Contacts of the helix formed by residues 104 - 129 (chain B) in PDB entry 1IZO
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 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU 3.5 15.3 - - - +
101B SER* 4.0 14.6 - - - +
102B LEU 3.8 0.6 - - - -
103B MET* 1.3 79.5 - - - +
105B PRO* 1.3 77.5 - - + +
106B PRO* 3.1 17.8 - - - +
107B HIS* 3.1 16.9 + - - -
108B GLN* 2.9 20.4 + - - +
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Residues in contact with PRO 105 (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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104B THR* 1.3 89.4 - - - +
106B PRO* 1.3 67.2 - - + +
108B GLN* 3.0 21.9 + - - +
109B LYS* 3.0 46.8 + - - +
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Residues in contact with PRO 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B THR* 3.1 16.8 - - - +
105B PRO* 1.3 97.3 - - + +
107B HIS* 1.3 63.5 + - + +
109B LYS* 3.3 17.4 + - + +
110B ARG* 3.1 23.0 + - - +
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Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B SER 3.1 27.9 + - - -
102B LEU* 3.3 29.8 - - + +
103B MET* 4.1 1.6 - - - -
104B THR* 3.1 20.9 + - - +
106B PRO* 1.3 82.9 - - + +
108B GLN* 1.3 62.2 + - - +
110B ARG* 3.6 6.3 + - + +
111B LEU* 3.2 28.2 + - - +
149B TRP* 3.7 24.9 + + + +
211B GLY* 2.9 28.0 + - - -
212B THR* 5.7 2.0 - - + -
368B ILE* 5.1 2.2 - - + -
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Residues in contact with GLN 108 (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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103B MET 2.5 26.5 + - - +
104B THR* 2.9 19.1 - - - +
105B PRO* 3.0 20.5 + - + +
107B HIS* 1.3 76.2 - - - +
109B LYS* 1.3 66.8 + - + +
111B LEU* 3.7 2.6 + - - +
112B ALA* 3.2 22.2 + - - +
367B GLY* 3.0 31.4 - - - +
368B ILE* 3.6 23.2 - - + +
371B GLU* 3.7 24.6 - - + +
372B VAL* 5.7 0.3 - - - +
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Residues in contact with LYS 109 (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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105B PRO* 3.0 39.9 + - - +
106B PRO* 3.3 14.9 + - + +
108B GLN* 1.3 75.0 - - + +
110B ARG* 1.3 57.5 + - - +
112B ALA* 3.0 6.9 + - - +
113B GLU* 2.7 54.4 + - - +
371B GLU* 5.5 8.3 - - + +
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PRO 3.1 14.1 + - - +
107B HIS* 3.6 11.2 - - + +
109B LYS* 1.3 79.2 - - - +
111B LEU* 1.3 56.7 - - - +
113B GLU* 3.5 19.3 + - - +
114B LEU* 2.9 57.3 + - + +
148B TYR* 4.1 25.9 + - - -
149B TRP* 3.8 20.1 - - + +
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Residues in contact with LEU 111 (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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107B HIS 3.2 14.1 + - - +
108B GLN 4.0 3.8 - - - +
110B ARG* 1.3 74.9 - - - +
112B ALA* 1.3 62.1 + - - +
114B LEU* 3.3 4.0 + - + +
115B MET* 2.9 35.1 + - - +
145B VAL* 3.7 20.8 - - + +
146B ALA* 4.8 2.9 - - - -
149B TRP* 3.3 46.7 - - + -
244B ILE* 4.0 22.9 - - + -
368B ILE* 3.5 41.1 - - + -
372B VAL* 4.4 11.7 - - + -
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Residues in contact with ALA 112 (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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108B GLN 3.2 12.7 + - - +
109B LYS* 3.0 10.4 + - - +
111B LEU* 1.3 78.2 - - - +
113B GLU* 1.3 59.1 + - + +
115B MET* 3.2 7.0 + - - +
116B THR* 2.9 32.9 + - - -
371B GLU* 3.9 21.5 - - + +
372B VAL* 4.7 4.6 - - - +
375B ALA* 3.8 22.6 - - + +
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Residues in contact with GLU 113 (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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109B LYS* 2.7 39.3 + - - +
110B ARG* 3.7 19.6 + - - +
112B ALA* 1.3 71.6 - - + +
114B LEU* 1.3 64.0 + - + +
116B THR* 3.2 9.6 + - - -
117B GLU* 3.2 22.7 + - - +
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Residues in contact with LEU 114 (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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110B ARG* 2.9 59.8 + - + +
111B LEU* 3.5 0.7 - - - +
113B GLU* 1.3 77.2 - - + +
115B MET* 1.3 64.2 + - - +
117B GLU* 3.4 22.1 + - - +
118B GLU* 3.1 24.8 + - - +
145B VAL* 3.5 31.2 - - + -
148B TYR* 4.1 30.7 - - + -
149B TRP* 4.1 20.6 - - + -
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Residues in contact with MET 115 (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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111B LEU 2.9 22.2 + - - +
112B ALA* 3.5 7.4 - - - +
114B LEU* 1.3 75.0 - - - +
116B THR* 1.3 60.3 + - - +
118B GLU* 3.8 2.7 - - - +
119B TRP* 2.7 66.1 + - + +
141B ILE* 3.5 19.1 - - + -
142B LEU* 3.2 35.9 - - + -
145B VAL* 3.6 28.3 - - + -
244B ILE* 6.3 0.2 - - - -
251B LEU* 4.5 0.7 - - + -
372B VAL* 4.2 18.6 - - + -
375B ALA* 5.2 3.4 - - + -
376B SER* 4.1 9.2 - - - +
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA 2.9 20.1 + - - -
113B GLU* 3.2 13.7 + - - -
115B MET* 1.3 76.1 - - - +
117B GLU* 1.3 63.6 + - - +
119B TRP* 3.0 12.6 + - - +
120B LYS* 3.0 49.2 + - + +
375B ALA* 3.7 19.1 + - - +
383B GLN* 5.7 2.0 - - - +
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Residues in contact with GLU 117 (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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113B GLU 3.2 7.5 + - - +
114B LEU* 3.4 29.1 - - - +
116B THR* 1.3 81.8 - - - +
118B GLU* 1.3 63.7 + - + +
120B LYS* 3.3 10.1 + - - +
121B ALA* 2.9 28.2 + - + +
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Residues in contact with GLU 118 (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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114B LEU* 3.1 17.9 + - + +
115B MET 3.8 4.5 - - - +
116B THR 3.3 0.2 - - - -
117B GLU* 1.3 77.4 - - + +
119B TRP* 1.3 58.0 + - - +
121B ALA* 3.4 7.3 + - - +
122B ALA* 2.9 29.8 + - - +
141B ILE* 3.7 28.0 - - + +
144B ARG* 3.1 44.2 + - - +
145B VAL* 3.7 21.3 - - + +
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Residues in contact with TRP 119 (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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115B MET* 2.7 52.1 + - + +
116B THR* 3.0 11.3 + - - +
118B GLU* 1.3 73.3 - - - +
120B LYS* 1.3 68.4 + - + +
122B ALA* 3.1 11.2 + - + +
123B VAL 3.4 6.9 + - - -
126B TRP* 3.4 31.2 - + - -
134B LEU* 4.1 21.3 - - + -
137B GLU* 5.1 1.3 - - + -
138B ALA* 4.5 12.1 - - + -
141B ILE* 3.8 19.7 - - + -
251B LEU* 4.0 12.1 - - + -
375B ALA 4.7 1.1 - - - -
376B SER* 3.1 42.3 + - - -
379B PHE* 3.4 57.0 - + + -
380B LEU* 6.0 0.9 - - + -
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Residues in contact with LYS 120 (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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116B THR* 3.0 37.0 + - + +
117B GLU* 3.6 10.1 - - - +
119B TRP* 1.3 74.2 - - + +
121B ALA* 1.3 67.2 + - - +
122B ALA 2.8 1.7 + - - -
123B VAL* 2.9 28.8 + - - +
124B THR* 4.3 2.1 + - - -
379B PHE* 4.8 1.6 - - - -
383B GLN* 4.0 34.1 - - + +
415B ARG* 4.6 6.4 + - - +
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Residues in contact with ALA 121 (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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117B GLU* 2.9 20.1 + - + +
118B GLU* 3.7 9.2 - - - +
120B LYS* 1.3 76.3 - - - +
122B ALA* 1.3 59.9 + - - +
123B VAL 3.5 0.3 + - - -
124B THR* 3.8 19.3 + - - -
125B ARG* 4.6 4.7 + - - +
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Residues in contact with ALA 122 (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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118B GLU 2.9 17.8 + - - +
119B TRP* 3.5 9.9 - - + +
120B LYS 2.8 1.2 + - - -
121B ALA* 1.3 75.5 - - - +
123B VAL* 1.3 65.4 + - - +
124B THR 3.2 0.4 - - - -
125B ARG* 3.2 23.8 + - - +
126B TRP* 3.0 50.0 + - + +
141B ILE* 4.4 10.3 - - + -
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Residues in contact with VAL 123 (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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119B TRP 3.4 10.5 + - - +
120B LYS* 2.9 20.3 + - - +
122B ALA* 1.3 77.0 - - - +
124B THR* 1.3 64.4 + - - +
126B TRP* 3.0 8.4 + - - -
127B GLU* 2.8 54.9 + - + +
379B PHE* 3.8 18.2 - - + -
383B GLN* 5.2 3.6 - - + +
384B ILE* 3.9 17.7 - - + -
413B ILE* 5.1 1.8 - - + -
414B ARG 4.9 0.2 - - - -
415B ARG* 3.8 33.4 - - + +
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Residues in contact with THR 124 (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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120B LYS 4.3 1.4 + - - -
121B ALA* 3.8 15.3 + - - -
122B ALA 3.2 0.2 - - - -
123B VAL* 1.3 79.8 - - - +
125B ARG* 1.3 62.6 + - + +
127B GLU* 3.9 10.7 + - - +
128B LYS* 2.9 48.6 + - - +
415B ARG* 4.0 12.9 + - - +
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Residues in contact with ARG 125 (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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121B ALA 5.1 3.7 + - - +
122B ALA* 3.2 24.5 + - - +
123B VAL 3.2 0.4 - - - -
124B THR* 1.3 79.9 - - + +
126B TRP* 1.3 71.7 + - + +
128B LYS* 3.2 12.2 + - - +
129B ALA* 3.1 21.6 + - - +
137B GLU* 4.0 19.2 + - - -
140B GLU* 5.8 1.6 + - - -
141B ILE* 5.4 3.6 - - - +
144B ARG* 4.2 22.0 - - - +
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Residues in contact with TRP 126 (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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119B TRP* 3.4 35.9 - + - -
122B ALA* 3.0 33.2 + - + +
123B VAL* 3.6 5.4 - - - +
125B ARG* 1.3 81.9 - - + +
127B GLU* 1.3 63.7 + - - +
129B ALA* 2.9 25.7 + - + +
132B VAL* 3.7 17.7 - - + -
134B LEU* 4.9 8.7 - - + -
137B GLU* 3.0 43.8 + - + -
141B ILE* 5.1 0.7 - - + -
379B PHE* 3.2 32.8 - + - -
380B LEU* 5.3 0.9 - - + -
384B ILE* 3.8 8.1 - - + -
410B MET* 4.3 11.9 - - + -
413B ILE* 3.5 49.2 - - + +
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Residues in contact with GLU 127 (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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123B VAL* 2.8 43.3 + - + +
124B THR* 4.1 6.9 - - - +
126B TRP* 1.3 77.3 - - - +
128B LYS* 1.3 62.5 + - + +
129B ALA 3.3 6.4 + - - +
413B ILE* 3.7 23.4 + - + +
414B ARG* 3.7 6.7 - - - +
415B ARG* 3.2 40.7 + - - +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B THR* 2.9 48.0 + - - +
125B ARG* 3.2 14.8 + - - +
127B GLU* 1.3 77.5 - - + +
129B ALA* 1.3 57.7 + - - +
130B ASP 4.2 0.3 + - - -
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Residues in contact with ALA 129 (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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125B ARG 3.1 10.4 + - - +
126B TRP* 2.9 20.3 + - - +
127B GLU 3.7 5.5 - - - +
128B LYS* 1.3 81.5 - - - +
130B ASP* 1.3 66.2 + - - +
131B GLU 4.5 4.9 - - - +
132B VAL* 3.9 21.3 - - + -
412B GLY* 5.3 2.8 + - - -
413B ILE* 5.5 1.7 + - - +
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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