Contacts of the helix formed by residues 112 - 137 (chain B) in PDB entry 3BUM
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 ASN 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B THR* 3.0 10.3 + - + +
109B LEU* 3.0 19.6 + - + +
111B GLU* 1.3 75.1 - - - +
113B GLU* 1.3 61.7 + - - +
114B TYR* 3.3 12.6 + - - +
115B PHE* 3.0 31.5 + - + +
116B ARG* 2.9 30.1 + - - +
169B PHE* 4.2 3.0 - - - -
174B PHE* 3.5 45.1 - - - +
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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
----------------------------------------------------------
111B GLU 3.2 3.8 + - - +
112B ASN* 1.3 71.5 - - - +
114B TYR* 1.3 62.9 + - - +
116B ARG* 3.5 24.5 + - - +
117B VAL* 2.8 34.0 + - + +
197B LYS* 3.1 28.9 + - - -
198B THR 5.3 1.6 + - - -
199B ILE* 3.9 21.1 + - + +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 3.3 7.6 + - - +
113B GLU* 1.3 78.8 - - - +
115B PHE* 1.3 61.0 + - - +
117B VAL* 3.2 4.7 + - - +
118B PHE* 2.9 48.3 + - + +
164B GLU* 2.8 46.4 + - + +
165B LEU* 3.5 15.6 + - + -
168B ILE* 3.5 34.8 - - + -
169B PHE* 3.7 20.9 - + - -
174B PHE* 4.1 4.7 - - + -
198B THR* 3.8 31.8 - - + -
199B ILE* 4.3 25.9 - - + +
237B SER* 4.5 4.5 - - - -
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.0 27.4 - - + -
56B VAL* 5.0 8.3 - - + -
95B LEU* 3.9 24.9 - - + -
98B ILE* 4.2 16.2 - - + -
99B LEU* 5.3 4.3 - - + -
106B MET* 6.1 0.9 - - + -
109B LEU* 3.6 48.2 - - + +
110B GLY* 5.6 0.2 - - - -
112B ASN* 3.0 22.5 + - + +
113B GLU 3.4 0.2 - - - -
114B TYR* 1.3 81.4 - - - +
116B ARG* 1.3 56.6 + - - +
118B PHE* 3.6 3.3 - + - +
119B MET* 2.8 52.6 + - + +
165B LEU* 4.5 7.4 - - + -
169B PHE* 3.7 20.4 - + + -
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 2.7 38.1 + - + +
49B GLY 2.9 29.2 - - - +
50B THR* 3.4 4.9 + - - +
51B VAL* 3.4 14.3 - - + +
55B MET* 5.8 0.2 - - - +
110B GLY 3.1 23.1 - - - +
111B GLU* 2.6 35.6 + - - +
112B ASN 2.9 25.3 + - - +
113B GLU* 3.8 23.7 + - - +
114B TYR 3.3 0.2 - - - -
115B PHE* 1.3 75.8 - - - +
117B VAL* 1.3 59.8 + - + +
119B MET* 3.4 1.9 + - - +
120B GLU* 2.9 30.5 + - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 4.0 24.9 - - + -
113B GLU* 2.8 24.0 + - + +
114B TYR 3.5 5.4 - - - +
116B ARG* 1.3 75.8 - - + +
118B PHE* 1.3 58.5 + - - +
120B GLU* 3.3 4.5 + - - +
121B ASN* 2.9 28.2 + - - +
199B ILE* 3.6 28.5 - - + -
233B ASN* 3.6 12.3 - - + +
235B TYR* 3.4 37.9 - - + -
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B THR* 4.7 8.1 - - + -
95B LEU* 4.4 6.5 - - + -
114B TYR* 2.9 50.2 + - + +
115B PHE* 3.6 5.8 - + - +
117B VAL* 1.3 73.8 - - - +
119B MET* 1.3 69.2 + - + +
121B ASN* 3.1 9.4 + - + +
122B LEU* 2.8 54.0 + - + +
161B MET* 3.3 45.0 - - + +
164B GLU* 3.9 7.6 - - - -
165B LEU* 3.7 39.0 - - + -
231B THR* 6.0 0.2 - - + -
233B ASN* 5.6 2.0 - - - +
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 3.8 26.9 - - + -
55B MET* 4.2 12.8 - - + -
56B VAL* 3.9 29.2 - - + -
59B CYS* 3.8 32.6 - - + -
95B LEU* 4.0 28.5 - - + -
115B PHE* 2.8 38.2 + - + +
116B ARG 3.9 3.1 - - - +
118B PHE* 1.3 80.0 - - - +
120B GLU* 1.3 63.6 + - - +
122B LEU* 3.7 9.7 - - + +
123B MET* 3.1 25.1 + - - +
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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
----------------------------------------------------------
48B PRO* 3.0 41.5 - - + +
49B GLY 4.7 1.0 + - - -
55B MET* 5.1 3.7 - - - -
116B ARG 2.9 18.5 + - - +
117B VAL* 3.5 6.2 - - - +
119B MET* 1.3 76.8 - - - +
121B ASN* 1.3 64.3 + - - +
123B MET* 3.6 7.8 + - - +
124B LYS* 3.1 24.9 + - + +
235B TYR* 5.1 5.9 - - - -
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Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL 2.9 17.6 + - - +
118B PHE* 3.5 9.2 - - + +
120B GLU* 1.3 76.7 - - - +
122B LEU* 1.3 54.5 + - - +
124B LYS* 3.2 6.7 + - - +
125B LYS* 2.8 63.9 + - - +
161B MET* 3.5 21.6 - - - +
231B THR* 3.0 32.1 + - - -
233B ASN* 3.5 25.3 - - + +
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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
----------------------------------------------------------
59B CYS* 4.2 2.9 - - - -
63B MET* 3.4 36.8 - - + -
88B LEU* 5.3 0.7 - - + -
91B THR* 4.2 10.3 - - + -
95B LEU* 3.7 19.7 - - + -
118B PHE* 2.8 36.0 + - + +
119B MET* 3.7 15.7 - - + +
121B ASN* 1.3 76.7 - - - +
123B MET* 1.3 62.6 + - - +
125B LYS* 3.3 3.8 + - - -
126B THR* 2.9 45.1 + - + +
158B PHE* 4.1 16.8 - - + -
161B MET* 4.8 8.7 - - + -
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B MET* 3.6 39.5 - - + +
58B LYS* 5.3 8.3 - - + -
59B CYS* 3.5 25.2 - - - +
62B LEU* 3.8 20.9 - - + -
119B MET 3.1 12.3 + - - +
120B GLU* 3.8 6.3 - - - +
122B LEU* 1.3 76.8 - - - +
124B LYS* 1.3 62.1 + - - +
126B THR* 2.8 19.7 + - - -
127B LYS* 3.0 38.9 + - + +
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Residues in contact with LYS 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 GLU* 3.1 21.1 + - + +
121B ASN* 3.4 11.0 - - - +
123B MET* 1.3 78.3 - - - +
125B LYS* 1.3 62.7 + - - +
127B LYS* 3.5 8.4 + - - +
128B GLN* 2.5 74.2 + - + +
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Residues in contact with LYS 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 ASN* 2.8 42.1 + - - +
122B LEU 3.9 3.1 - - - +
124B LYS* 1.3 75.6 - - - +
126B THR* 1.3 63.0 + - - +
128B GLN* 3.4 32.3 + - - +
129B THR* 2.9 28.9 + - - -
154B LEU* 4.8 5.2 - - + +
157B ILE* 3.8 23.6 - - + -
158B PHE* 3.8 9.6 - - + -
161B MET* 3.9 26.5 - - + -
231B THR 3.5 15.3 - - - -
232B CYS* 2.8 33.5 + - - +
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Residues in contact with THR 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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59B CYS* 5.0 1.2 + - - +
62B LEU* 3.5 23.9 - - + +
63B MET* 3.8 22.9 - - + +
66B VAL* 3.7 10.0 - - + +
88B LEU* 5.2 0.4 - - + -
122B LEU* 2.9 37.4 + - + +
123B MET* 2.8 24.3 + - - -
125B LYS* 1.3 75.8 - - - +
127B LYS* 1.3 61.7 + - - +
129B THR* 3.4 3.7 + - - -
130B ILE* 3.1 29.6 + - - +
158B PHE* 3.9 15.5 - - + -
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Residues in contact with LYS 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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58B LYS* 4.6 13.3 - - - +
62B LEU* 4.0 30.7 - - + -
123B MET* 3.0 39.6 + - + +
124B LYS* 3.7 7.2 - - - +
126B THR* 1.3 76.4 + - - +
128B GLN* 1.3 64.2 + - - +
130B ILE* 3.2 9.6 + - + +
131B SER* 3.0 29.2 + - - +
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Residues in contact with GLN 128 (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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124B LYS* 2.5 67.5 + - + +
125B LYS* 3.6 33.8 + - - +
126B THR 3.3 0.2 - - - -
127B LYS* 1.3 75.1 - - - +
129B THR* 1.3 58.5 + - - +
131B SER* 3.3 7.2 + - - -
132B LEU* 2.9 29.7 + - - +
154B LEU* 4.0 21.3 - - + +
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Residues in contact with THR 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B VAL* 3.5 31.2 - - + -
69B LEU* 5.9 0.2 - - + -
84B ILE* 4.7 2.5 - - + -
125B LYS 2.9 14.1 + - - -
126B THR* 3.5 8.7 - - - -
127B LYS 3.2 0.2 - - - -
128B GLN* 1.3 79.4 - - - +
130B ILE* 1.3 62.1 + - - +
132B LEU* 3.3 5.3 + - + +
133B PHE* 3.3 27.9 + - + -
151B LEU* 4.1 24.9 - - + -
154B LEU* 3.6 18.4 - - + +
158B PHE* 3.5 16.2 - - + -
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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
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62B LEU* 3.9 36.1 - - + +
65B LYS* 3.6 51.4 - - + +
66B VAL* 3.8 12.1 - - + -
69B LEU* 4.2 13.9 - - + +
126B THR 3.1 17.5 + - - +
127B LYS* 3.2 9.2 + - + +
129B THR* 1.3 75.2 - - - +
131B SER* 1.3 65.8 + - - +
133B PHE* 3.3 5.4 + - - +
134B LYS* 3.2 22.7 + - + +
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Residues in contact with SER 131 (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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127B LYS* 3.0 18.7 + - - +
128B GLN* 3.6 6.9 - - - -
130B ILE* 1.3 75.6 - - - +
132B LEU* 1.3 61.8 + - - +
134B LYS* 4.6 5.8 - - - -
135B GLU* 3.0 55.3 + - - +
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Residues in contact with LEU 132 (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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128B GLN 2.9 17.1 + - - +
129B THR 3.5 6.5 - - - +
130B ILE 3.2 0.2 - - - -
131B SER* 1.3 78.0 - - - +
133B PHE* 1.3 56.1 + - - +
135B GLU* 5.1 1.3 - - - -
136B GLY* 2.9 29.0 + - - -
140B MET* 3.9 16.6 - - + +
147B PRO* 3.6 15.5 - - + +
150B ASN* 3.6 32.3 - - + +
151B LEU* 3.5 33.7 - - + +
154B LEU* 3.8 17.7 - - + -
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Residues in contact with PHE 133 (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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66B VAL* 5.5 0.2 - - + -
69B LEU* 3.7 47.3 - - + -
70B CYS* 3.7 23.1 - - - -
75B LEU* 3.6 33.2 - - + -
129B THR* 3.3 22.3 + - + -
130B ILE 3.3 8.5 + - - +
132B LEU* 1.3 80.8 - - + +
134B LYS* 1.3 57.0 + - - +
136B GLY 4.0 0.3 - - - -
137B LYS* 3.1 24.6 + - - +
140B MET* 4.1 29.2 - - + +
141B TYR* 4.9 11.0 - + - -
151B LEU* 3.9 23.6 - - + -
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Residues in contact with LYS 134 (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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130B ILE* 3.2 14.8 + - + +
131B SER* 4.0 3.4 - - - +
132B LEU 3.3 0.2 - - - -
133B PHE* 1.3 79.3 - - - +
135B GLU* 1.3 83.5 + - + +
137B LYS* 3.0 36.3 + - - +
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Residues in contact with GLU 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 SER* 3.0 38.7 + - - +
132B LEU* 4.6 1.3 - - - +
134B LYS* 1.3 95.8 - - + +
136B GLY* 1.3 57.4 + - - +
137B LYS* 3.4 18.0 - - - +
139B ARG* 5.4 3.1 + - - -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 2.9 18.6 + - - -
133B PHE 4.0 0.4 - - - -
135B GLU* 1.3 76.3 - - - +
137B LYS* 1.3 59.5 + - - +
138B GLU* 3.3 0.9 + - - +
139B ARG* 2.7 45.6 + - - +
140B MET* 4.3 3.4 - - - -
147B PRO* 4.5 19.7 - - - -
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Residues in contact with LYS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE 3.1 15.2 + - - +
134B LYS* 3.0 23.5 + - - +
135B GLU* 4.0 18.7 - - - +
136B GLY* 1.3 77.7 - - - +
138B GLU* 1.3 78.2 + - - +
139B ARG 3.0 5.4 + - - -
140B MET* 3.3 18.2 + - - +
141B TYR* 4.1 8.0 + - - -
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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