Contacts of the helix formed by residues 126 - 149 (chain A) in PDB entry 4NEF
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 THR 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 4.1 1.1 - - - -
124A SER 4.5 6.7 - - - +
125A THR* 1.3 75.2 - - - +
127A ALA* 1.4 53.2 + - - +
128A GLY* 3.8 4.1 + - - -
129A GLN* 3.0 37.2 + - - +
130A ALA* 2.8 32.1 + - - +
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Residues in contact with ALA 127 (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 LEU* 3.6 20.7 - - + +
126A THR* 1.4 72.0 - - - +
128A GLY* 1.3 55.6 + - - +
130A ALA* 3.7 4.9 - - - +
131A VAL* 2.9 31.8 + - - +
200A ASP* 4.9 5.8 - - + +
202A TRP* 3.7 26.9 - - + +
203A VAL* 3.7 12.5 - - + +
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 3.2 5.2 + - - -
127A ALA* 1.3 75.6 - - - +
129A GLN* 1.4 56.9 + - - +
131A VAL* 3.4 15.9 - - - +
132A THR* 2.7 27.9 + - - -
202A TRP* 5.0 3.1 - - - -
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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
----------------------------------------------------------
124A SER 4.8 0.7 - - - +
125A THR* 3.8 10.6 - - + +
126A THR* 3.0 41.3 + - - +
128A GLY* 1.4 74.4 - - - +
130A ALA* 1.3 63.8 + - - +
132A THR* 3.4 3.5 + - - -
133A VAL* 3.2 18.4 + - - +
106D GLU* 3.2 28.0 + - - +
107D ILE* 3.4 43.6 - - - +
108D THR 3.9 10.1 + - - -
109D PRO* 4.2 10.6 - - - +
113D ARG* 4.5 6.3 - - - +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.3 8.3 - - + -
125A THR* 3.8 12.9 - - + +
126A THR 2.8 15.0 + - - +
127A ALA* 3.7 9.0 - - - +
129A GLN* 1.3 75.1 - - - +
131A VAL* 1.4 58.7 + - - +
133A VAL* 3.2 8.7 + - - +
134A GLU* 3.0 31.7 + - - +
178A TYR* 5.2 0.7 - - - -
179A THR* 3.6 26.3 - - + +
203A VAL* 3.8 8.5 - - + -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ALA 2.9 20.1 + - - +
128A GLY* 3.4 20.9 - - - +
130A ALA* 1.4 71.8 - - - +
132A THR* 1.4 58.1 + - - +
134A GLU* 4.5 1.3 - - - -
135A LEU* 3.1 27.5 + - - +
202A TRP* 3.8 28.3 - - + -
203A VAL* 3.6 15.6 - - + +
206A ILE* 3.9 10.8 - - + -
207A GLY* 3.4 28.8 - - - +
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Residues in contact with THR 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 GLY 2.7 21.5 + - - -
129A GLN* 3.5 9.5 - - - -
130A ALA 3.2 0.6 - - - -
131A VAL* 1.4 76.5 - - - +
133A VAL* 1.4 63.4 + - - +
135A LEU* 3.4 10.5 - - + +
136A PHE* 3.2 45.4 + - + -
103D LEU* 4.4 4.7 - - + -
107D ILE* 3.6 20.0 - - + -
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Residues in contact with VAL 133 (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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129A GLN 3.2 16.4 + - - +
130A ALA* 3.2 7.9 + - - +
132A THR* 1.4 73.4 - - - +
134A GLU* 1.4 57.5 + - + +
136A PHE* 3.0 6.4 + - - +
137A LEU* 2.9 54.2 + - + +
174A LEU* 4.4 9.6 - - + -
175A GLY* 4.5 1.6 - - - -
178A TYR* 3.8 41.1 - - + -
179A THR* 5.5 1.3 - - - +
25D PHE* 4.6 5.3 - - + -
107D ILE* 3.7 31.9 - - + -
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Residues in contact with GLU 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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130A ALA 3.0 18.5 + - - +
131A VAL 3.9 0.4 - - - +
133A VAL* 1.4 74.4 - - + +
135A LEU* 1.4 58.1 + - - +
137A LEU* 3.7 14.7 - - + +
138A THR* 2.9 32.7 + - - -
179A THR* 2.7 34.2 + - + +
182A SER* 3.0 28.0 + - - -
183A MET* 2.8 28.2 + - - -
203A VAL* 4.3 12.6 - - + +
204A PHE* 4.8 1.8 - - + -
207A GLY* 3.8 23.5 - - - +
208A PRO* 3.5 9.0 - - + +
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Residues in contact with LEU 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 VAL 3.1 14.6 + - - +
132A THR* 3.4 15.5 - - + +
134A GLU* 1.4 74.9 - - - +
136A PHE* 1.4 84.9 + - + +
139A LEU* 2.9 32.7 + - + +
207A GLY* 3.4 13.6 + - - +
210A VAL* 3.7 26.5 - - + -
211A GLY* 3.3 22.4 - - - +
214A LEU* 4.3 18.8 - - + -
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Residues in contact with PHE 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 THR* 3.2 30.0 + - + -
133A VAL 3.0 7.1 + - - +
135A LEU* 1.4 94.3 - - + +
137A LEU* 1.4 63.3 + - - +
139A LEU* 3.9 12.6 - - + +
140A GLN* 3.3 24.8 + - - +
18D LEU* 5.9 3.4 - - + -
21D LEU* 4.2 18.4 - - + -
22D LEU* 3.7 23.5 - - + +
25D PHE* 3.7 27.6 - + + -
26D PHE* 3.6 6.6 - - + -
103D LEU* 3.6 41.3 - - + -
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Residues in contact with LEU 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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133A VAL* 2.9 24.3 + - + +
134A GLU* 3.7 32.5 - - - +
135A LEU 3.3 0.2 - - - -
136A PHE* 1.4 74.1 - - - +
138A THR* 1.4 61.1 + - - +
140A GLN* 2.7 31.6 + - - +
141A LEU 3.4 0.9 + - - -
171A GLY* 3.3 23.8 - - - +
174A LEU* 3.9 13.9 - - + -
175A GLY* 3.8 21.5 - - - +
181A CYS* 4.0 11.9 - - - -
183A MET* 3.2 19.2 - - + +
26D PHE* 3.5 25.4 - - + -
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Residues in contact with THR 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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68A ASN* 5.2 0.4 - - - +
70A ALA* 4.0 5.4 - - + -
71A VAL* 5.7 0.4 - - + -
134A GLU 2.9 17.3 + - - -
135A LEU 4.1 2.2 - - - -
137A LEU* 1.4 74.1 - - - +
139A LEU* 1.4 56.7 + - - +
141A LEU* 3.4 9.1 + - + -
142A VAL* 3.0 34.5 + - + +
183A MET* 3.4 33.3 - - + +
208A PRO* 3.3 36.7 - - + +
211A GLY 4.2 2.2 - - - -
212A ALA* 4.0 14.1 - - + -
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Residues in contact with LEU 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 LEU* 2.9 25.5 + - + +
136A PHE* 3.9 14.6 - - + +
137A LEU 3.4 0.2 - - - -
138A THR* 1.4 76.5 - - - +
140A GLN* 1.4 62.0 + - - +
142A VAL* 3.4 2.3 + - - +
143A LEU* 3.1 33.5 + - + +
211A GLY 3.4 10.7 + - - +
214A LEU* 3.7 27.4 - - + -
215A GLY* 3.6 27.1 - - - +
218A LEU* 4.3 8.5 - - + -
18D LEU* 4.6 11.0 - - + -
22D LEU* 3.9 35.2 - - + -
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Residues in contact with GLN 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 PHE 3.3 12.4 + - - +
137A LEU* 2.7 22.9 + - - +
139A LEU* 1.4 75.5 - - - +
141A LEU* 1.4 72.0 - - - +
143A LEU* 3.2 13.2 + - - +
144A CYS* 3.0 23.2 + - - +
167A SER* 2.9 38.2 + - - +
170A LEU* 3.3 25.8 - - + +
171A GLY* 4.1 5.9 - - - -
183A MET* 3.3 11.9 - - - +
22D LEU* 4.4 17.3 - - + -
26D PHE* 3.4 19.7 - - + -
54D THR* 3.4 9.9 - - + +
55D LEU* 5.6 3.8 - - + -
58D ALA* 5.1 0.5 - - - +
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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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52A ILE* 5.6 0.2 - - + -
68A ASN* 4.3 20.0 - - - +
71A VAL* 4.7 5.4 - - + -
137A LEU 3.4 9.8 + - - +
138A THR* 3.6 11.7 - - + +
139A LEU 3.3 0.2 - - - -
140A GLN* 1.4 81.4 - - - +
142A VAL* 1.3 57.4 + - + +
144A CYS* 3.1 5.5 + - - +
145A ILE* 2.9 56.0 + - + +
164A ILE* 4.2 4.5 - - + +
167A SER* 3.4 19.3 - - - +
168A VAL* 3.6 31.4 - - + +
183A MET* 3.8 29.4 - - + +
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Residues in contact with VAL 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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71A VAL* 4.3 20.6 - - + -
74A ALA* 3.9 7.6 - - + -
138A THR* 3.0 23.7 + - + +
139A LEU 3.9 3.4 - - - +
141A LEU* 1.3 73.7 - - + +
143A LEU* 1.3 56.6 + - - +
145A ILE* 4.4 5.6 - - + -
146A PHE* 3.0 61.2 + - + -
212A ALA* 3.6 43.1 - - + +
215A GLY* 3.8 3.6 - - - -
216A SER 3.7 11.0 - - - +
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Residues in contact with LEU 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 LEU* 3.1 25.1 + - + +
140A GLN* 3.2 11.2 + - - +
142A VAL* 1.3 75.7 - - - +
144A CYS* 1.3 59.8 + - - +
146A PHE* 3.7 4.3 + - - +
147A ALA* 3.3 23.2 + - - +
215A GLY* 3.3 33.9 - - - +
218A LEU* 4.7 7.6 - - + -
219A TYR* 4.2 15.3 - - + -
223A LEU* 4.6 9.4 - - + -
18D LEU* 4.0 26.2 - - + -
22D LEU* 4.3 18.2 - - + -
55D LEU* 5.7 0.9 - - + -
58D ALA* 3.8 17.3 - - + +
59D LEU* 4.7 9.0 - - + -
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Residues in contact with CYS 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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140A GLN 3.0 7.6 + - - +
141A LEU 3.5 7.6 - - - +
143A LEU* 1.3 73.8 - - - +
145A ILE* 1.4 52.7 + - - +
147A ALA* 3.3 2.4 + - - +
148A SER* 2.8 42.8 + - - -
163A SER* 3.6 30.3 - - - -
164A ILE* 3.9 3.8 - - - -
167A SER* 3.6 20.6 - - - +
54D THR* 4.0 14.8 - - + +
57D GLN* 3.7 23.8 - - - -
58D ALA* 3.9 8.9 - - - +
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Residues in contact with ILE 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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52A ILE* 6.1 0.4 - - + -
64A GLY 6.0 2.0 - - - +
65A ALA 5.9 2.0 - - - +
66A HIS 5.5 1.6 - - - +
71A VAL* 3.6 43.7 - - + -
75A CYS* 5.7 5.4 - - - -
141A LEU* 2.9 39.8 + - + +
142A VAL* 3.9 7.0 - - + +
144A CYS* 1.4 70.7 - - - +
146A PHE* 1.3 62.5 + - + +
148A SER 3.4 0.7 + - - -
149A THR* 2.8 46.1 + - + +
164A ILE* 3.7 37.5 - - + -
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Residues in contact with PHE 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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71A VAL* 6.4 0.7 - - + -
74A ALA* 3.6 33.9 - - + -
75A CYS* 4.2 9.9 - - - -
80A HIS* 3.1 38.1 - + - -
142A VAL* 3.0 50.4 + - + +
143A LEU 4.0 1.6 - - - +
145A ILE* 1.3 82.3 - - + +
147A ALA* 1.4 58.3 + - - +
149A THR* 3.7 7.0 + - - -
150A ASP* 3.3 22.3 + - - +
216A SER* 3.7 9.6 - - - -
219A TYR* 3.6 33.3 + + + -
220A ASN* 3.2 23.8 - - - -
302A ZN 4.4 0.9 - - - -
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Residues in contact with ALA 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 LEU 3.3 15.2 + - - +
144A CYS 3.3 3.7 + - - +
146A PHE* 1.4 74.2 - - - +
148A SER* 1.3 60.5 + - - +
149A THR 3.3 0.2 - - - -
150A ASP* 3.3 7.8 + - - +
153A ARG* 2.8 36.4 + - - +
219A TYR* 3.5 18.8 + - + +
57D GLN* 3.3 27.1 - - + +
58D ALA* 3.8 11.9 - - - +
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Residues in contact with SER 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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144A CYS* 2.8 24.0 + - - -
145A ILE 3.4 0.9 + - - -
147A ALA* 1.3 77.0 - - - +
149A THR* 1.3 58.0 + - - +
150A ASP 3.4 2.4 + - - +
153A ARG* 4.2 2.5 + - - +
155A GLU* 5.4 1.6 - - - +
160A PRO* 3.4 35.6 + - - +
164A ILE* 3.7 28.3 - - - +
57D GLN* 2.8 30.7 + - - +
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Residues in contact with THR 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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56A VAL* 6.0 2.9 - - + -
64A GLY 5.4 8.1 - - - +
145A ILE* 2.8 31.0 + - + +
146A PHE* 3.7 8.6 + - - -
147A ALA 3.3 0.2 - - - -
148A SER* 1.3 79.5 - - - +
150A ASP* 1.4 60.9 + - - +
151A GLU* 3.6 14.0 + - - +
160A PRO* 6.2 0.4 - - + -
164A ILE* 4.7 13.2 - - + -
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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
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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