Contacts of the helix formed by residues 102 - 137 (chain B) in PDB entry 2M59
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 LYS 102 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 5.8 6.3 - - - +
7A ILE* 4.7 18.5 - - - +
101B GLU* 1.3 70.1 - - - +
103B THR* 1.3 70.3 + - + +
105B LEU* 2.9 11.6 + - - +
106B GLU* 2.9 38.0 + - + +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 5.8 6.3 - - - +
3A THR* 4.8 18.4 - - + -
6A GLU* 5.9 1.6 - - + -
101B GLU* 4.0 12.8 + - - +
102B LYS* 1.3 78.4 - - + +
104B ASN* 1.3 79.5 + - - +
106B GLU* 2.7 23.3 + - + +
107B ILE* 2.9 26.6 + - - +
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Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU* 3.7 40.0 + - - +
102B LYS 3.4 0.4 - - - -
103B THR* 1.3 87.9 + - - +
105B LEU* 1.3 58.9 + - - +
107B ILE* 3.7 8.3 + - - +
108B ILE* 2.9 40.0 + - + +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU 3.1 16.0 + - - +
102B LYS* 2.9 12.4 + - - +
104B ASN* 1.3 74.9 - - - +
106B GLU* 1.3 71.8 + - - +
108B ILE* 3.1 16.8 + - + +
109B ILE* 2.8 50.8 + - + +
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A THR* 5.9 2.0 - - + -
6A GLU* 3.3 58.4 - - + +
7A ILE* 3.9 11.3 + - + +
10A LEU* 4.0 12.3 - - - +
102B LYS* 2.9 34.1 + - + +
103B THR* 2.7 16.9 + - + +
105B LEU* 1.3 77.4 - - - +
107B ILE* 1.3 60.9 + - + +
109B ILE* 3.8 5.5 - - - +
110B LEU* 3.2 30.4 + - - +
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 4.8 15.5 - - - +
6A GLU* 4.3 11.0 - - + +
103B THR* 2.9 41.6 + - - +
104B ASN* 4.0 9.0 - - - +
106B GLU* 1.3 76.2 - - + +
108B ILE* 1.3 69.9 + - + +
110B LEU* 3.2 8.0 + - - +
111B VAL* 3.1 31.3 + - + +
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN* 2.9 34.5 + - + +
105B LEU* 3.1 19.2 + - + +
107B ILE* 1.3 79.1 - - + +
109B ILE* 1.3 66.5 + - + +
111B VAL* 3.2 10.7 + - - +
112B GLY* 3.1 18.0 + - - -
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.2 38.4 - - + -
105B LEU* 2.8 43.9 + - + +
106B GLU* 3.8 7.4 - - - +
108B ILE* 1.3 76.1 - - + +
110B LEU* 1.3 52.5 + - - +
112B GLY* 3.0 4.2 + - - +
113B THR* 2.5 49.8 + - + +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 4.0 15.7 - - - +
9A ILE* 3.2 34.5 - - + -
10A LEU* 3.1 36.1 - - + -
13A THR* 5.5 1.8 - - + +
106B GLU 3.2 12.9 + - - +
107B ILE* 3.2 11.0 + - - +
109B ILE* 1.3 77.4 - - - +
111B VAL* 1.3 53.5 + - + +
113B THR* 2.7 8.3 + - - +
114B ALA* 2.7 38.6 + - + +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE* 3.1 24.3 + - + +
108B ILE* 3.4 9.9 - - + +
109B ILE 3.2 0.2 - - - -
110B LEU* 1.3 77.8 - - + +
112B GLY* 1.3 63.3 + - - +
114B ALA* 3.7 5.4 - - - +
115B VAL* 3.2 36.7 + - + +
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Residues in contact with GLY 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ILE 3.1 6.8 + - - -
109B ILE* 3.0 6.2 + - - -
111B VAL* 1.3 81.2 - - - +
113B THR* 1.3 62.3 + - - +
115B VAL* 3.6 5.4 + - - +
116B ILE* 3.1 31.1 + - - +
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Residues in contact with THR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 5.5 1.1 - - + -
13A THR* 4.0 39.7 - - - +
14A ALA* 5.6 0.7 - - - +
17A ALA* 6.2 2.5 - - + -
109B ILE* 2.5 40.6 + - + +
110B LEU* 2.7 19.2 + - - +
112B GLY* 1.3 68.6 - - - +
114B ALA* 1.3 59.1 + - - +
116B ILE* 3.5 5.3 + - - +
117B ALA* 3.0 30.5 + - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 6.2 0.7 - - - -
110B LEU* 2.7 22.6 + - + +
111B VAL* 3.7 6.7 - - - +
112B GLY 3.3 0.2 - - - -
113B THR* 1.3 73.8 - - - +
115B VAL* 1.3 63.8 + - + +
117B ALA* 3.3 6.3 + - - +
118B MET* 3.1 22.7 + - - +
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B VAL* 3.2 26.8 + - + +
112B GLY* 4.0 5.6 - - - +
114B ALA* 1.3 77.5 - - + +
116B ILE* 1.3 67.7 + - + +
118B MET* 3.1 8.5 + - + +
119B PHE* 3.1 33.5 + - + +
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 5.8 5.8 - - + -
112B GLY 3.1 19.4 + - - +
113B THR* 3.9 6.1 - - - +
115B VAL* 1.3 80.2 - - + +
117B ALA* 1.3 62.8 + - - +
119B PHE* 3.3 12.9 + - + +
120B PHE* 3.1 50.5 + - + -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 6.2 3.1 - - + -
16A ILE* 5.8 4.0 - - + -
20A PHE* 5.0 13.4 - - + -
113B THR 3.0 19.5 + - - +
114B ALA* 3.5 7.2 - - - +
115B VAL 3.2 0.2 - - - -
116B ILE* 1.3 79.5 - - - +
118B MET* 1.3 61.3 + - - +
120B PHE* 3.4 8.8 + - - +
121B TRP* 3.1 23.1 + - - +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ALA 3.1 13.0 + - - +
115B VAL* 3.5 10.5 - - + +
117B ALA* 1.3 76.6 - - - +
119B PHE* 1.3 62.0 + - - +
121B TRP* 3.4 10.4 + - - +
122B LEU* 3.0 45.7 + - + +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.1 24.4 + - + +
116B ILE* 3.5 16.8 - - + +
117B ALA 3.2 0.2 - - - -
118B MET* 1.3 73.8 - - - +
120B PHE* 1.3 58.7 + - + +
122B LEU* 3.1 8.8 + - + +
123B LEU* 2.8 45.0 + - + +
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Residues in contact with PHE 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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17A ALA* 5.0 11.9 - - + -
20A PHE* 4.1 42.1 - + + -
21A TRP* 3.3 42.2 - + - -
24A LEU* 4.4 10.8 - - + -
116B ILE* 3.1 45.4 + - + +
117B ALA* 3.4 5.8 + - - +
119B PHE* 1.3 80.9 - - + +
121B TRP* 1.3 54.7 + - - +
123B LEU* 3.3 21.4 - - + +
124B LEU* 2.7 37.4 + - - +
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Residues in contact with TRP 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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20A PHE* 3.3 42.0 - + - -
117B ALA 3.1 13.0 + - - +
118B MET* 3.5 17.3 - - - +
119B PHE 3.1 0.8 - - - -
120B PHE* 1.3 76.7 - - - +
122B LEU* 1.3 68.7 + - + +
124B LEU* 3.3 17.2 + - + +
125B VAL* 3.1 34.9 + - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET* 3.0 42.2 + - + +
119B PHE* 3.1 11.3 + - + +
121B TRP* 1.3 85.9 - - + +
123B LEU* 1.3 64.9 + - - +
125B VAL* 3.1 17.6 + - - +
126B ILE* 3.1 24.6 + - + +
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.1 41.1 - - + -
119B PHE* 2.8 29.2 + - + +
120B PHE* 3.3 25.6 - - + +
122B LEU* 1.3 73.2 - - - +
124B LEU* 1.3 78.0 + - + +
126B ILE* 3.4 11.6 + - - +
127B ILE* 3.0 37.0 + - + +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 4.4 10.5 - - + -
23A LEU* 3.1 40.6 - - + -
24A LEU* 4.9 5.8 - - + -
27A ILE* 3.5 19.7 - - + -
120B PHE 2.7 23.3 + - - +
121B TRP* 3.5 29.8 - - + +
123B LEU* 1.3 79.0 - - + +
125B VAL* 1.3 63.8 + - + +
127B ILE* 3.4 5.6 + - + +
128B LEU* 3.1 45.6 + - + +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B TRP* 3.1 27.7 + - + +
122B LEU* 3.1 11.3 + - - +
124B LEU* 1.3 75.2 - - + +
126B ILE* 1.3 60.5 + - + +
128B LEU* 3.2 11.1 + - + +
129B ARG* 2.8 69.2 + - + +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B LEU* 3.1 22.6 + - + +
123B LEU* 3.7 9.4 - - - +
125B VAL* 1.3 76.3 - - + +
127B ILE* 1.3 63.9 + - + +
129B ARG* 3.2 21.8 + - + +
130B THR* 3.1 24.1 + - - -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.5 31.9 - - + -
27A ILE* 3.2 38.4 - - + -
28A LEU* 4.8 15.0 - - + -
31A VAL* 5.0 2.7 - - + -
123B LEU* 3.0 31.4 + - + +
124B LEU* 3.6 9.0 - - + +
125B VAL 3.2 0.2 - - - -
126B ILE* 1.3 78.8 - - + +
128B LEU* 1.3 61.2 + - + +
129B ARG 3.3 0.2 + - - -
130B THR* 3.5 5.2 + - + +
131B VAL* 2.9 36.1 + - + +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 4.8 22.4 - - + -
124B LEU* 3.1 42.0 + - + +
125B VAL* 3.7 8.7 - - + +
127B ILE* 1.3 76.3 - - + +
129B ARG* 1.3 59.0 + - + +
131B VAL* 3.9 8.1 - - + +
132B LYS* 2.9 33.5 + - - +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 2.8 43.6 + - + +
126B ILE* 3.3 23.6 - - + +
127B ILE 3.1 0.2 - - - -
128B LEU* 1.3 75.5 - - - +
130B THR* 1.3 61.2 + - - +
132B LYS* 3.3 9.4 + - - +
133B ARG* 3.0 33.1 + - - +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 5.7 6.7 - - + -
126B ILE* 3.1 13.0 + - - -
127B ILE* 4.0 6.7 - - - +
129B ARG* 1.3 79.7 - - - +
131B VAL* 1.3 69.8 + - + +
133B ARG* 3.4 9.1 + - - +
134B ALA* 3.4 20.3 + - - +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 5.0 3.1 - - + -
30A THR* 5.7 5.8 - - + -
31A VAL* 3.7 30.7 - - + -
127B ILE* 2.9 30.4 + - + +
128B LEU* 3.9 9.6 - - + +
130B THR* 1.3 85.0 - - + +
132B LYS* 1.3 62.0 + - - +
134B ALA* 3.5 6.6 + - - +
135B ASN* 3.3 22.7 + - - +
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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 LEU* 2.9 22.1 + - - +
129B ARG* 3.8 8.1 - - - +
131B VAL* 1.3 74.9 - - - +
133B ARG* 1.3 65.2 + - - +
134B ALA 3.3 0.4 + - - -
135B ASN* 3.6 15.8 + - + +
136B GLY* 3.6 8.5 + - - -
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG 3.0 18.7 + - - +
130B THR* 3.6 10.3 - - - +
131B VAL 3.2 0.2 - - - -
132B LYS* 1.3 79.3 - - - +
134B ALA* 1.3 59.7 + - - +
136B GLY* 3.6 2.1 + - - -
137B GLY 3.6 19.8 + - - -
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR 3.4 10.0 + - - +
131B VAL* 3.5 9.4 + - - +
132B LYS 3.3 0.2 - - - -
133B ARG* 1.3 75.8 - - - +
135B ASN* 1.3 64.7 - - - +
136B GLY 3.1 3.4 + - - -
137B GLY* 3.4 13.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B VAL* 3.3 13.9 + - - +
132B LYS* 3.7 15.2 - - + +
133B ARG 3.4 0.2 - - - -
134B ALA* 1.3 78.8 - - - +
136B GLY* 1.3 62.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LYS 3.6 6.3 + - - -
133B ARG 3.6 5.6 + - - -
134B ALA 3.1 0.8 - - - -
135B ASN* 1.3 81.9 - - - +
137B GLY* 1.3 58.1 + - - +
----------------------------------------------------------
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Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 3.6 12.4 + - - -
134B ALA* 3.4 12.9 + - - -
136B GLY* 1.3 78.2 - - - +
----------------------------------------------------------
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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