Contacts of the helix formed by residues 113 - 145 (chain B) in PDB entry 3BVI
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 113 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.8 16.7 - - - +
3B SER* 5.1 3.8 + - - +
6B ILE* 3.9 15.3 - - + +
108B ALA* 2.8 26.2 + - - +
111B SER* 3.2 16.8 - - - +
112B LYS* 1.3 70.1 - - - +
114B HIS* 1.3 57.8 + - - +
115B ALA* 3.7 8.5 + - - +
116B THR* 2.6 34.3 + - - -
117B PHE* 3.1 19.9 + - - +
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Residues in contact with HIS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 5.2 0.2 - - - -
109B ILE* 4.6 29.6 + - + -
112B LYS* 3.3 32.1 + - + +
113B ASP* 1.3 69.8 + - - +
115B ALA* 1.3 60.8 + - - +
116B THR 3.2 0.9 - - - -
117B PHE* 3.6 19.6 - + + +
118B ASN* 2.9 30.8 + - - +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 6.0 2.2 - - + -
60B PHE* 4.4 8.6 - - + -
113B ASP* 3.4 8.6 + - - +
114B HIS* 1.3 76.1 - - - +
116B THR* 1.3 58.9 + - - +
118B ASN* 3.7 4.9 - - - +
119B PHE* 2.9 27.4 + - - +
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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
----------------------------------------------------------
2B LEU* 3.6 16.1 - - - +
6B ILE* 4.1 17.9 - - + +
10B LEU* 4.4 12.3 - - + -
60B PHE* 3.8 15.2 - - + -
104B ILE* 5.0 0.4 - - + -
108B ALA* 4.4 8.3 - - + -
113B ASP* 2.6 35.1 + - - +
114B HIS 3.2 0.2 - - - -
115B ALA* 1.3 75.3 - - - +
117B PHE* 1.3 64.7 + - - +
119B PHE* 3.2 1.6 + - - +
120B LEU* 2.9 43.8 + - + +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.3 35.0 - - + -
108B ALA* 4.1 8.7 - - + +
109B ILE* 3.6 33.2 - - + -
113B ASP 3.1 14.0 + - - +
114B HIS* 3.6 26.0 - + - +
116B THR* 1.3 77.8 - - - +
118B ASN* 1.3 66.4 + - + +
120B LEU* 3.2 10.3 + - - +
121B GLN* 3.0 46.5 + - + -
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Residues in contact with ASN 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B HIS 2.9 19.2 + - - +
115B ALA* 3.7 6.0 - - - +
117B PHE* 1.3 80.2 - - + +
119B PHE* 1.3 66.9 + - - +
121B GLN* 3.3 25.3 + - - +
122B TRP* 4.8 0.7 + - - -
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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
----------------------------------------------------------
10B LEU* 5.5 0.7 - - + -
56B LYS* 3.5 17.0 - - + -
57B LEU* 3.9 22.7 - - + -
60B PHE* 3.4 63.3 - + + -
63B GLU* 6.1 0.2 - - - -
115B ALA 2.9 19.0 + - - +
116B THR* 3.2 4.4 + - + +
118B ASN* 1.3 79.9 + - - +
120B LEU* 1.3 67.9 + - + +
121B GLN 3.2 0.7 + - - -
122B TRP* 2.7 65.1 + + - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.1 20.4 - - + -
57B LEU* 4.4 3.8 - - + -
101B ILE* 5.5 1.1 - - + -
104B ILE* 3.7 32.1 - - + -
105B VAL* 3.8 31.4 - - + +
108B ALA* 5.2 0.4 - - + -
116B THR* 2.9 31.9 + - + +
117B PHE* 3.2 6.8 + - - +
119B PHE* 1.3 87.0 - - + +
121B GLN* 1.3 58.3 + - - +
122B TRP 3.4 0.7 - - - -
123B TYR* 2.9 34.1 + - + +
124B VAL* 2.9 29.1 + - + +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 4.4 9.1 - - - +
117B PHE* 3.0 59.0 + - + +
118B ASN* 3.6 19.5 - - - +
119B PHE 3.2 2.2 - - - -
120B LEU* 1.3 80.0 - - - +
122B TRP* 1.3 62.0 + - - +
124B VAL* 3.4 16.9 + - - +
125B ALA* 3.1 23.2 + - - +
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Residues in contact with TRP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B HIS* 3.9 32.5 - + - -
56B LYS* 3.6 46.4 - - + -
57B LEU* 4.8 2.9 - - + -
118B ASN 4.8 0.6 + - - -
119B PHE* 2.7 60.6 + + - -
121B GLN* 1.3 76.2 - - - +
123B TYR* 1.3 97.8 + + + +
125B ALA* 3.5 5.3 + - - +
126B GLU* 2.9 54.7 + - - +
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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
----------------------------------------------------------
13B GLN* 3.0 32.2 + - + +
17B GLU* 2.4 37.4 + - - +
53B HIS* 4.1 17.5 - + + -
57B LEU* 4.3 15.9 - - + -
101B ILE* 3.5 34.9 - - + +
104B ILE* 5.4 1.1 - - + -
120B LEU* 2.9 33.8 + - + +
122B TRP* 1.3 114.6 - + + +
124B VAL* 1.3 62.3 + - - +
126B GLU* 4.8 0.9 - - + -
127B GLN* 3.0 29.2 + - + +
1006B FE 4.0 7.0 - - - -
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 3.8 25.1 - - + -
102B ASN* 5.1 11.0 - - - +
105B VAL* 3.8 20.0 - - + -
120B LEU 2.9 18.9 + - - +
121B GLN* 3.7 20.2 - - - +
123B TYR* 1.3 76.2 - - - +
125B ALA* 1.3 60.6 + - - +
127B GLN* 4.0 2.7 - - - +
128B HIS* 3.1 25.5 + - + +
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLN 3.1 17.1 + - - +
122B TRP* 3.6 7.0 - - - +
123B TYR 3.2 0.2 - - - -
124B VAL* 1.3 76.4 - - - +
126B GLU* 1.3 66.8 + - + +
128B HIS* 3.3 8.0 + - - +
129B GLU* 3.0 22.2 + - - +
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Residues in contact with GLU 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 4.7 5.9 - - - +
53B HIS* 3.2 32.0 + - + +
56B LYS* 4.5 10.7 + - - -
122B TRP* 2.9 40.3 + - + +
123B TYR* 4.2 2.7 - - - +
125B ALA* 1.3 76.0 - - + +
127B GLN* 1.3 57.5 - - - +
129B GLU* 3.2 14.8 + - - +
130B GLU* 2.9 36.2 + - - +
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B HIS* 5.4 1.7 - - + -
94B GLU* 2.8 45.2 + - - +
97B ILE* 3.6 10.5 - - - +
98B SER* 3.0 23.2 + - - +
101B ILE* 3.6 23.6 - - + -
123B TYR* 3.0 22.3 + - + +
124B VAL* 4.0 3.6 - - - +
126B GLU* 1.3 74.9 - - - +
128B HIS* 1.3 57.8 + - - +
130B GLU* 3.1 5.0 + - - +
131B GLU* 2.7 28.7 + - - +
1006B FE 3.1 7.1 - - - -
1007B FE 2.4 26.4 - - - -
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER* 5.1 0.4 - - - -
124B VAL* 3.1 21.0 + - + +
125B ALA* 3.6 7.0 - - - +
127B GLN* 1.3 77.8 - - - +
129B GLU* 1.3 64.2 + - - +
131B GLU* 3.3 15.5 + - - +
132B VAL* 3.0 48.6 + - + +
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ALA 3.0 14.9 + - - +
126B GLU* 3.2 17.9 + - - +
128B HIS* 1.3 78.3 - - - +
130B GLU* 1.3 58.8 + - - +
132B VAL* 3.4 6.1 + - - +
133B LEU* 2.9 28.3 + - + +
165B ARG* 2.8 39.2 + - - +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 3.3 23.2 - - + +
49B GLU* 4.2 11.3 - - - +
50B GLU* 3.2 7.5 - - - +
53B HIS* 2.9 30.1 + - - -
94B GLU* 4.3 2.7 - - - +
126B GLU* 2.9 21.0 + - - +
127B GLN* 3.3 10.2 - - - +
129B GLU* 1.3 82.4 - - - +
131B GLU* 1.3 61.7 + - - +
133B LEU* 3.2 10.6 + - + +
134B PHE* 3.1 31.2 + - - -
165B ARG* 5.0 6.5 - - - +
1007B FE 2.2 37.1 - - - -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 3.6 22.3 + - + -
94B GLU* 4.3 19.0 - - + +
95B GLN* 3.6 22.8 - - - +
98B SER* 2.6 36.7 + - - +
127B GLN* 2.7 22.0 + - - +
128B HIS* 3.7 15.0 + - - +
130B GLU* 1.3 71.8 - - - +
132B VAL* 1.3 62.5 + - + +
134B PHE* 3.4 1.5 + - - -
135B LYS* 3.1 22.7 + - - +
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B HIS* 3.0 48.6 + - + +
129B GLU* 3.8 6.1 - - - +
131B GLU* 1.3 73.0 - - + +
133B LEU* 1.3 66.4 + - - +
135B LYS* 3.3 24.1 + - - +
136B ASP* 2.9 35.6 + - - +
----------------------------------------------------------
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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
----------------------------------------------------------
42B PHE* 3.7 21.8 - - + -
46B HIS* 6.1 1.6 - - - +
129B GLU* 2.9 14.5 + - + +
130B GLU* 3.2 15.2 + - + +
132B VAL* 1.3 77.9 - - - +
134B PHE* 1.3 59.5 + - + +
136B ASP* 3.2 11.4 + - + +
137B ILE* 3.0 45.0 + - + +
161B ILE* 4.0 26.5 - - + -
165B ARG* 3.5 43.1 - - - +
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.8 10.8 - + - -
42B PHE* 3.5 24.9 - + - -
43B LEU* 4.0 3.4 - - + -
46B HIS* 3.6 44.9 - + - -
87B PHE* 3.8 32.2 - + - +
90B ALA* 3.6 32.3 - - + -
91B TYR* 4.2 19.7 - - + +
94B GLU* 3.9 13.5 - - + -
130B GLU* 3.1 27.3 + - + +
131B GLU 4.0 4.0 - - - +
132B VAL 3.3 0.4 - - - -
133B LEU* 1.3 76.3 - - + +
135B LYS* 1.3 60.7 + - - +
137B ILE* 4.0 4.4 - - - +
138B LEU* 3.0 30.3 + - - +
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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
----------------------------------------------------------
91B TYR* 3.7 34.8 - - + +
131B GLU 3.1 14.2 + - - +
132B VAL* 3.4 25.1 - - - +
134B PHE* 1.3 76.7 - - - +
136B ASP* 1.3 79.3 + - - +
138B LEU* 3.5 3.7 + - - +
139B ASP* 2.9 48.6 + - - +
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 2.9 25.8 + - - +
133B LEU* 3.5 14.8 - - + +
135B LYS* 1.3 106.5 + - - +
137B ILE* 1.3 60.0 + - + +
139B ASP* 3.4 9.1 + - - +
140B LYS* 3.0 31.9 + - - +
157B TYR* 5.2 6.9 - - + +
161B ILE* 6.1 1.8 - - + -
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B PHE* 3.3 44.9 - - + -
87B PHE* 3.6 27.1 - - + -
133B LEU* 3.0 23.8 + - + +
134B PHE* 4.0 5.2 - - - +
136B ASP* 1.3 73.4 - - + +
138B LEU* 1.3 61.3 + - - +
140B LYS* 3.2 6.7 + - - +
141B ILE* 2.9 35.0 + - + +
157B TYR* 4.9 2.2 - - + -
158B VAL* 3.7 24.9 - - + -
161B ILE* 3.8 24.5 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 4.3 10.1 - - + +
87B PHE* 3.9 20.3 - - + +
88B GLN* 3.8 44.0 - - + +
91B TYR* 4.1 22.9 - - + -
134B PHE 3.0 18.5 + - - +
135B LYS* 3.8 4.9 - - - +
137B ILE* 1.3 75.5 - - - +
139B ASP* 1.3 65.9 + - - +
141B ILE* 3.2 10.3 + - + +
142B GLU* 3.0 46.7 + - + +
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LYS* 2.9 38.7 + - - +
136B ASP* 3.4 9.2 - - - +
138B LEU* 1.3 76.8 - - - +
140B LYS* 1.3 59.1 + - - +
142B GLU* 3.4 6.8 + - - +
143B LEU* 2.9 28.3 + - - +
----------------------------------------------------------
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Residues in contact with LYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP 3.0 19.0 + - - +
137B ILE 3.2 4.7 + - - +
139B ASP* 1.3 75.3 - - - +
141B ILE* 1.3 60.0 + - + +
143B LEU* 3.2 25.9 + - + +
144B ILE* 2.9 49.7 + - + +
157B TYR* 3.6 55.4 - - + -
----------------------------------------------------------
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 4.1 26.5 - - + +
84B THR* 3.3 35.2 + - + +
87B PHE* 3.6 42.4 - - + -
137B ILE* 2.9 33.9 + - + +
138B LEU* 3.7 5.8 - - + +
140B LYS* 1.3 72.4 - - + +
142B GLU* 1.3 58.2 + - - +
144B ILE* 3.6 1.6 + - + +
145B GLY* 3.0 27.3 + - - +
146B ASN* 5.8 1.6 - - - +
151B LEU* 6.3 0.7 - - + -
154B ALA* 4.4 16.4 - - + -
157B TYR* 6.6 0.2 - - + -
158B VAL* 4.9 4.9 - - + -
----------------------------------------------------------
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 3.8 18.7 + - + +
88B GLN* 3.8 20.8 + - - +
138B LEU* 3.0 26.9 + - + +
139B ASP* 3.6 9.2 - - - +
141B ILE* 1.3 75.8 - - - +
143B LEU* 1.3 64.3 + - - +
145B GLY* 3.6 10.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASP 2.9 17.4 + - - +
140B LYS* 3.2 32.1 + - + +
142B GLU* 1.3 74.9 - - - +
144B ILE* 1.3 69.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LYS* 2.9 39.9 + - + +
141B ILE 4.0 3.1 - - - +
143B LEU* 1.3 81.4 - - + +
145B GLY* 1.3 63.9 + - - +
147B GLU* 5.3 3.1 - - - +
150B GLY* 3.2 34.0 - - - +
153B LEU* 4.1 19.3 - - + +
154B ALA* 3.6 29.6 - - + +
157B TYR* 4.7 6.1 - - + -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ILE 3.0 17.7 + - - +
142B GLU* 4.0 8.3 - - - -
143B LEU 3.3 2.0 - - - -
144B ILE* 1.3 84.8 - - - +
146B ASN* 1.3 62.8 + - - +
147B GLU* 3.6 6.7 - - - -
150B GLY* 3.5 20.2 - - - +
151B LEU* 5.0 0.3 - - - -
----------------------------------------------------------
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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