Contacts of the helix formed by residues 127 - 152 (chain D) in PDB entry 2CHP
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 127 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLN* 5.5 1.7 - - - +
13D VAL* 4.3 6.1 - - + +
67D ARG* 2.9 26.0 + - - -
71D ILE* 3.9 17.6 - - - +
122D ALA* 2.8 31.6 + - - +
123D GLU* 4.6 0.8 + - - +
125D ASN* 4.2 13.3 - - + +
126D GLN* 1.3 71.4 - - - +
128D ASN* 1.3 61.5 + - - +
129D ALA* 3.8 1.4 + - - +
130D THR* 2.6 31.6 + - - +
131D ALA* 3.2 14.4 + - - +
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Residues in contact with ASN 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D GLU* 5.3 10.2 - - - +
126D GLN* 3.6 13.5 + - - +
127D ASP* 1.3 75.8 - - - +
129D ALA* 1.3 58.9 + - - +
131D ALA* 3.3 8.7 + - - +
132D ASP* 2.9 30.4 + - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ARG* 3.5 30.3 + - - +
127D ASP* 3.3 1.0 + - - -
128D ASN* 1.3 76.2 - - - +
130D THR* 1.3 64.4 + - - +
132D ASP* 3.3 15.2 + - - +
133D LEU* 3.3 13.3 + - - +
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Residues in contact with THR 130 (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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13D VAL* 4.4 4.5 - - + -
17D LEU* 3.9 34.3 - - + -
67D ARG* 2.9 30.1 + - + +
71D ILE* 4.0 4.7 - - - +
118D VAL* 4.5 1.6 - - + -
122D ALA* 4.0 12.3 - - + -
127D ASP* 2.6 35.3 + - - +
129D ALA* 1.3 72.7 - - - +
131D ALA* 1.3 68.3 + - - +
132D ASP 3.2 0.5 + - - -
133D LEU* 3.3 17.5 + - - +
134D PHE* 3.3 15.6 - - + -
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Residues in contact with ALA 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D ILE* 3.6 29.7 - - + +
122D ALA* 3.7 14.5 - - + +
123D GLU* 4.2 15.7 - - + +
127D ASP 3.2 12.4 + - - +
128D ASN* 3.4 11.2 - - - +
130D THR* 1.3 77.6 - - - +
132D ASP* 1.3 57.9 + - - +
134D PHE* 3.2 3.9 + - - -
135D VAL* 3.0 31.5 + - + +
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Residues in contact with ASP 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D ASN 2.9 17.2 + - - +
129D ALA* 3.6 9.1 - - - +
130D THR 3.2 0.2 - - - -
131D ALA* 1.3 75.6 - - - +
133D LEU* 1.3 62.7 + - - +
135D VAL* 3.3 13.4 + - - +
136D GLY* 3.1 20.1 + - - -
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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
----------------------------------------------------------
17D LEU* 5.8 0.4 - - + -
60D THR* 6.4 0.4 - - + -
63D THR* 3.5 38.6 - - + +
64D ILE* 4.3 8.7 - - + -
67D ARG* 3.7 34.1 - - + -
129D ALA 3.3 9.1 + - - +
130D THR* 3.3 10.5 - - - +
132D ASP* 1.3 79.5 + - - +
134D PHE* 1.3 73.6 + - + +
136D GLY* 3.4 3.3 + - - -
137D LEU* 3.1 36.8 + - + +
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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
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17D LEU* 4.0 24.9 - - + -
20D GLN* 4.0 28.9 - - + -
24D TRP* 5.6 0.9 - - - -
64D ILE* 4.1 20.2 - - + -
115D SER* 3.7 26.4 - - - +
118D VAL* 3.6 26.5 - - + -
119D ILE* 3.9 17.3 - - + -
130D THR* 3.3 17.5 - - + +
131D ALA 3.2 7.2 + - - +
133D LEU* 1.3 94.9 - - + +
135D VAL* 1.3 65.0 + - - +
137D LEU* 3.2 20.5 + - + +
138D ILE* 3.0 28.8 + - - +
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Residues in contact with VAL 135 (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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119D ILE* 3.5 26.8 - - + +
131D ALA* 3.0 22.8 + - + +
132D ASP* 3.3 16.5 + - - +
134D PHE* 1.3 74.6 - - - +
136D GLY* 1.3 63.5 + - - +
138D ILE* 3.4 6.6 + - - +
139D GLU* 3.2 36.0 + - + +
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Residues in contact with GLY 136 (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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132D ASP 3.1 14.1 + - - -
133D LEU 3.8 3.6 - - - -
135D VAL* 1.3 76.5 - - - +
137D LEU* 1.3 60.9 + - - +
139D GLU* 3.3 19.1 + - - +
140D GLU* 3.2 19.9 + - - +
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Residues in contact with LEU 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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24D TRP* 4.1 17.7 - - + +
56D HIS* 4.3 12.1 - - - +
60D THR* 3.6 43.3 - - + +
64D ILE* 4.0 17.9 - - + -
111D ILE* 6.1 0.4 - - + -
115D SER* 5.1 5.6 - - - +
133D LEU* 3.1 24.6 + - + +
134D PHE* 3.2 27.8 + - + +
136D GLY* 1.3 73.9 - - - +
138D ILE* 1.3 60.5 + - - +
140D GLU* 3.3 3.3 + - + +
141D VAL* 2.9 36.6 + - + +
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Residues in contact with ILE 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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112D SER* 3.7 13.7 - - - +
115D SER* 3.8 21.8 - - - -
116D LYS* 3.5 35.2 - - + -
119D ILE* 3.6 26.9 - - + -
134D PHE 3.0 12.9 + - - +
135D VAL* 3.7 7.9 - - - +
136D GLY 3.3 0.2 - - - -
137D LEU* 1.3 75.6 - - - +
139D GLU* 1.4 66.0 + - + +
141D VAL* 4.3 7.0 - - - -
142D GLU* 3.0 50.8 + - - +
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Residues in contact with GLU 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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135D VAL* 3.2 29.7 + - + +
136D GLY* 3.5 15.1 - - - +
137D LEU 3.3 0.2 - - - -
138D ILE* 1.4 82.6 - - + +
140D GLU* 1.3 62.8 + - - +
142D GLU* 4.1 2.2 - - - +
143D LYS* 3.3 20.6 + - - +
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D HIS* 3.6 38.5 - - + +
136D GLY 3.2 10.0 + - - +
137D LEU* 3.3 7.8 + - + +
139D GLU* 1.3 78.8 - - - +
141D VAL* 1.3 62.2 + - - +
143D LYS* 3.3 22.5 + - - +
144D GLN* 3.0 51.0 + - + +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TRP* 3.7 36.3 - - + -
56D HIS* 4.9 4.0 - - + -
108D TYR* 3.6 41.5 - - + +
111D ILE* 4.5 4.5 - - + -
112D SER* 3.9 20.9 - - - +
137D LEU 2.9 24.2 + - - +
138D ILE* 3.8 9.2 - - - +
140D GLU* 1.3 73.6 - - - +
142D GLU* 1.3 61.7 + - + +
144D GLN* 3.2 9.1 + - - +
145D VAL* 2.8 31.0 + - + +
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Residues in contact with GLU 142 (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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112D SER* 2.6 34.3 + - - +
116D LYS* 3.3 16.4 + - - -
138D ILE* 3.0 29.6 + - - +
139D GLU* 4.3 3.2 - - - +
141D VAL* 1.3 73.1 - - + +
143D LYS* 1.3 64.4 + - - +
145D VAL* 3.8 10.7 - - + +
146D TRP* 3.1 22.3 + - - +
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Residues in contact with LYS 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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139D GLU 3.3 13.6 + - - +
140D GLU* 3.6 26.0 + - - +
141D VAL 3.2 0.4 - - - -
142D GLU* 1.3 75.0 - - - +
144D GLN* 1.3 83.3 + - - +
146D TRP* 3.2 16.2 + - + +
147D MET* 3.0 47.1 + - + +
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Residues in contact with GLN 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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49D LYS* 2.7 38.3 + - - +
53D LEU* 3.6 20.7 - - + +
56D HIS* 6.0 2.0 - - + +
108D TYR* 4.3 20.0 - - + -
140D GLU* 3.0 39.1 + - + +
141D VAL* 3.2 10.8 + - - +
143D LYS* 1.3 98.9 - - - +
145D VAL* 1.3 57.8 + - - +
147D MET* 3.4 6.2 + - - +
148D LEU* 2.8 40.3 + - + +
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Residues in contact with VAL 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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105D VAL* 4.1 9.4 - - + +
108D TYR* 3.4 28.0 - - + -
109D LYS* 3.7 43.3 - - + +
112D SER* 6.5 0.2 - - - -
141D VAL* 2.8 21.7 + - + +
142D GLU* 3.8 11.9 - - + +
143D LYS 3.2 0.4 - - - -
144D GLN* 1.3 77.0 - - - +
146D TRP* 1.3 56.7 + - - +
148D LEU* 4.1 5.3 - - - +
149D SER* 2.7 46.3 + - - +
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Residues in contact with TRP 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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142D GLU 3.1 14.0 + - - +
143D LYS* 3.2 18.1 + - + +
145D VAL* 1.3 79.2 - - - +
147D MET* 1.3 90.9 + - + +
149D SER* 3.8 3.7 - - - -
150D SER* 2.8 55.2 + - - -
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Residues in contact with MET 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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49D LYS* 3.9 14.4 - - - +
143D LYS* 3.0 33.8 + - - +
144D GLN* 3.6 34.1 - - - +
146D TRP* 1.3 101.3 - - + +
148D LEU* 1.3 59.6 + - + +
150D SER* 3.3 7.1 + - - -
151D TYR* 3.0 25.1 + - - +
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Residues in contact with LEU 148 (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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46D LEU* 5.5 3.6 - - + -
49D LYS* 5.0 13.0 - - + -
50D PHE* 5.1 2.9 - - + -
53D LEU* 4.5 11.4 - - + -
101D VAL* 3.6 34.9 - - + +
104D LEU* 3.9 24.9 - - + -
105D VAL* 3.8 17.5 - - + -
108D TYR* 3.8 33.2 - - + -
144D GLN* 2.8 27.0 + - + +
145D VAL* 4.1 1.3 - - - +
147D MET* 1.3 73.3 - - + +
149D SER* 1.3 66.5 + - - +
151D TYR* 3.3 22.0 + - + +
152D LEU* 3.3 6.4 + - - +
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Residues in contact with SER 149 (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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105D VAL* 3.9 16.4 - - - +
109D LYS* 5.1 3.1 + - - -
145D VAL* 2.7 39.4 + - - +
146D TRP* 3.8 6.1 - - - -
148D LEU* 1.3 72.7 - - - +
150D SER* 1.3 63.9 + - - +
152D LEU* 3.1 19.7 + - - +
153D GLY* 3.2 11.8 + - - -
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Residues in contact with SER 150 (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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146D TRP* 2.8 49.5 + - - -
147D MET* 3.5 7.4 - - - -
149D SER* 1.3 76.6 - - - +
151D TYR* 1.3 62.6 + - - +
153D GLY* 3.0 16.5 + - - +
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Residues in contact with TYR 151 (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 HIS* 3.4 39.9 - + + -
45D THR* 5.8 4.9 - - + -
46D LEU* 3.6 35.9 - - + +
97D ALA* 3.8 10.5 - - - +
98D SER* 4.7 7.5 + - - -
101D VAL* 4.2 20.0 - - + -
147D MET 3.0 13.2 + - - +
148D LEU* 3.3 14.4 - - + +
150D SER* 1.3 77.0 - - - +
152D LEU* 1.4 79.5 + - + +
153D GLY 3.5 3.3 + - - +
1154D PO4 5.7 0.9 - - - -
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Residues in contact with LEU 152 (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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98D SER* 4.0 36.6 - - - +
101D VAL* 3.9 17.9 - - + -
102D GLN* 3.5 33.7 - - + +
105D VAL* 4.5 7.9 - - + -
148D LEU 3.3 10.3 + - - +
149D SER* 3.1 11.9 + - - +
151D TYR* 1.4 87.1 - - + +
153D GLY* 1.3 64.3 + - - +
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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
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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) + - + + + + + -
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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