Contacts of the helix formed by residues 120 - 145 (chain D) 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 LEU 120 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU* 4.3 17.3 - - + -
57D LEU* 4.5 3.6 - - + -
101D ILE* 5.1 4.5 - - + -
104D ILE* 3.9 24.0 - - + +
105D VAL* 3.9 28.9 - - + +
108D ALA* 5.0 0.4 - - + -
116D THR* 3.1 38.5 + - + +
117D PHE* 3.8 6.5 - - - +
118D ASN 3.2 0.6 - - - -
119D PHE* 1.3 85.9 - - + +
121D GLN* 1.3 59.4 + - - +
122D TRP 3.4 0.7 - - - -
123D TYR* 3.0 32.6 + - + +
124D VAL* 2.9 30.5 + - + +
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Residues in contact with GLN 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D VAL* 4.6 8.5 - - - +
117D PHE* 3.1 55.7 + - + +
118D ASN* 3.6 19.1 - - - +
119D PHE 3.2 1.0 - - - -
120D LEU* 1.3 77.0 - - - +
122D TRP* 1.3 66.2 + - - +
124D VAL* 3.4 9.5 + - - +
125D ALA* 3.0 20.6 + - - +
114E HIS* 4.9 2.4 + - - +
117E PHE* 4.2 8.1 - - - -
118E ASN* 3.0 48.8 + - - +
121E GLN* 5.5 1.6 - - - +
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Residues in contact with TRP 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D HIS* 3.7 33.9 - + - -
56D LYS* 3.6 47.1 - - + -
57D LEU* 4.8 3.8 - - + -
118D ASN 4.8 0.2 + - - -
119D PHE* 2.6 61.6 + + - -
121D GLN* 1.3 77.6 - - - +
123D TYR* 1.3 96.5 + + + +
125D ALA* 3.5 5.8 + - - +
126D GLU* 3.0 49.8 + - + +
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Residues in contact with TYR 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN* 2.9 32.1 + - + +
17D GLU* 2.4 37.8 + - - +
53D HIS* 4.0 16.2 - + + -
57D LEU* 4.2 15.9 - - + -
101D ILE* 3.5 30.6 - - + +
104D ILE* 5.4 0.7 - - + -
120D LEU* 3.0 32.7 + - + +
122D TRP* 1.3 114.8 - + + +
124D VAL* 1.3 65.0 + - - +
126D GLU* 3.4 0.8 + - - -
127D GLN* 2.9 28.8 + - + +
1006D FE 3.6 12.3 - - - -
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ILE* 3.7 25.5 - - + +
102D ASN* 5.0 3.6 - - - +
105D VAL* 3.8 18.2 - - + -
120D LEU 2.9 21.1 + - - +
121D GLN* 3.4 11.9 + - - +
123D TYR* 1.3 76.4 - - - +
125D ALA* 1.3 61.9 + - - +
127D GLN* 3.6 3.6 + - - +
128D HIS* 3.1 23.6 + - - +
114E HIS* 3.4 39.9 - - + +
115E ALA* 3.7 9.6 - - + +
118E ASN* 4.1 8.3 - - + -
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Residues in contact with ALA 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D GLN 3.0 17.5 + - - +
122D TRP* 3.7 5.8 - - - +
124D VAL* 1.3 78.6 - - - +
126D GLU* 1.3 64.0 + - + +
128D HIS* 3.4 6.4 + - - +
129D GLU* 3.2 22.6 + - - +
115E ALA* 6.3 0.2 - - - +
118E ASN* 3.5 22.2 - - - +
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Residues in contact with GLU 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU* 4.1 6.6 - - - +
53D HIS* 3.4 26.8 + - - +
56D LYS* 4.9 9.1 + - - -
122D TRP* 3.0 41.5 + - + +
123D TYR* 4.1 2.9 - - - +
125D ALA* 1.3 75.1 - - + +
127D GLN* 1.3 59.8 - - - +
129D GLU* 3.4 14.1 + - - +
130D GLU* 3.0 35.5 + - - +
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Residues in contact with GLN 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D HIS* 5.2 1.2 - - - -
94D GLU* 2.9 45.2 + - - +
97D ILE* 3.7 10.7 - - - +
98D SER* 3.3 22.0 + - - +
101D ILE* 3.6 26.0 - - + -
123D TYR* 2.9 18.3 + - + +
124D VAL* 4.1 3.1 - - - +
126D GLU* 1.3 74.0 - - - +
128D HIS* 1.3 60.9 + - - +
130D GLU* 3.3 3.7 + - - +
131D GLU* 2.9 26.4 + - - +
1006D FE 2.7 14.5 - - - -
1007D FE 2.3 26.3 - - - -
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Residues in contact with HIS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D SER* 5.1 0.7 - - - -
124D VAL 3.1 19.0 + - - +
125D ALA* 3.6 7.2 - - - +
126D GLU 3.3 0.2 - - - -
127D GLN* 1.3 76.9 - - - +
129D GLU* 1.3 57.5 + - - +
131D GLU* 3.2 17.3 + - - +
132D VAL* 2.9 49.6 + - + +
1E MET* 4.5 4.0 - - + -
2E LEU* 5.5 1.3 - - + -
60E PHE* 3.9 15.8 - + - -
63E GLU* 5.3 4.5 + - - -
64E ASN* 3.1 36.3 + - - -
115E ALA* 3.5 33.5 - - + +
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D ALA 3.2 11.6 + - - +
126D GLU* 3.6 16.4 - - - +
128D HIS* 1.3 82.9 - - - +
130D GLU* 1.3 55.6 + - + +
132D VAL* 3.5 7.5 + - - +
133D LEU* 3.0 28.3 + - + +
165D ARG* 2.8 38.5 + - - +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D HIS* 3.2 24.4 - - + +
49D GLU* 3.9 10.4 - - - +
50D GLU* 3.1 6.8 - - - +
53D HIS* 2.8 29.2 + - - -
94D GLU* 4.1 4.3 - - - +
126D GLU* 3.0 19.7 + - - +
127D GLN* 3.3 9.7 - - - +
129D GLU* 1.3 74.8 - - + +
131D GLU* 1.3 63.6 + - - +
133D LEU* 3.1 11.7 + - + +
134D PHE* 3.0 30.1 + - - -
165D ARG* 5.1 11.0 - - - +
1006D FE 3.5 1.4 - - - -
1007D FE 2.2 36.6 - - - -
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TYR* 3.5 21.4 + - + -
94D GLU* 4.2 20.1 + - + -
95D GLN* 3.5 22.4 - - + +
98D SER* 2.5 35.1 + - - +
127D GLN* 2.9 19.3 + - - +
128D HIS* 3.5 12.8 + - - +
130D GLU* 1.3 74.8 - - - +
132D VAL* 1.3 60.3 + - - +
134D PHE* 3.4 1.3 + - - +
135D LYS 3.1 17.3 + - - -
1E MET* 3.7 24.6 - - + +
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Residues in contact with VAL 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D HIS* 2.9 40.3 + - + +
129D GLU* 3.7 7.2 - - - +
131D GLU* 1.3 72.1 - - - +
133D LEU* 1.3 67.6 + - - +
135D LYS* 3.2 5.6 + - - +
136D ASP* 2.9 35.9 + - - +
1E MET* 3.6 22.4 - - + -
63E GLU* 3.6 37.7 - - + +
64E ASN* 4.5 1.6 - - - +
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Residues in contact with LEU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.7 24.9 - - + -
46D HIS* 6.2 1.1 - - - +
129D GLU 3.0 14.7 + - - +
130D GLU* 3.1 14.8 + - + +
132D VAL* 1.3 77.6 - - - +
134D PHE* 1.3 59.1 + - + +
136D ASP* 3.2 11.5 + - + +
137D ILE* 3.0 36.6 + - + +
161D ILE* 3.8 26.9 - - + -
165D ARG* 3.4 48.2 - - - +
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Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 4.0 8.7 - + - -
42D PHE* 3.7 31.0 - + - -
43D LEU* 4.1 4.5 - - + -
46D HIS* 3.5 46.9 - + - -
87D PHE* 3.9 21.6 - + - -
90D ALA* 3.6 33.7 - - + -
91D TYR* 4.2 20.1 - - + +
94D GLU* 3.9 13.9 - - + -
130D GLU* 3.0 26.0 + - + -
131D GLU 3.9 6.7 - - - +
132D VAL 3.3 0.4 - - - -
133D LEU* 1.3 75.8 - - + +
135D LYS* 1.3 60.9 + - - +
137D ILE* 3.9 4.6 - - - +
138D LEU* 2.9 31.4 + - - +
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Residues in contact with LYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TYR* 3.6 25.6 - - + +
131D GLU 3.1 15.1 + - - +
132D VAL* 3.5 8.9 - - - +
134D PHE* 1.3 74.5 - - - +
136D ASP* 1.3 81.2 + - - +
138D LEU* 3.7 3.8 - - - +
139D ASP* 2.9 35.9 + - - +
1E MET* 3.6 19.7 - - + -
62E ASN 4.2 2.0 + - - -
63E GLU* 2.5 32.6 + - - +
65E ASN* 3.1 35.3 + - - +
1002E GLN* 3.8 23.7 - - + +
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Residues in contact with ASP 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 5.9 7.1 - - - +
132D VAL* 2.9 26.7 + - - +
133D LEU* 3.5 15.3 - - + +
135D LYS* 1.3 105.2 + - - +
137D ILE* 1.3 60.5 + - + +
139D ASP* 3.5 6.4 + - - +
140D LYS* 3.0 31.9 + - - +
157D TYR* 5.0 6.8 + - + +
63E GLU* 6.1 0.2 - - - -
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Residues in contact with ILE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.4 46.2 - - + -
87D PHE* 3.6 24.2 - - + -
133D LEU* 3.0 26.4 + - + +
134D PHE* 4.0 4.3 - - - +
136D ASP* 1.3 73.4 - - + +
138D LEU* 1.3 67.3 + - - +
140D LYS* 3.1 5.9 + - - +
141D ILE* 2.9 37.1 + - + +
157D TYR* 5.0 2.9 - - + -
158D VAL* 3.7 19.7 - - + -
161D ILE* 4.0 24.7 - - + -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D THR* 4.2 13.2 - - + +
87D PHE* 3.8 21.4 - - + +
88D GLN* 3.9 33.9 - - + +
91D TYR* 4.1 14.4 - - + -
134D PHE 2.9 19.0 + - - +
135D LYS* 3.7 4.0 - - - +
137D ILE* 1.3 77.9 - - - +
139D ASP* 1.3 61.0 + - - +
141D ILE* 3.3 7.8 + - + +
142D GLU* 3.1 37.8 + - + +
1002E GLN* 3.4 33.4 - - - +
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Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR 5.1 0.3 - - - +
35B SER* 3.5 33.9 + - - +
135D LYS* 2.9 23.7 + - - +
136D ASP* 3.6 8.9 - - - +
138D LEU* 1.3 75.6 - - - +
140D LYS* 1.3 57.6 + - + +
142D GLU* 3.5 6.5 + - - +
143D LEU* 3.0 27.9 + - - +
65E ASN* 3.3 24.1 + - - +
1002E GLN* 2.8 37.8 + - - +
1003E SER* 3.5 4.3 - - - -
1004E HIS 4.3 1.4 - - - +
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Residues in contact with LYS 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 2.9 21.3 + - - +
37B ASP* 2.5 31.1 + - - +
152B TYR* 4.3 17.9 - - + -
155B ASP* 2.9 19.4 + - - -
156B GLN* 3.6 22.9 - - - +
159B LYS* 4.1 4.0 - - - +
136D ASP 3.0 17.9 + - - +
137D ILE 3.1 3.6 + - - +
139D ASP* 1.3 75.1 - - + +
141D ILE* 1.3 66.6 + - + +
143D LEU* 3.4 8.9 + - + +
144D ILE* 3.0 34.0 + - + +
157D TYR* 3.5 37.7 - - + +
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Residues in contact with ILE 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D LEU* 4.1 18.6 - - + +
84D THR* 3.4 34.5 - - + +
87D PHE* 3.6 39.3 - - + -
137D ILE* 2.9 34.0 + - + +
138D LEU* 3.7 5.4 - - + +
140D LYS* 1.3 77.3 - - + +
142D GLU* 1.3 57.7 + - - +
144D ILE* 3.4 5.3 + - - +
145D GLY* 3.0 28.1 + - - +
151D LEU* 6.1 1.1 - - + -
154D ALA* 4.3 19.7 - - + +
157D TYR* 6.4 0.7 - - + -
158D VAL* 4.9 5.6 - - + -
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Residues in contact with GLU 142 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D THR* 3.5 27.1 - - + +
88D GLN* 3.5 13.0 + - - -
138D LEU* 3.1 26.1 + - + +
139D ASP* 3.9 2.2 - - - +
140D LYS 3.4 0.2 - - - -
141D ILE* 1.3 72.2 - - - +
143D LEU* 1.3 65.6 + - - +
144D ILE 3.4 0.2 + - - -
145D GLY* 3.6 10.9 + - - -
1002E GLN* 5.4 4.4 - - - +
1004E HIS* 3.7 41.2 + - + +
1005E HIS* 3.9 11.1 - - + +
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 3.6 25.8 - - - +
36B LEU* 4.1 19.3 - - + -
148B ASN 4.7 8.3 - - - +
149B HIS* 4.9 2.3 - - - -
151B LEU* 4.1 15.1 - - + +
152B TYR* 3.9 29.5 + - + +
155B ASP* 5.0 0.9 - - + -
139D ASP 3.0 18.3 + - - +
140D LYS* 3.7 19.7 - - + +
141D ILE 3.3 0.4 - - - -
142D GLU* 1.3 76.9 - - - +
144D ILE* 1.3 62.8 + - - +
1005E HIS* 3.5 43.6 + - + +
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Residues in contact with ILE 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ASN* 4.6 2.4 - - - +
149B HIS* 3.6 31.7 + - + +
152B TYR* 3.6 45.3 - - + -
140D LYS* 3.0 23.8 + - + +
141D ILE 3.8 3.4 - - - +
143D LEU* 1.3 79.4 - - - +
145D GLY* 1.3 61.3 + - - +
147D GLU* 5.3 2.3 + - - +
150D GLY* 3.2 34.8 - - - +
153D LEU* 4.1 8.5 - - + +
154D ALA* 3.7 29.2 - - + +
157D TYR* 4.8 3.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ILE* 3.0 16.0 + - - +
142D GLU* 3.6 8.0 + - - -
143D LEU 3.5 1.8 - - - -
144D ILE* 1.3 83.2 - - - +
146D ASN* 1.3 61.6 + - - -
147D GLU* 3.6 2.9 - - - -
150D GLY* 3.5 20.5 - - - -
151D LEU* 3.9 1.4 + - - +
154D ALA* 5.5 1.4 - - - +
----------------------------------------------------------
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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