Contacts of the helix formed by residues 126 - 152 (chain A) in PDB entry 2X9D
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 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A THR* 4.3 1.9 - - - +
124A GLY 3.9 2.0 + - - -
125A PHE* 1.3 80.2 - - - +
127A LEU* 1.3 60.1 + - - +
128A ARG* 3.7 6.9 + - - +
129A ASP* 2.9 37.2 + - - -
130A GLY* 2.9 21.8 + - - -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.2 33.0 - - + +
121A THR* 4.0 20.6 - - + +
126A SER* 1.3 74.3 - - - +
128A ARG* 1.3 54.0 + - - +
130A GLY* 3.5 0.7 + - - -
131A LEU* 2.8 35.7 + - + +
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A SER* 4.0 6.9 - - - +
127A LEU* 1.3 75.9 - - - +
129A ASP* 1.3 65.7 + - - +
130A GLY 3.1 1.3 - - - -
131A LEU* 3.0 9.3 + - - +
132A TYR* 2.7 77.4 + - + -
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Residues in contact with ASP 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 3.9 17.4 - - + -
126A SER* 2.9 24.0 + - - +
128A ARG* 1.3 84.9 - - - +
130A GLY* 1.3 63.7 + - - +
132A TYR* 3.8 13.1 - - - +
133A ALA* 3.2 23.9 + - - +
200A GLN* 4.9 18.7 - - + +
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.9 5.4 - - - -
120A MET* 4.2 15.0 - - - +
121A THR* 5.9 0.4 - - - -
125A PHE* 3.8 18.1 - - - +
126A SER 2.9 19.3 + - - -
127A LEU* 3.8 1.3 - - - -
129A ASP* 1.3 77.7 - - - +
131A LEU* 1.3 61.3 + - - +
133A ALA* 3.5 3.6 + - - +
134A ILE* 3.2 27.3 + - - +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.8 28.1 - - + +
127A LEU* 2.8 21.6 + - + +
128A ARG* 3.3 7.6 - - - +
130A GLY* 1.3 73.5 - - - +
132A TYR* 1.3 75.0 + - + +
133A ALA 3.2 0.2 + - - -
134A ILE* 3.2 2.4 + - - +
135A SER* 2.8 47.2 + - - +
1209A ITC 4.2 15.0 - - + -
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Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 2.7 72.5 + - + +
129A ASP* 4.1 11.0 - - - +
130A GLY 3.4 0.2 - - - -
131A LEU* 1.3 89.7 - - + +
133A ALA* 1.3 56.6 + - - +
135A SER* 3.9 6.9 - - - -
136A ALA* 2.9 30.1 + - - +
197A PHE* 5.2 0.7 - - - -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.6 1.3 - - + -
120A MET* 4.1 15.0 - - + -
125A PHE* 4.7 3.1 - - + -
129A ASP 3.2 17.7 + - - +
130A GLY 3.9 3.8 - - - +
131A LEU 3.2 0.2 - - - -
132A TYR* 1.3 76.1 - - - +
134A ILE* 1.3 57.8 + - - +
137A VAL* 3.0 26.1 + - - +
197A PHE* 3.1 53.0 - - + -
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Residues in contact with ILE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE* 4.9 2.9 - - + -
79A LEU* 3.7 23.8 - - + -
113A VAL* 6.0 0.9 - - + -
116A GLN* 4.0 31.6 - - + +
117A LEU* 4.5 12.6 - - + +
120A MET* 3.8 25.1 - - + -
130A GLY 3.2 12.6 + - - +
131A LEU* 3.2 4.6 + - - +
133A ALA* 1.3 77.3 - - - +
135A SER* 1.3 58.9 + - - +
137A VAL* 3.4 7.4 + - - +
138A SER* 2.7 32.4 + - - -
1209A ITC 3.5 43.7 - - + -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 2.8 41.2 + - - +
132A TYR* 3.9 7.7 - - - -
134A ILE* 1.3 72.4 - - - +
136A ALA* 1.3 52.7 + - - +
138A SER* 3.0 4.5 + - - -
139A HIS* 2.8 51.6 + - - -
1209A ITC 3.9 24.5 - - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A TYR 2.9 20.7 + - - +
135A SER* 1.3 73.8 - - - +
137A VAL* 1.3 66.3 + - - +
139A HIS* 4.1 5.8 - - - +
140A PHE* 3.0 27.7 + - - +
193A LEU* 3.8 12.7 - - + +
197A PHE* 3.4 24.2 - - + -
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.3 27.6 - - + +
83A ALA* 3.5 34.1 - - + -
133A ALA 3.0 19.3 + - - +
134A ILE* 3.7 9.0 - - - +
135A SER 3.3 0.2 - - - -
136A ALA* 1.3 74.3 - - - +
138A SER* 1.3 52.9 + - - +
140A PHE* 3.7 1.4 - - + +
141A THR* 2.8 42.0 + - - +
190A LEU* 4.8 7.9 - - + -
193A LEU* 3.9 13.9 - - + -
194A ILE* 5.3 1.3 - - + -
197A PHE* 3.8 15.7 - - + -
1209A ITC 4.5 14.1 - - - -
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE* 4.0 19.1 - - - -
134A ILE 2.7 18.1 + - - -
135A SER 3.0 8.4 + - - -
137A VAL* 1.3 78.7 - - - +
139A HIS* 1.3 59.5 + - - +
141A THR* 4.5 0.4 - - - -
142A LEU* 2.9 30.1 + - - +
1209A ITC 3.2 55.8 - - - +
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Residues in contact with HIS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A SER* 2.8 36.2 + - - +
136A ALA* 4.1 4.8 + - - +
138A SER* 1.3 73.0 - - - +
140A PHE* 1.3 61.9 + - - +
142A LEU* 3.9 12.4 - - + +
143A GLY* 2.9 27.2 + - - -
1209A ITC 3.6 25.1 - - + +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA 3.0 18.2 + - - +
137A VAL 3.7 1.6 - - - +
139A HIS* 1.3 76.8 - - - +
141A THR* 1.3 66.4 + - - +
143A GLY* 3.4 0.5 + - - -
144A ALA* 3.0 29.3 + - + +
185A ALA 4.4 2.0 - - - -
186A PHE* 3.1 60.1 - + - -
189A GLY* 3.8 11.0 - - - -
190A LEU* 3.6 22.2 - - + -
193A LEU* 3.8 22.2 - - + -
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Residues in contact with THR 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.8 15.1 - - - +
86A PHE* 3.7 25.6 - - + -
87A ARG* 3.7 34.8 - - + +
90A LEU* 4.7 1.6 - - + -
137A VAL* 2.8 29.6 + - - +
138A SER 4.0 3.1 - - - -
140A PHE* 1.3 75.0 - - - +
142A LEU* 1.3 63.0 + - - +
144A ALA* 3.4 1.7 + - - +
145A VAL* 3.1 24.8 + - + +
186A PHE* 3.5 24.3 - - + -
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A PHE* 4.7 3.6 - - + -
90A LEU* 4.2 14.8 - - + +
97A ALA* 3.7 30.3 - - + +
100A HIS* 4.8 17.3 - - + -
101A LEU* 4.4 21.5 - - + -
138A SER 2.9 19.0 + - - +
139A HIS* 3.9 13.7 - - + +
141A THR* 1.3 76.5 - - - +
143A GLY* 1.3 57.4 + - - +
145A VAL* 3.4 1.6 + - - +
146A LEU* 2.9 61.3 + - + +
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A HIS 2.9 18.3 + - - -
140A PHE 3.9 0.7 - - - -
142A LEU* 1.3 79.4 - - - +
144A ALA* 1.3 55.2 + - - +
146A LEU* 3.4 8.8 + - - +
147A GLU* 3.0 37.1 + - - +
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Residues in contact with ALA 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 5.6 2.5 - - - +
140A PHE* 3.0 24.6 + - + +
141A THR 3.9 2.9 - - - +
143A GLY* 1.3 76.6 - - - +
145A VAL* 1.3 60.6 + - + +
147A GLU* 4.1 4.5 - - - +
148A GLN* 3.1 25.3 + - - +
182A GLY* 5.7 1.4 - - - +
186A PHE* 4.1 28.7 - - + -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 3.7 45.1 - - + +
90A LEU* 3.8 23.8 - - + -
91A LEU* 3.6 15.0 - - + -
97A ALA* 3.9 3.4 - - + -
141A THR 3.1 17.7 + - - +
142A LEU 4.0 2.7 - - - +
143A GLY 3.3 0.2 - - - -
144A ALA* 1.3 73.4 - - - +
146A LEU* 1.3 57.5 + - - +
148A GLN* 3.3 5.0 + - - +
149A GLN* 2.7 61.1 + - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ALA* 3.3 24.2 - - + -
98A LYS* 3.7 33.7 - - + +
101A LEU* 4.8 14.1 - - + -
142A LEU* 2.9 47.2 + - + +
143A GLY* 3.7 7.9 - - - +
145A VAL* 1.3 75.2 - - - +
147A GLU* 1.3 58.0 + - + +
149A GLN* 3.8 3.3 - - - +
150A GLU* 3.0 34.1 + - - +
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A GLY* 3.0 21.2 + - - +
144A ALA* 4.1 4.5 - - - +
146A LEU* 1.3 73.4 - - + +
148A GLN* 1.3 60.8 + - - +
150A GLU* 4.0 4.6 - - - +
151A HIS* 2.9 32.2 + - - +
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Residues in contact with GLN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 5.3 0.9 - - - +
91A LEU* 4.1 18.4 - - + -
144A ALA 3.1 19.8 + - - +
145A VAL* 3.5 4.9 - - - +
147A GLU* 1.3 78.8 - - - +
149A GLN* 1.3 63.5 + - + +
150A GLU 3.1 1.6 + - - -
151A HIS* 3.2 13.4 + - - +
152A THR* 3.5 13.0 + - - +
181A ASP* 3.3 33.4 - - + +
182A GLY* 5.1 5.2 - - - -
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Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 2.7 26.3 + - - -
91A LEU* 3.5 22.1 + - + +
93A TYR 3.0 19.0 + - - -
94A ARG* 4.9 0.8 - - - +
95A ASP* 4.1 17.2 - - - +
96A GLY 3.6 4.9 + - - +
97A ALA* 3.3 25.8 + - - +
98A LYS 4.8 0.2 + - - -
145A VAL* 2.7 34.3 + - + +
146A LEU* 4.0 3.5 - - - +
148A GLN* 1.3 74.7 - - + +
150A GLU* 1.3 60.3 + - - +
152A THR* 3.7 19.3 - - - -
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASP* 4.7 6.5 - - - +
98A LYS* 2.8 38.7 + - - +
146A LEU 3.0 18.9 + - - +
147A GLU* 4.0 6.3 - - - +
149A GLN* 1.3 77.5 - - - +
151A HIS* 1.3 59.1 + - - +
152A THR 3.0 15.3 + - - +
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Residues in contact with HIS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLU* 2.9 18.6 + - - +
148A GLN* 3.2 8.3 + - - +
150A GLU* 1.3 74.4 - - - +
152A THR* 1.3 59.9 + - - +
174A LEU 5.9 0.2 + - - -
177A MET* 5.8 5.1 - - + +
178A ASP* 4.5 30.3 + - + +
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Residues in contact with THR 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A GLN* 3.5 10.3 + - - +
149A GLN* 3.7 18.2 - - - -
150A GLU* 3.0 14.1 - - - +
151A HIS* 1.3 81.0 - - - +
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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