Contacts of the helix formed by residues 109 - 139 (chain X) in PDB entry 2DE0
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 GLY 109 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X LEU* 1.3 77.6 - - - +
110X LYS* 1.3 71.4 + - - +
111X ASP 3.4 1.3 - - - -
112X HIS* 3.3 4.5 + - - +
113X GLU* 3.3 23.9 + - - +
174X ASP* 3.3 36.9 + - - -
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Residues in contact with LYS 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X LEU 3.8 1.6 + - - -
109X GLY* 1.3 75.3 - - - +
111X ASP* 1.3 74.4 + - - +
112X HIS 3.1 0.2 + - - -
113X GLU* 3.1 4.0 + - - +
114X ILE* 3.1 42.8 + - + +
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Residues in contact with ASP 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109X GLY 3.4 0.2 - - - -
110X LYS* 1.3 89.3 + - - +
112X HIS* 1.3 62.2 + - - +
114X ILE* 3.8 12.4 - - - +
115X LEU* 2.9 33.8 + - + +
173X THR* 3.2 29.9 - - + +
174X ASP* 5.4 1.3 + - - +
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Residues in contact with HIS 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108X LEU* 4.2 10.1 - - + +
109X GLY* 3.3 12.6 + - - +
110X LYS 3.1 0.6 + - - -
111X ASP* 1.3 79.1 - - - +
113X GLU* 1.3 76.8 + - - +
116X ARG* 2.7 47.9 + - + +
170X LEU* 3.4 37.9 - - + +
173X THR* 3.8 19.1 + - - +
174X ASP* 4.0 21.8 - - - +
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Residues in contact with GLU 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108X LEU* 3.1 39.3 - - + +
109X GLY 3.3 14.4 - - - +
110X LYS* 3.1 6.6 + - - +
112X HIS* 1.3 95.0 + - - +
114X ILE* 1.3 68.1 + - + +
116X ARG* 3.2 32.9 + - - +
117X ARG* 3.0 49.5 + - - +
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Residues in contact with ILE 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X LYS* 3.1 39.8 + - + +
111X ASP* 3.8 14.8 - - - +
113X GLU* 1.3 78.3 - - + +
115X LEU* 1.3 55.0 + - + +
117X ARG* 3.1 19.5 + - - +
118X ARG* 2.8 59.5 + - + +
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Residues in contact with LEU 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X ASP* 2.9 29.1 + - + +
112X HIS 3.7 2.9 - - - +
114X ILE* 1.3 73.3 - - + +
116X ARG* 1.3 65.8 + - - +
117X ARG 3.1 0.2 + - - -
118X ARG* 3.1 20.4 + - - +
119X ILE* 2.8 30.1 + - + +
166X ASP* 4.0 26.0 - - - +
169X TYR* 3.6 45.1 - - + +
170X LEU* 3.8 16.2 - - + +
173X THR* 4.0 17.0 - - + +
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Residues in contact with ARG 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112X HIS* 2.7 30.2 + - + +
113X GLU* 3.2 33.1 + - - +
114X ILE 3.3 0.4 - - - -
115X LEU* 1.3 76.1 - - - +
117X ARG* 1.3 83.1 + - - +
119X ILE* 3.2 11.2 + - + +
120X GLU* 3.1 49.5 + - + +
170X LEU* 4.2 11.6 - - + +
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Residues in contact with ARG 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113X GLU* 3.0 45.8 + - - +
114X ILE* 3.7 24.6 - - - +
116X ARG* 1.3 93.5 - - - +
118X ARG* 1.3 57.3 + - - +
120X GLU* 3.3 12.7 + - - +
121X ASN* 2.6 39.7 + - + +
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Residues in contact with ARG 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114X ILE* 2.8 44.2 + - + +
115X LEU* 3.8 17.4 - - - +
117X ARG* 1.3 75.6 - - - +
119X ILE* 1.3 52.8 + - - +
121X ASN* 4.3 4.9 - - + +
122X GLY* 2.7 32.6 + - - +
166X ASP* 3.1 34.2 + - - +
169X TYR* 5.8 2.0 - - - -
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Residues in contact with ILE 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115X LEU 2.8 27.4 + - - +
116X ARG* 3.5 9.0 - - - +
118X ARG* 1.3 75.5 - - - +
120X GLU* 1.3 67.4 + - - +
122X GLY* 3.2 2.3 + - - -
123X ALA* 3.0 24.0 + - + +
163X ILE* 4.2 22.8 - - + +
166X ASP* 3.5 26.0 - - + +
167X LEU* 3.6 47.6 - - + +
170X LEU* 4.3 11.9 - - + -
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Residues in contact with GLU 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116X ARG* 3.1 35.8 + - + +
117X ARG* 3.6 12.2 - - - +
119X ILE* 1.3 80.4 - - - +
121X ASN* 1.3 61.5 + - - +
123X ALA* 3.4 6.1 + - - +
124X LYS* 3.2 28.4 + - + +
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Residues in contact with ASN 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117X ARG* 2.6 22.4 + - + +
118X ARG* 4.2 4.7 - - + +
120X GLU* 1.3 74.3 - - - +
122X GLY* 1.3 57.7 + - - +
124X LYS* 3.2 26.4 + - - +
125X GLU* 2.9 47.5 + - - +
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Residues in contact with GLY 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118X ARG* 2.7 25.2 + - - +
119X ILE 3.6 1.6 - - - -
121X ASN* 1.3 72.8 - - - +
123X ALA* 1.3 55.0 + - - +
125X GLU* 3.6 2.6 + - - -
126X LEU* 3.0 10.2 + - - +
159X HIS* 2.8 31.0 + - - -
162X SER* 5.9 1.1 - - - -
163X ILE* 3.6 14.6 - - - -
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Residues in contact with ALA 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119X ILE* 3.0 16.9 + - + +
120X GLU* 3.9 5.8 - - - +
121X ASN 3.3 0.4 - - - -
122X GLY* 1.3 73.1 - - - +
124X LYS* 1.3 60.2 + - - +
126X LEU* 3.7 6.8 - - + +
127X TRP* 2.9 27.3 + - - +
163X ILE* 3.6 16.7 - - + +
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Residues in contact with LYS 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120X GLU* 3.2 19.9 + - + +
121X ASN* 3.5 26.5 - - - +
123X ALA* 1.3 72.5 - - - +
125X GLU* 1.3 68.0 + - - +
127X TRP* 2.8 12.2 + - + +
128X PHE* 2.8 57.6 + - + -
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Residues in contact with GLU 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121X ASN* 2.9 38.9 + - - +
122X GLY* 3.9 5.4 - - - +
124X LYS* 1.3 75.9 - - - +
126X LEU* 1.3 62.2 + - - +
128X PHE* 2.9 32.0 + - - +
129X PHE* 2.8 24.4 + - - +
159X HIS* 3.8 13.0 - - + -
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Residues in contact with LEU 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X GLY 3.0 19.5 + - - +
123X ALA* 3.7 8.7 - - + +
125X GLU* 1.3 73.1 - - - +
127X TRP* 1.3 57.0 + - - +
129X PHE* 3.3 5.1 + - + +
130X LEU* 2.8 46.7 + - + +
156X LEU* 3.7 34.1 - - + +
159X HIS* 3.2 34.9 - - + +
160X GLU* 5.0 11.0 - - + +
163X ILE* 4.3 15.7 - - + -
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Residues in contact with TRP 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123X ALA 2.9 17.7 + - - +
124X LYS* 2.8 15.0 + - + +
126X LEU* 1.3 73.4 - - - +
128X PHE* 1.3 65.6 + + - +
130X LEU* 3.7 27.4 - - + -
131X GLN* 2.7 71.8 + - + +
134X LEU* 6.2 3.1 - - + -
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Residues in contact with PHE 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X ASN* 6.0 0.2 - - - -
124X LYS* 2.8 58.2 + - + -
125X GLU* 2.9 35.6 + - - +
127X TRP* 1.3 77.7 - + - +
129X PHE* 1.3 63.9 + - - +
131X GLN* 3.3 15.8 + - - +
132X SER* 3.0 25.8 + - - -
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Residues in contact with PHE 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X GLU 2.8 16.5 + - - +
126X LEU* 3.5 7.0 - - + +
128X PHE* 1.3 75.5 - - - +
130X LEU* 1.3 58.0 + - - +
132X SER* 4.4 4.7 - - - -
133X GLU* 2.9 67.7 + - + +
152X PHE* 3.9 20.6 - + - -
155X ASP* 3.9 33.2 - - + -
156X LEU* 4.1 21.3 - - + -
159X HIS* 4.7 15.7 - - + -
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Residues in contact with LEU 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126X LEU* 2.8 38.0 + - + +
127X TRP* 3.5 34.3 - - + +
128X PHE 3.1 0.2 - - - -
129X PHE* 1.3 77.4 - - - +
131X GLN* 1.3 59.8 + - - +
133X GLU* 3.8 0.7 - - - +
134X LEU* 2.9 43.5 + - + +
152X PHE* 4.1 13.6 - - + -
156X LEU* 3.6 27.6 - - + -
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Residues in contact with GLN 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X TRP* 2.7 70.8 + - + +
128X PHE* 3.7 16.6 - - - +
130X LEU* 1.3 74.6 - - - +
132X SER* 1.3 63.9 + - - +
134X LEU* 4.0 7.5 - - - +
135X LYS* 3.2 20.4 + - - +
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Residues in contact with SER 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X PHE 3.0 19.9 + - - -
129X PHE* 3.7 6.7 - - - -
131X GLN* 1.3 76.2 - - - +
133X GLU* 1.3 65.1 + - - +
135X LYS* 2.8 22.9 + - - +
136X LYS* 3.2 25.6 + - - +
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Residues in contact with GLU 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X PHE* 2.9 56.9 + - + +
132X SER* 1.3 73.6 - - - +
134X LEU* 1.3 61.5 + - - +
135X LYS 3.2 0.2 - - - -
136X LYS* 3.4 30.2 + - - +
137X LEU* 3.1 20.3 + - - +
148X HIS* 3.2 32.8 + - + -
152X PHE* 3.7 25.6 - - + -
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Residues in contact with LEU 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127X TRP* 6.2 3.1 - - + -
130X LEU* 2.9 32.1 + - + +
131X GLN* 4.1 7.2 - - - +
133X GLU* 1.3 78.4 - - - +
135X LYS* 1.3 61.6 + - - +
137X LEU* 3.4 22.3 + - + +
138X LYS* 3.3 19.3 + - - +
152X PHE* 3.5 25.1 - - + -
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Residues in contact with LYS 135 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131X GLN 3.2 15.9 + - - +
132X SER* 2.8 6.7 + - - +
134X LEU* 1.3 76.1 - - - +
136X LYS* 1.3 66.7 + - - +
138X LYS* 3.5 36.0 + - - +
139X ASN* 3.4 18.9 + - - +
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Residues in contact with LYS 136 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132X SER* 3.2 20.5 + - - +
133X GLU* 3.4 38.9 + - - +
134X LEU 3.3 0.2 - - - -
135X LYS* 1.3 77.0 - - - +
137X LEU* 1.3 62.2 + - - +
139X ASN* 3.0 24.3 + - - +
140X LEU* 3.3 16.2 - - + +
148X HIS* 3.8 13.2 - - + +
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Residues in contact with LEU 137 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133X GLU 3.1 8.3 + - - +
134X LEU* 3.7 26.5 - - + +
135X LYS 3.4 0.4 - - - -
136X LYS* 1.3 75.4 - - - +
138X LYS* 1.3 61.4 + - + +
139X ASN 3.2 0.9 + - - -
140X LEU* 3.3 20.1 + - + +
145X LEU* 3.4 40.4 - - + +
148X HIS* 2.9 33.2 + - + +
149X ALA* 4.0 12.8 - - + +
152X PHE* 3.6 30.3 - - + -
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Residues in contact with LYS 138 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134X LEU 3.3 17.5 - - - +
135X LYS* 3.6 34.2 - - - +
136X LYS 3.1 0.4 + - - -
137X LEU* 1.3 76.4 - - + +
139X ASN* 1.3 65.2 + - - +
140X LEU 3.4 4.0 + - - +
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Residues in contact with ASN 139 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135X LYS* 3.4 21.4 + - - +
136X LYS* 3.0 10.4 + - - +
138X LYS* 1.3 84.8 - - - +
140X LEU* 1.3 71.6 + - - +
141X GLU* 5.8 0.9 - - - -
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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