Contacts of the helix formed by residues 118 - 143 (chain B) in PDB entry 2DSA
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 SER 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A SER* 4.1 10.6 + - - -
120A GLU* 4.2 20.8 - - - +
116B ALA 3.5 3.3 + - - -
117B SER* 1.3 77.5 - - - +
119B ASP* 1.3 63.3 + - - +
120B GLU* 3.3 8.6 - - - +
121B TRP* 3.4 22.0 + - - +
122B LYS* 3.2 25.6 + - - +
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Residues in contact with ASP 119 (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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118B SER* 1.3 72.3 - - - +
120B GLU* 1.3 64.4 + - - +
121B TRP 3.3 0.4 - - - -
122B LYS* 3.8 23.8 + - - +
123B ASN* 3.3 38.5 + - - +
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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
----------------------------------------------------------
116A ALA 5.0 4.8 - - - +
118A SER* 3.8 26.3 + - - +
121A TRP* 5.7 0.2 - - - -
118B SER* 3.3 7.0 - - - +
119B ASP* 1.3 75.7 - - - +
121B TRP* 1.3 66.6 + - - +
123B ASN* 4.4 3.0 - - - +
124B ALA* 3.6 18.4 + - - +
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Residues in contact with TRP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 4.7 7.7 + - - +
120A GLU* 4.6 4.3 - - + -
121A TRP* 3.4 67.6 - + + +
124A ALA* 4.0 29.6 - - + -
125A VAL* 5.9 2.0 - - + -
111B PRO* 3.7 28.3 - - + +
114B ASN* 5.2 8.5 - - - -
117B SER* 3.6 30.1 - - - -
118B SER* 3.4 22.3 + - - +
120B GLU* 1.3 76.6 - - - +
122B LYS* 1.3 67.3 + - - +
124B ALA* 3.1 15.0 + - - +
125B VAL* 3.2 26.6 + - + +
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Residues in contact with LYS 122 (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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111B PRO* 3.8 13.0 - - - +
112B LEU* 3.7 30.9 - - + +
114B ASN 3.7 11.3 + - - -
115B PRO* 5.1 4.6 + - - +
117B SER* 3.5 36.1 + - - +
118B SER 3.2 14.9 + - - +
119B ASP* 3.8 22.3 + - - +
121B TRP* 1.3 82.6 - - + +
123B ASN* 1.3 62.1 + - - +
125B VAL* 3.3 4.6 + - - +
126B ARG* 2.9 43.0 + - - +
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Residues in contact with ASN 123 (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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119B ASP* 3.3 26.6 + - - +
120B GLU* 4.4 3.6 - - - +
121B TRP 3.3 1.0 - - - -
122B LYS* 1.3 78.0 - - - +
124B ALA* 1.3 64.1 + - - +
126B ARG* 3.6 17.4 + - - +
127B GLN* 3.2 23.6 + - - +
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Residues in contact with ALA 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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121A TRP* 4.1 21.1 - - + -
120B GLU 3.6 12.3 + - - +
121B TRP 3.1 10.0 + - - +
123B ASN* 1.3 77.3 - - - +
125B VAL* 1.3 62.9 + - - +
127B GLN* 3.4 7.5 + - - +
128B SER* 3.2 25.5 + - - -
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TRP* 4.1 15.9 - - + -
108B SER* 3.0 45.5 - - - +
111B PRO* 4.2 8.1 - - + -
112B LEU* 4.5 7.9 - - + -
121B TRP* 3.2 36.4 + - + +
122B LYS* 3.6 9.4 - - - +
124B ALA* 1.3 75.2 - - - +
126B ARG* 1.3 57.4 + - - +
128B SER* 3.3 8.1 + - - -
129B LEU* 2.9 29.1 + - + +
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Residues in contact with ARG 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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112B LEU* 3.9 29.9 + - + +
122B LYS* 2.9 30.2 + - - +
123B ASN* 3.8 20.1 + - - +
124B ALA 3.3 0.2 - - - -
125B VAL* 1.3 75.4 - - - +
127B GLN* 1.3 57.3 + - - +
129B LEU* 3.6 7.4 + - - +
130B ASN* 3.1 37.9 + - - +
168B VAL* 2.6 39.2 + - - +
169B ASN* 4.0 11.2 + - - +
170B ILE* 3.7 20.8 - - + +
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Residues in contact with GLN 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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123B ASN 3.2 14.3 + - - +
124B ALA* 3.6 11.2 - - - +
126B ARG* 1.3 74.3 - - - +
128B SER* 1.3 65.7 + - - +
130B ASN* 3.4 10.9 + - + +
131B THR* 3.2 28.0 + - - +
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Residues in contact with SER 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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108B SER* 5.1 7.0 - - - -
124B ALA 3.2 12.4 + - - -
125B VAL* 3.3 10.4 + - - -
127B GLN* 1.3 77.3 - - - +
129B LEU* 1.3 57.8 + - - +
131B THR* 3.2 7.7 + - - -
132B ARG* 2.9 38.8 + - - +
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Residues in contact with LEU 129 (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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104B GLU 4.3 0.9 - - - +
105B LEU* 3.8 26.9 - - + +
108B SER* 3.5 30.9 + - - +
109B PHE* 3.8 37.0 - - + -
112B LEU* 3.9 27.8 - - + -
125B VAL 2.9 14.7 + - - +
126B ARG* 3.8 7.0 - - - +
127B GLN 3.3 0.2 - - - -
128B SER* 1.3 72.8 - - - +
130B ASN* 1.3 55.7 + - - +
132B ARG* 3.1 4.7 + - - +
133B LEU* 2.7 50.1 + - + +
170B ILE* 4.1 10.8 - - + -
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Residues in contact with ASN 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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126B ARG* 3.1 26.1 + - - +
127B GLN* 3.4 9.4 + - + +
129B LEU* 1.3 76.0 - - - +
131B THR* 1.3 58.0 + - - +
133B LEU* 3.6 8.9 + - - +
134B GLY* 3.0 24.6 + - - -
170B ILE* 5.2 6.2 - - - +
175B TRP* 3.8 29.4 + - + -
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Residues in contact with THR 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 GLN* 3.2 14.1 + - - +
128B SER* 3.2 11.0 + - - -
129B LEU 3.2 0.4 - - - -
130B ASN* 1.3 78.3 - - - +
132B ARG* 1.3 79.3 + - - +
134B GLY* 3.3 3.9 + - - -
135B GLN* 3.2 19.4 + - - +
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Residues in contact with ARG 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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49A ALA* 3.2 29.1 + - - +
51A TYR* 3.6 26.9 - - - -
1224A GSH 5.5 6.1 + - - -
100B PHE* 3.8 24.2 - - + -
104B GLU* 3.1 36.1 + - - +
105B LEU* 3.8 19.3 - - + -
128B SER* 2.9 25.9 + - - +
129B LEU 3.9 2.5 - - - +
131B THR* 1.3 92.2 - - - +
133B LEU* 1.3 57.6 + - - +
135B GLN* 3.3 10.2 + - - +
136B VAL* 3.1 32.6 + - - +
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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
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105B LEU* 4.1 17.3 - - + -
109B PHE* 5.1 7.0 - - + -
129B LEU* 2.7 46.4 + - + +
130B ASN* 3.8 7.4 - - - +
132B ARG* 1.3 70.0 - - - +
134B GLY* 1.3 55.8 + - - +
136B VAL* 3.3 7.0 + - + +
137B ALA* 2.8 36.1 + - - +
162B LEU* 3.8 28.7 - - + -
170B ILE* 4.4 18.8 - - + -
172B LEU* 4.8 3.8 - - + -
175B TRP* 3.9 32.1 - - + -
178B LEU* 3.9 12.2 - - + +
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Residues in contact with GLY 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 ASN 3.0 14.2 + - - -
131B THR* 3.3 5.3 + - - -
133B LEU* 1.3 75.0 - - - +
135B GLN* 1.3 55.5 + - - +
137B ALA* 3.4 2.8 - - - +
138B ARG* 3.0 36.5 + - - +
175B TRP* 3.7 20.9 - - - +
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Residues in contact with GLN 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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47A ASN* 4.7 2.6 - - - +
48A PRO* 4.0 24.0 + - + +
49A ALA* 3.3 40.2 + - - +
97B TRP* 4.8 10.7 - - + -
100B PHE* 3.5 27.4 - - + -
131B THR* 3.2 10.9 + - - +
132B ARG* 3.5 15.2 - - - +
133B LEU 3.3 0.2 - - - -
134B GLY* 1.3 75.0 - - - +
136B VAL* 1.3 62.0 + - - +
138B ARG* 3.3 8.5 + - - +
139B GLN* 3.2 19.9 + - - +
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Residues in contact with VAL 136 (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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97B TRP* 4.1 8.7 - - + -
100B PHE* 3.3 27.6 - - + -
101B ILE* 6.3 0.4 - - + -
105B LEU* 4.0 14.8 - - + -
132B ARG 3.1 18.1 + - - +
133B LEU* 3.8 7.6 - - + +
135B GLN* 1.3 74.0 - - - +
137B ALA* 1.3 63.2 + - - +
139B GLN* 3.2 8.8 + - - +
140B LEU* 3.0 24.2 + - + +
146B LEU* 4.1 12.6 - - + -
158B LEU* 3.6 35.7 - - + -
162B LEU* 6.3 0.2 - - + -
178B LEU* 4.1 7.0 - - + -
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Residues in contact with ALA 137 (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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133B LEU 2.8 18.6 + - - +
134B GLY 3.4 6.3 - - - +
136B VAL* 1.3 77.1 - - - +
138B ARG* 1.3 62.4 + - + +
140B LEU 3.2 8.5 + - - -
141B GLU* 3.3 8.2 + - - +
175B TRP* 3.6 32.3 - - + -
177B SER* 2.7 29.6 + - - +
178B LEU* 3.7 11.7 - - + +
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Residues in contact with ARG 138 (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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134B GLY 3.0 23.9 + - - +
135B GLN* 3.7 7.6 - - - +
136B VAL 3.3 0.2 - - - -
137B ALA* 1.3 73.0 - - - +
139B GLN* 1.3 66.9 - - - +
141B GLU* 3.0 47.7 + - - +
142B HIS* 3.2 19.3 + - + -
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Residues in contact with GLN 139 (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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93B HIS* 4.6 9.0 + - - -
97B TRP* 3.4 38.5 + - + -
135B GLN 3.2 9.5 + - - +
136B VAL 3.2 10.5 + - - +
138B ARG* 1.3 77.3 - - - +
140B LEU* 1.3 58.3 + - - +
142B HIS* 3.2 38.2 + - - +
143B ALA* 4.0 2.9 + - - +
145B TYR 5.2 1.4 - - - +
146B LEU* 3.1 35.5 - - + +
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Residues in contact with LEU 140 (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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136B VAL* 3.0 15.2 + - + +
137B ALA 3.2 6.5 + - - +
138B ARG 3.2 0.6 - - - -
139B GLN* 1.3 73.4 - - - +
141B GLU* 1.3 58.2 + - - +
142B HIS 3.5 0.4 - - - -
143B ALA 3.3 12.4 - - - +
144B PRO* 3.8 8.9 - - - +
145B TYR* 3.5 38.8 - - - +
146B LEU* 3.5 16.2 - - + +
158B LEU* 3.8 20.4 - - + -
177B SER* 3.5 21.9 - - - +
178B LEU* 3.9 18.2 - - + -
181B PHE* 3.7 31.0 - - + -
184B ARG* 5.0 5.2 + - - +
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Residues in contact with GLU 141 (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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137B ALA 3.3 10.3 + - - +
138B ARG* 3.0 53.8 + - - +
140B LEU* 1.3 76.6 - - - +
142B HIS* 1.3 66.7 + - + +
143B ALA 3.4 1.8 + - - -
177B SER* 4.2 12.1 + - - +
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Residues in contact with HIS 142 (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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138B ARG* 3.2 28.7 + - + -
139B GLN* 3.2 22.1 + - - +
141B GLU* 1.3 82.3 - - + +
143B ALA* 1.3 62.5 + - + +
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Residues in contact with ALA 143 (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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139B GLN 4.0 2.1 + - - +
140B LEU* 3.3 24.4 - - - +
141B GLU 3.4 1.8 - - - -
142B HIS* 1.3 82.0 - - + +
144B PRO* 1.3 75.5 - - + +
145B TYR 3.1 8.0 + - - +
148B GLY* 3.4 30.3 - - - +
149B ASP* 4.2 4.3 - - - +
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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