Contacts of the helix formed by residues 123 - 150 (chain A) in PDB entry 3W8I
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 123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASP 5.6 1.3 + - - +
120A GLU* 2.9 8.9 + - - +
121A ILE 3.2 1.5 - - - -
122A ASN* 1.3 79.0 - - - +
124A ARG* 1.3 60.7 + - - +
125A VAL* 3.3 21.5 + - - +
126A ARG* 3.2 37.4 + - + +
127A PHE* 2.9 26.0 + - - +
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Residues in contact with ARG 124 (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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121A ILE 4.4 6.9 + - - -
122A ASN 4.0 3.4 + - - -
123A ASP* 1.3 73.7 + - - +
125A VAL* 1.3 58.5 + - + +
127A PHE* 4.3 11.2 - - - -
128A LEU* 2.9 50.9 + - + +
181A TYR* 3.5 37.2 + - - -
182A PHE* 3.4 35.0 + - - +
185A GLY* 5.8 2.8 - - - -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 3.3 11.4 - - - +
124A ARG* 1.3 77.8 - - + +
126A ARG* 1.3 66.0 + - + +
128A LEU* 3.1 11.8 + - + +
129A GLN* 3.0 21.6 + - + +
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Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASP 5.1 2.9 - - - -
120A GLU* 3.6 33.6 - - + +
123A ASP* 3.2 35.3 + - - +
125A VAL* 1.3 80.0 - - + +
127A PHE* 1.3 52.9 + - - +
129A GLN* 3.0 11.3 + - - +
130A THR* 2.7 34.6 + - - -
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 4.3 21.3 - - + -
120A GLU* 3.3 14.5 + - + +
121A ILE* 3.8 41.7 - - + +
123A ASP 2.9 12.2 + - - +
124A ARG* 3.9 13.7 - - - +
126A ARG* 1.3 76.2 - - - +
128A LEU* 1.3 58.1 + - - +
130A THR* 3.0 17.0 + - + -
131A ILE* 2.9 50.6 + - + +
134A ILE* 5.9 1.1 - - + -
174A PHE* 6.0 0.4 - + - -
178A LEU* 3.8 22.4 - - + -
181A TYR* 3.6 32.3 - + - -
182A PHE* 4.0 7.4 - + - -
190A VAL* 4.3 4.5 - - + -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 2.9 39.6 + - + +
125A VAL* 3.1 9.4 + - + +
127A PHE* 1.3 76.6 - - - +
129A GLN* 1.3 60.0 + - - +
131A ILE* 3.7 9.7 + - + +
132A LYS* 3.5 26.1 + - - +
182A PHE* 4.2 26.5 - - + -
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU* 6.0 0.2 - - - +
125A VAL* 3.0 12.0 + - + +
126A ARG* 3.0 12.8 + - - +
128A LEU* 1.3 76.7 - - - +
130A THR* 1.3 64.6 + - - +
132A LYS* 3.2 29.5 + - - +
133A ASP* 2.8 57.6 + - - +
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Residues in contact with THR 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.3 14.8 - - + +
117A ILE* 4.3 16.4 - - + -
120A GLU* 2.1 42.8 + - + +
126A ARG 2.7 14.0 + - - -
127A PHE* 3.0 20.2 + - + -
129A GLN* 1.3 76.0 - - - +
131A ILE* 1.3 57.9 + - - +
133A ASP* 3.2 10.4 + - - +
134A ILE* 2.9 51.7 + - + +
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Residues in contact with ILE 131 (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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127A PHE* 2.9 36.8 + - + +
128A LEU* 3.9 13.9 - - + +
129A GLN 3.2 0.4 - - - -
130A THR* 1.3 76.1 - - - +
132A LYS* 1.3 59.7 + - + +
134A ILE* 3.2 10.8 + - + +
135A ALA* 2.9 29.8 + - + +
178A LEU* 3.8 29.2 - - + -
182A PHE* 3.5 38.4 - - + -
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Residues in contact with LYS 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 LEU 3.5 18.1 + - - +
129A GLN* 3.2 30.4 + - - +
131A ILE* 1.3 78.7 - - + +
133A ASP* 1.3 63.6 + - - +
135A ALA* 3.3 7.5 + - - +
136A SER* 2.9 24.1 + - - -
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.8 24.3 - - + +
120A GLU* 5.4 1.2 - - - +
129A GLN* 2.8 48.2 + - - +
130A THR* 3.2 11.4 + - - +
132A LYS* 1.3 77.0 - - - +
134A ILE* 1.3 56.6 + - - +
136A SER* 3.3 7.7 + - - -
137A ALA* 2.9 28.8 + - - +
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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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110A LEU* 4.6 3.1 - - + -
113A ILE* 3.6 19.7 - - + -
114A LEU* 3.9 21.3 - - + -
117A ILE* 3.9 12.3 - - + -
127A PHE* 5.9 1.3 - - + -
130A THR* 2.9 32.0 + - + +
131A ILE* 3.2 10.3 + - + +
133A ASP* 1.3 72.1 - - - +
135A ALA* 1.3 67.4 + - - +
137A ALA* 3.2 5.3 + - - +
138A ILE* 2.9 44.9 + - + +
174A PHE* 3.8 38.6 - - + -
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Residues in contact with ALA 135 (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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131A ILE* 2.9 15.4 + - + +
132A LYS* 3.3 11.4 + - - +
134A ILE* 1.3 76.5 - - - +
136A SER* 1.3 57.8 + - - +
138A ILE* 3.4 7.5 + - - +
139A LYS* 2.9 30.2 + - - +
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Residues in contact with SER 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 LYS 2.9 14.0 + - - -
133A ASP* 3.5 11.2 - - - -
135A ALA* 1.3 76.3 - - - +
137A ALA* 1.3 57.6 + - - +
139A LYS* 3.3 8.3 + - - +
140A GLU* 2.9 44.9 + - - +
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Residues in contact with ALA 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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106A LYS* 5.0 3.2 - - - +
109A ALA* 4.9 4.0 - - + -
110A LEU* 4.1 27.6 - - + +
113A ILE* 3.7 21.5 - - + -
133A ASP 2.9 17.2 + - - +
134A ILE* 3.7 5.2 - - - +
136A SER* 1.3 76.0 - - - +
138A ILE* 1.3 57.4 + - - +
140A GLU* 3.4 7.8 + - - +
141A LEU* 2.9 29.6 + - - +
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Residues in contact with ILE 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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110A LEU* 4.0 21.1 - - + -
134A ILE* 2.9 37.0 + - + +
135A ALA* 3.7 6.5 - - - +
137A ALA* 1.3 73.6 - - - +
139A LYS* 1.3 67.0 + - - +
141A LEU* 3.3 6.4 + - - +
142A LEU* 2.9 40.9 + - + +
167A PHE* 4.0 4.9 - - + -
171A SER* 3.7 31.0 - - - +
174A PHE* 5.2 3.4 - - + -
197A LEU* 3.9 20.0 - - + -
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Residues in contact with LYS 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 ALA 2.9 17.4 + - - +
136A SER* 3.4 9.4 - - - +
138A ILE* 1.3 78.6 - - - +
140A GLU* 1.3 63.1 + - + +
142A LEU* 3.4 8.5 + - - +
143A ASP* 2.9 57.9 + - - +
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Residues in contact with GLU 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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106A LYS* 3.4 33.1 + - + +
136A SER* 2.9 31.4 + - - +
137A ALA* 3.9 6.2 - - - +
139A LYS* 1.3 78.6 - - + +
141A LEU* 1.3 61.5 + - - +
143A ASP* 3.2 13.2 + - - +
144A THR* 2.9 32.2 + - - -
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Residues in contact with LEU 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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103A LEU* 3.8 22.4 - - + -
106A LYS* 3.6 27.9 - - + +
107A ALA* 3.6 20.6 - - + +
110A LEU* 4.6 7.2 - - + -
137A ALA 2.9 18.5 + - - +
138A ILE* 3.3 7.6 + - - +
140A GLU* 1.3 75.6 - - - +
142A LEU* 1.3 58.1 + - - +
144A THR* 3.2 4.8 + - - -
145A VAL* 2.9 44.4 + - + +
167A PHE* 3.5 39.0 - - + -
201A THR* 5.3 4.0 - - + +
204A ILE* 5.1 8.1 - - + -
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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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138A ILE* 2.9 37.0 + - + +
139A LYS* 3.6 7.9 - - - +
141A LEU* 1.3 74.2 - - - +
143A ASP* 1.3 66.7 + - - +
145A VAL* 3.2 8.8 + - + +
146A ASN* 2.9 32.4 + - - +
164A LYS* 4.3 23.1 - - + -
167A PHE* 4.0 19.3 - - + -
168A VAL* 3.8 31.2 - - + -
171A SER* 5.5 1.1 - - - +
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Residues in contact with ASP 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 LYS* 2.9 53.2 + - - +
140A GLU* 3.2 17.2 - - - +
142A LEU* 1.3 75.4 - - - +
144A THR* 1.3 59.0 + - - +
146A ASN* 3.2 14.9 + - - +
147A ASN* 2.9 36.5 + - - +
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Residues in contact with THR 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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99A GLU* 3.7 9.4 - - - +
102A ASP* 3.4 20.0 + - + -
103A LEU* 3.3 42.8 - - + +
106A LYS* 3.5 17.5 - - - +
140A GLU 2.9 13.5 + - - -
141A LEU* 3.4 9.9 - - - -
143A ASP* 1.3 75.6 - - - +
145A VAL* 1.3 60.7 + - - +
147A ASN* 3.1 12.9 + - + +
148A VAL* 2.9 26.7 + - - +
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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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103A LEU* 4.5 7.9 - - + -
141A LEU* 2.9 35.8 + - + +
142A LEU* 3.2 11.4 + - + +
144A THR* 1.3 74.7 - - - +
146A ASN* 1.3 64.8 + - - +
148A VAL* 3.0 12.1 + - - +
149A PHE* 3.0 38.5 + - + -
164A LYS* 4.4 17.9 - - + -
167A PHE* 6.1 0.4 - - + -
204A ILE* 4.4 20.6 - - + -
208A PHE* 3.6 23.6 - - + -
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Residues in contact with ASN 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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142A LEU* 2.9 23.0 + - - +
143A ASP* 3.3 14.8 + - - +
145A VAL* 1.3 76.2 - - - +
147A ASN* 1.3 64.0 + - - +
149A PHE* 3.3 20.1 + - - +
150A LYS* 3.5 16.7 + - - +
164A LYS* 3.0 37.9 + - - +
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Residues in contact with ASN 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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99A GLU* 3.6 23.4 - - + +
102A ASP* 4.5 10.3 + - - +
143A ASP* 2.9 26.9 + - - +
144A THR* 3.1 13.6 + - + +
146A ASN* 1.3 75.4 - - - +
148A VAL* 1.3 64.2 + - - +
150A LYS* 3.3 44.0 + - - +
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 3.9 33.8 - - + +
100A PHE* 4.0 20.6 - - + -
103A LEU* 4.2 12.6 - - + -
144A THR 2.9 21.2 + - - +
145A VAL* 3.0 8.0 + - - +
147A ASN* 1.3 78.0 - - - +
149A PHE* 1.3 65.7 + - + +
150A LYS 3.0 6.8 + - - -
208A PHE* 3.5 34.5 - - + -
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Residues in contact with PHE 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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145A VAL* 3.0 26.6 + - + -
146A ASN* 3.3 19.4 + - - +
148A VAL* 1.3 79.5 - - + +
150A LYS* 1.3 58.0 + - - +
160A LEU* 3.2 51.4 - - + -
161A GLU* 3.9 20.6 - - + -
164A LYS* 3.9 19.3 - - + -
208A PHE* 3.4 31.6 - + - -
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Residues in contact with LYS 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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99A GLU* 6.1 0.9 - - - -
146A ASN* 3.7 7.4 - - - +
147A ASN* 3.3 46.8 + - - +
148A VAL 3.0 7.8 + - - +
149A PHE* 1.3 82.3 - - - +
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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