRP* 3.2 20.3 - - - +
141B SER* 3.5 1.4 - - - -
142B ILE* 3.0 45.4 + - - +
145B VAL* 3.6 19.6 - - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LYS* 3.1 8.8 + - + +
133B GLU* 3.8 9.0 - - - +
135B ASN* 1.3 78.3 - - - +
137B ASN* 1.3 63.8 + - + +
138B GLY 3.2 1.1 + - - -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR* 5.7 3.2 - - - +
75B ASN* 4.1 10.2 - - - +
133B GLU 2.9 15.2 + - - +
134B GLY 3.9 4.0 - - - +
135B ASN 2.9 0.8 + - - -
136B LEU* 1.3 83.3 - - + +
138B GLY* 1.3 63.1 + - - +
139B GLU* 3.3 26.1 + - + +
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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