Contacts of the helix formed by residues 126 - 149 (chain D) in PDB entry 1QGH
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 126 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLY* 3.6 7.7 - - - +
125D ASP* 1.3 69.2 - - - +
127D VAL* 1.3 68.7 + - + +
129D ASN* 3.1 9.2 + - - +
130D ASP* 2.9 20.8 + - - +
114F LYS* 2.6 36.3 + - - +
117F ILE* 3.7 19.9 - - + +
129F ASN* 5.5 0.7 + - - -
133F ILE* 3.4 34.7 - - + +
136F LYS* 5.3 5.0 - - - +
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Residues in contact with VAL 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ARG* 3.1 39.5 - - + +
125D ASP* 3.2 1.2 + - - -
126D ASP* 1.3 80.8 - - + +
128D THR* 1.3 63.9 + - - +
130D ASP* 3.1 9.7 + - - +
131D MET* 3.1 15.9 + - + +
133F ILE* 3.5 31.9 - - + +
136F LYS* 3.7 28.2 - - + +
137F ALA* 3.6 30.7 - - + +
140F ASP* 4.2 0.7 - - - +
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Residues in contact with THR 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D THR* 4.0 8.3 - - + +
13D LEU* 3.8 28.7 - - + +
63D ARG* 2.9 20.8 + - - +
67D ILE* 4.6 0.5 - - - +
120D THR* 3.5 5.6 - - - +
125D ASP* 2.5 34.5 + - - -
127D VAL* 1.3 75.1 - - - +
129D ASN* 1.3 64.6 + - - +
131D MET* 3.1 29.3 - - + +
132D LEU* 3.1 27.2 + - + +
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Residues in contact with ASN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 3.3 40.8 + - - +
120D THR* 3.2 15.0 + - + +
121D ASP* 4.0 15.7 - - - +
125D ASP 3.0 19.7 + - - +
126D ASP* 3.2 10.4 - - - +
128D THR* 1.3 80.1 - - - +
130D ASP* 1.3 66.7 + - - +
132D LEU* 3.5 3.4 + - - +
133D ILE* 2.9 40.5 + - - +
133F ILE* 6.0 0.9 - - - +
126K ASP* 5.8 0.2 + - - -
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ASP 2.9 10.9 + - - +
127D VAL 3.7 6.5 - - - +
129D ASN* 1.3 83.6 - - - +
131D MET* 1.3 66.7 + - - +
133D ILE* 3.1 7.8 + - - +
134D ALA* 3.0 23.4 + - - +
130F ASP* 3.3 32.9 - - - +
133F ILE* 4.0 24.1 - - + +
134F ALA* 5.3 1.7 + - - +
130K ASP* 3.4 22.4 - - - +
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Residues in contact with MET 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LEU* 4.4 4.7 - - + -
59D GLU* 4.0 17.3 - - - +
60D VAL* 4.1 17.5 - - + -
63D ARG* 3.8 38.8 - - + -
127D VAL* 3.1 16.8 + - + +
128D THR* 3.1 15.9 - - + +
130D ASP* 1.3 75.7 - - - +
132D LEU* 1.3 87.3 - - + +
134D ALA* 3.0 9.9 + - - +
135D PHE* 2.9 44.7 + - + -
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 3.8 34.1 - - + -
13D LEU* 4.5 3.1 - - + -
16D GLN* 6.0 0.4 - - + -
60D VAL* 5.1 2.7 - - + -
113D TYR* 4.0 18.1 - - + +
116D GLY 4.1 18.2 - - - +
117D ILE* 3.7 17.9 - - + +
120D THR* 4.5 3.4 - - + -
128D THR* 3.1 29.5 + - + +
129D ASN 3.6 7.2 - - - +
131D MET* 1.3 99.4 - - + +
133D ILE* 1.3 57.8 + - - +
135D PHE* 3.3 16.2 + - + +
136D LYS* 2.8 30.1 + - - +
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 4.1 20.4 - - + -
129D ASN* 2.9 41.0 + - - +
130D ASP* 3.5 17.0 - - - +
131D MET 3.1 1.2 - - - -
132D LEU* 1.3 74.7 - - - +
134D ALA* 1.3 58.6 + - - +
136D LYS* 3.1 3.8 + - - +
137D ALA* 2.8 27.0 + - + +
126K ASP* 3.6 27.6 - - + +
127K VAL* 3.5 30.1 - - + +
129K ASN* 6.2 0.2 - - - +
130K ASP* 3.8 22.0 - - + +
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASP 3.0 10.7 + - - +
131D MET* 3.0 9.8 + - - +
133D ILE* 1.3 78.3 - - - +
135D PHE* 1.3 69.6 + - + +
137D ALA* 3.1 17.1 + - - +
138D SER* 3.3 10.2 + - - -
130K ASP* 5.4 1.3 + - - +
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Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D GLN* 3.4 50.9 - - + +
59D GLU* 3.7 33.9 - - + -
60D VAL* 3.3 28.3 - - + -
113D TYR* 3.3 29.4 - + + -
131D MET* 2.9 34.9 + - + -
132D LEU* 3.7 8.5 - - + +
134D ALA* 1.3 80.0 - - + +
136D LYS* 1.3 65.5 + - - +
138D SER* 3.0 7.2 + - - +
139D ILE* 2.9 24.7 + - - +
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Residues in contact with LYS 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 4.2 33.9 - - + +
113D TYR* 4.2 6.2 - - + -
114D LYS* 4.7 14.1 - - + +
117D ILE* 4.1 20.0 - - + -
132D LEU 2.8 20.7 + - - +
133D ILE* 3.1 6.9 + - - +
135D PHE* 1.3 73.6 - - - +
137D ALA* 1.3 66.1 + - - +
139D ILE* 3.1 9.0 + - - +
140D ASP* 2.9 53.9 + - - +
63K ARG* 4.4 6.2 - - - +
125K ASP* 5.3 0.9 + - - -
126K ASP* 5.2 4.0 - - - +
127K VAL* 3.7 22.1 - - + +
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE* 2.8 12.6 + - + +
134D ALA* 3.4 13.7 - - - +
136D LYS* 1.3 78.6 - - - +
138D SER* 1.3 63.0 + - - +
140D ASP* 3.4 4.5 + - - +
141D LYS* 3.3 18.7 + - - +
63K ARG* 4.9 1.2 + - - -
127K VAL* 3.6 28.4 - - + +
131K MET* 6.5 0.2 - - + -
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Residues in contact with SER 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D GLU* 2.6 28.7 + - - -
56D GLN* 4.7 3.7 + - - -
134D ALA 3.3 6.6 + - - -
135D PHE* 3.0 11.5 + - - -
137D ALA* 1.3 78.1 - - - +
139D ILE* 1.3 66.5 + - - +
141D LYS* 3.0 11.0 + - - +
142D HIS* 2.8 34.4 + - - -
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Residues in contact with ILE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D PHE* 4.0 25.8 - - + -
56D GLN* 4.5 1.3 - - - +
106D LEU* 3.6 30.5 - - + +
109D LEU* 4.2 16.2 - - + -
110D ARG* 3.9 13.7 - - + +
113D TYR* 3.8 33.4 - - + -
135D PHE 2.9 15.5 + - - +
136D LYS* 3.6 8.1 - - - +
138D SER* 1.3 75.0 + - - +
140D ASP* 1.3 53.2 + - - +
142D HIS* 3.0 11.0 + - - +
143D ILE* 2.7 46.6 + - + +
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Residues in contact with ASP 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ARG* 3.2 33.6 + - - +
136D LYS* 2.9 38.9 + - - +
137D ALA 3.6 6.1 - - - +
139D ILE* 1.3 77.0 - - - +
141D LYS* 1.3 57.8 + - - +
143D ILE* 3.4 8.3 + - - +
144D TRP* 3.0 26.2 + - - +
154D PRO* 5.9 0.2 - - - +
63K ARG* 2.8 33.9 + - - +
66K ALA* 3.8 16.0 - - + +
67K ILE* 6.2 0.4 - - - -
127K VAL* 4.3 0.5 - - - +
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ALA 3.3 9.2 + - - +
138D SER* 3.0 11.7 + - - +
140D ASP* 1.3 76.0 - - - +
142D HIS* 1.3 70.8 + - + +
144D TRP* 3.0 24.9 + - + +
145D MET* 2.9 46.1 + - + +
43I HIS* 5.4 2.0 + - - -
62K GLU* 2.9 32.7 + - + +
66K ALA* 4.8 4.7 - - - -
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Residues in contact with HIS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 4.5 6.2 + - - -
49D LEU* 3.6 25.2 - - + +
52D GLU* 2.7 29.3 + - - -
53D PHE* 4.0 19.7 - + - -
106D LEU* 3.9 16.8 - - + -
138D SER* 2.8 36.0 + - - -
139D ILE* 3.3 6.5 - - - +
141D LYS* 1.3 80.6 - - + +
143D ILE* 1.3 58.7 + - - +
145D MET* 3.0 21.3 + - + +
146D PHE* 2.8 41.9 + + + -
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Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D VAL* 4.8 4.9 - - + +
106D LEU* 3.8 23.3 - - + -
107D GLU* 3.9 26.5 - - + +
110D ARG* 3.7 34.8 - - - +
139D ILE* 2.7 40.8 + - + +
140D ASP* 3.7 7.0 - - - +
142D HIS* 1.3 72.4 - - - +
144D TRP* 1.3 63.2 + - - +
146D PHE* 4.7 1.8 - - - +
147D LYS* 3.1 29.2 + - + +
154D PRO* 4.0 23.1 - - + +
155D LEU* 5.5 0.9 - - + -
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Residues in contact with TRP 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D ASP 3.0 13.9 + - - +
141D LYS* 3.0 20.8 + - + +
143D ILE* 1.3 79.1 - - - +
145D MET* 1.3 82.2 + - + +
147D LYS* 3.8 1.6 - - - +
148D ALA* 2.9 35.4 + - + +
154D PRO* 4.1 30.4 - - + +
31I HIS 4.5 0.9 - - - -
32I TRP* 4.0 13.0 + - - -
34I MET 5.4 0.4 + - - -
39I PHE* 3.9 16.8 - + - -
43I HIS* 3.5 27.4 - + - -
62K GLU* 3.7 39.9 - - + -
65K LEU* 3.8 34.6 - - + +
66K ALA* 4.1 17.9 - - + -
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Residues in contact with MET 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LYS* 4.1 14.4 - - - +
141D LYS* 2.9 43.4 + - + +
142D HIS* 3.0 27.1 + - + +
144D TRP* 1.3 97.2 - - + +
146D PHE* 1.3 67.6 + - + +
148D ALA* 3.1 3.6 + - - +
149D PHE* 2.9 22.2 + - - +
39I PHE* 3.4 34.5 - - + -
40I PHE* 3.7 16.8 - - + -
43I HIS* 4.6 10.8 - - - -
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Residues in contact with PHE 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 4.7 2.0 - - + -
45D LYS* 3.9 14.6 - - + -
46D MET* 3.6 27.4 - - + -
49D LEU* 4.0 12.8 - - + -
99D MET* 3.8 23.8 - - + -
102D LEU* 3.7 23.8 - - + -
103D VAL* 3.4 25.1 - - + -
106D LEU* 4.3 5.8 - - + -
142D HIS* 2.8 48.5 + - + +
145D MET* 1.3 71.7 - - - +
147D LYS* 1.3 58.7 + - - +
149D PHE* 3.1 7.8 + - + +
150D LEU* 3.0 30.0 + - + +
40I PHE* 3.5 30.5 - + - -
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D VAL* 3.8 22.7 - - + -
107D GLU* 3.4 19.0 + - - -
143D ILE* 3.1 23.4 + - + +
144D TRP 3.9 2.5 - - - +
146D PHE* 1.3 75.1 - - - +
148D ALA* 1.3 63.7 + - - +
150D LEU* 3.0 11.9 + - + +
151D GLY 3.0 5.0 + - - -
152D LYS* 2.8 43.6 + - + +
153D ALA 3.2 12.8 - - - +
154D PRO* 3.1 22.4 - - + +
156D GLU* 2.8 41.8 + - - +
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D TRP* 2.9 24.8 + - + +
145D MET 3.1 4.2 + - - +
147D LYS* 1.3 76.5 - - - +
149D PHE* 1.3 56.8 + - - +
151D GLY 2.9 6.1 + - - -
152D LYS 3.6 10.7 + - - +
34I MET 3.7 12.8 - - - +
35I ARG* 3.3 9.6 - - + +
36I GLY 2.5 31.0 + - - -
39I PHE* 3.7 28.0 - - + -
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Residues in contact with PHE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASN* 4.0 6.7 - - - -
42D LEU* 3.4 28.5 - - + -
95D MET* 4.2 4.0 - - + -
96D ASP* 3.7 15.7 - - - -
99D MET* 3.5 31.0 - - + -
145D MET 2.9 12.7 + - - +
146D PHE* 3.2 10.1 - + - +
147D LYS 3.0 0.2 - - - -
148D ALA* 1.3 77.9 - - - +
150D LEU* 1.3 67.4 + - + +
151D GLY 3.2 2.4 + - - -
36I GLY* 3.1 29.4 - - - -
37I HIS* 3.2 64.7 + + + -
39I PHE* 4.0 3.8 - - + +
40I PHE* 3.8 28.3 - + + -
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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