Contacts of the helix formed by residues 137 - 167 (chain B) in PDB entry 5D0Y
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 ASN 137 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 1.3 76.9 - - - +
138B PHE* 1.3 82.9 + - - +
139B MET* 3.6 17.1 + - - +
140B VAL* 3.0 39.0 + - + +
141B ALA 3.3 4.5 + - - -
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Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 3.9 16.2 - - + -
124B GLY* 3.6 24.0 - - - -
127B THR* 3.7 19.5 - - + +
128B LEU* 3.9 23.8 - - + -
131B SER* 3.9 14.6 + - - +
136B THR 4.1 0.8 + - - -
137B ASN* 1.3 79.8 + - - +
139B MET* 1.3 85.9 + - + +
141B ALA* 3.3 5.5 - - - +
142B LEU* 2.9 35.9 + - + +
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Residues in contact with MET 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ASN* 3.3 14.9 + - - +
138B PHE* 1.3 95.8 - - + +
140B VAL* 1.3 60.9 + - - +
142B LEU* 3.4 29.3 - - + +
143B SER* 3.0 29.5 + - - -
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 4.1 19.5 - - + -
137B ASN* 3.0 35.9 + - + +
139B MET* 1.3 74.6 - - - +
141B ALA* 1.3 65.0 + - - +
143B SER* 3.1 17.4 + - - +
144B SER* 3.1 18.4 + - - +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 5.9 1.3 - - - -
127B THR* 3.6 17.7 - - + +
130B VAL* 4.5 10.8 - - + -
131B SER* 3.9 16.4 - - - +
136B THR* 3.8 20.5 + - - +
137B ASN 3.3 2.0 + - - -
138B PHE 3.3 9.4 - - - +
140B VAL* 1.3 80.2 - - - +
142B LEU* 1.3 63.9 + - - +
143B SER 3.0 1.2 + - - -
144B SER* 3.0 17.0 + - - -
145B ARG* 3.2 16.7 + - - +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 3.9 31.0 - - + +
127B THR* 3.7 18.1 - - + +
138B PHE* 2.9 29.1 + - + +
139B MET* 3.4 39.0 - - + +
140B VAL 3.3 0.4 - - - -
141B ALA* 1.3 72.5 - - - +
143B SER* 1.3 58.5 + - - +
145B ARG* 3.2 4.4 + - + +
146B ILE* 3.0 48.8 + - + +
149B GLU* 6.3 0.9 - - + -
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B MET 3.0 16.6 + - - -
140B VAL* 3.1 11.6 + - - +
141B ALA 3.0 0.6 + - - -
142B LEU* 1.3 79.1 - - - +
144B SER* 1.3 66.0 + - - +
145B ARG 3.4 0.2 + - - -
146B ILE* 3.7 19.0 + - - +
147B LEU* 5.1 2.3 + - - +
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Residues in contact with SER 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 4.8 11.2 - - - +
39B LEU* 3.4 14.1 - - - +
140B VAL* 3.1 17.7 + - - +
141B ALA* 3.0 7.9 + - - -
143B SER* 1.3 82.2 + - - +
145B ARG* 1.3 62.8 + - - +
147B LEU* 5.2 3.3 + - - +
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B THR* 4.1 21.5 - - + -
39B LEU* 3.6 22.5 - - + +
122B TYR 2.9 13.1 + - - -
123B ILE* 4.6 0.4 - - - +
126B ASN* 3.8 6.8 - - - +
127B THR* 2.5 54.4 + - - +
130B VAL* 4.5 8.2 - - - +
141B ALA 3.3 17.3 - - - +
142B LEU* 3.2 6.4 + - + +
144B SER* 1.3 80.8 - - - +
146B ILE* 1.3 62.0 + - - +
147B LEU 3.4 2.2 - - - -
148B LYS* 3.3 13.6 + - - +
149B GLU* 3.2 27.5 + - + +
201B FOL 2.5 58.0 + - - -
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Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 4.4 22.0 - - + -
142B LEU* 3.0 36.8 + - + +
143B SER* 3.7 15.7 - - - +
144B SER 3.7 1.4 - - - -
145B ARG* 1.3 75.3 - - - +
147B LEU* 1.3 72.7 + - + +
149B GLU* 3.1 6.4 + - + -
150B MET* 3.0 49.6 + - + +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.7 22.0 - - + -
143B SER 5.1 0.4 + - - -
144B SER 5.7 2.7 - - - +
145B ARG 3.4 1.0 - - - -
146B ILE* 1.3 83.4 - - + +
148B LYS* 1.3 62.7 + - - +
150B MET* 3.3 24.1 + - + +
151B ILE* 3.1 32.6 + - + +
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.8 36.0 - - + +
40B GLN 3.9 7.6 - - - +
41B VAL* 4.1 9.9 - - + +
122B TYR* 4.1 8.5 - - - -
145B ARG 3.3 11.3 + - - +
147B LEU* 1.3 78.8 - - - +
149B GLU* 1.3 84.3 + - - +
151B ILE* 3.1 3.6 + - - -
152B THR* 2.8 65.9 + - + -
156B HIS* 4.7 0.8 - - - -
201B FOL 3.2 50.7 + - - +
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Residues in contact with GLU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TRP* 4.9 1.6 - - - -
118B THR* 3.7 8.3 - - + +
122B TYR* 3.3 20.9 - - - +
123B ILE* 3.7 31.6 - - + +
142B LEU* 6.3 1.1 - - + -
145B ARG* 3.2 40.8 + - + +
146B ILE* 3.1 9.1 + - + +
148B LYS* 1.3 109.5 + - - +
150B MET* 1.3 60.2 + - - +
152B THR* 4.2 2.8 + - - -
153B PRO* 3.1 22.8 - - - +
201B FOL 2.6 22.0 - - - +
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Residues in contact with MET 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A MET 3.4 2.1 - - - +
151A ILE* 3.8 29.4 - - + +
154A TRP* 2.9 46.6 + - + +
155A ILE* 4.6 9.9 - - + -
123B ILE* 6.4 0.2 - - + -
146B ILE* 3.0 45.7 + - + +
147B LEU* 3.6 30.7 - - + +
148B LYS 3.2 0.2 - - - -
149B GLU* 1.3 81.1 - - - +
151B ILE* 1.3 59.1 + - - +
153B PRO* 3.5 3.0 - - - +
154B TRP* 3.2 13.5 + - - -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.7 28.7 - - + -
150A MET* 3.6 28.5 - - + -
151A ILE* 4.1 26.0 - - + -
147B LEU* 3.1 22.2 + - + +
148B LYS* 4.0 3.6 - - - +
150B MET* 1.3 76.1 - - - +
152B THR* 1.3 71.0 + - + +
153B PRO* 3.1 2.9 - - - -
154B TRP* 3.0 23.7 - - - -
155B ILE* 3.4 12.5 - - + +
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Residues in contact with THR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 4.6 13.7 - - + -
118B THR* 5.5 1.2 - - - +
122B TYR* 5.8 0.2 - - - -
148B LYS* 2.8 62.2 + - + +
149B GLU* 4.2 1.4 + - - -
151B ILE* 1.3 75.6 - - + +
153B PRO* 1.4 69.2 - - - +
155B ILE* 2.7 28.0 + - + +
156B HIS* 2.8 26.3 + - - +
201B FOL 5.5 0.2 - - - +
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Residues in contact with PRO 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TRP* 4.0 20.0 - - + -
114B VAL* 3.6 20.1 - - + +
115B ILE* 5.8 1.3 - - + -
118B THR* 4.1 15.9 - - + +
149B GLU 3.1 28.9 - - - +
150B MET 3.5 4.5 - - - +
151B ILE 3.1 6.5 - - - +
152B THR* 1.4 93.1 - - - +
154B TRP* 1.3 55.5 - - - +
156B HIS* 3.0 6.3 + - + +
157B MET* 2.8 45.9 + - + +
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Residues in contact with TRP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 3.7 38.6 - - + -
149A GLU 5.0 1.1 - - - -
150A MET* 3.0 46.8 + - + +
153A PRO* 4.0 22.0 - - + -
154A TRP* 3.1 38.4 - + - -
157A MET* 4.5 2.2 - - + -
150B MET 3.2 8.5 + - - -
151B ILE 3.0 24.0 - - - +
152B THR 3.1 0.6 - - - -
153B PRO* 1.3 73.6 - - - +
155B ILE* 1.3 66.1 + - + +
157B MET* 3.3 22.5 + - + +
158B VAL* 3.1 30.5 + - + +
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A MET* 4.3 11.4 - - - -
45B PHE* 5.6 0.9 - - + -
151B ILE* 3.4 32.1 - - + +
152B THR* 2.7 22.5 + - + +
154B TRP* 1.3 73.9 - - - +
156B HIS* 1.3 68.7 + - + +
158B VAL* 3.4 4.9 + - - +
159B VAL* 3.0 43.8 + - + +
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Residues in contact with HIS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLY 4.7 0.2 + - - -
45B PHE* 3.4 46.1 - + + -
96B TYR* 4.4 7.6 + - - +
114B VAL* 3.6 20.0 - - + +
118B THR* 4.7 2.0 + - - -
122B TYR* 3.8 37.7 + + - -
148B LYS* 4.7 5.8 - - - -
152B THR* 2.8 22.8 + - - +
153B PRO* 3.0 10.9 + - - +
155B ILE* 1.3 82.2 - - + +
157B MET* 1.3 52.9 + - - +
159B VAL* 3.4 1.6 + - - +
160B VAL* 2.7 41.2 + - + +
201B FOL 3.6 18.7 + - - -
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Residues in contact with MET 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TRP* 4.7 1.3 - - + -
110B VAL* 3.3 26.6 - - + +
111B ILE* 3.8 32.8 - - + +
114B VAL* 3.7 24.7 - - + -
115B ILE* 3.8 29.6 - - + -
153B PRO* 2.8 31.8 + - + +
154B TRP* 3.7 31.4 - - + +
156B HIS* 1.3 77.9 - - - +
158B VAL* 1.3 58.7 + - + +
160B VAL 3.2 0.3 + - - -
161B TRP* 2.9 26.5 + - - +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B TRP* 3.1 19.4 + - + +
155B ILE* 3.8 6.3 - - - +
157B MET* 1.3 73.6 - - + +
159B VAL* 1.3 70.3 + - + +
161B TRP* 3.1 16.7 + - - +
162B PHE* 3.1 41.6 + - + -
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 6.2 0.4 - - + -
45B PHE* 3.5 30.3 - - + -
46B ILE* 4.0 9.0 - - + -
155B ILE* 3.0 33.3 + - + +
156B HIS 3.7 2.7 - - - +
158B VAL* 1.3 78.5 - - + +
160B VAL* 1.3 62.2 + - - +
162B PHE* 3.4 8.3 + - + -
163B ILE* 3.0 48.1 + - + +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 4.6 9.0 - - + -
49B VAL* 4.1 28.5 - - + -
96B TYR* 4.3 1.8 - - + +
100B LEU* 4.6 7.2 - - + -
110B VAL* 3.5 26.2 - - + -
113B SER* 5.1 0.4 - - - +
114B VAL* 4.0 15.3 - - + -
156B HIS* 2.7 32.1 + - - +
157B MET 3.5 4.7 - - - +
159B VAL* 1.3 73.3 - - - +
161B TRP* 1.3 62.9 + - - +
163B ILE* 3.6 6.0 + - - +
164B LEU* 3.0 41.1 + - + +
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Residues in contact with TRP 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 3.6 28.0 - - + +
106B GLN 6.5 0.7 - - - -
107B ILE* 4.3 26.9 - - + -
110B VAL* 4.9 11.2 - - + -
157B MET 2.9 12.8 + - - +
158B VAL* 3.1 11.6 + - + +
160B VAL* 1.3 77.3 - - - +
162B PHE* 1.3 62.7 + + + +
164B LEU* 2.7 28.6 + - + -
165B GLU* 2.8 31.2 + - + +
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Residues in contact with PHE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.1 41.2 + - + -
159B VAL* 4.0 8.5 - - + +
161B TRP* 1.3 88.4 - + + +
163B ILE* 1.3 60.6 - - + +
165B GLU* 3.9 17.6 - - + +
166B GLY* 2.9 26.3 + - - -
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.7 30.3 - - + +
49B VAL* 4.6 11.9 - - + -
50B MET* 4.6 20.0 - - + +
53B TYR* 6.1 2.9 - - + -
159B VAL* 3.0 44.2 + - + +
160B VAL* 3.7 7.2 - - - +
162B PHE* 1.3 81.4 - - + +
164B LEU* 1.3 72.7 + - + +
167B LEU* 3.2 37.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B VAL* 4.1 14.6 - - + -
53B TYR* 4.0 37.5 + - + -
100B LEU* 3.4 29.6 - - + -
105B ILE* 3.5 44.9 - - + +
106B GLN 5.3 0.4 - - - +
110B VAL* 4.9 7.4 - - + -
160B VAL* 3.0 40.3 + - + +
161B TRP* 2.7 13.4 + - + +
163B ILE* 1.3 75.3 - - + +
165B GLU* 1.3 64.7 + - - +
167B LEU 3.9 9.4 + - - -
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 3.8 17.4 - - + +
161B TRP* 2.8 35.3 + - + +
162B PHE* 4.0 17.6 - - + +
164B LEU* 1.3 75.9 - - - +
166B GLY* 1.3 75.2 + - - +
167B LEU 3.0 9.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PHE 2.9 19.0 + - - -
163B ILE* 3.9 1.1 - - - -
165B GLU* 1.3 84.1 + - - +
167B LEU* 1.3 67.1 + - - +
----------------------------------------------------------
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET* 4.2 35.7 - - + -
53B TYR* 4.6 24.0 - - + -
54B LEU* 4.4 23.1 - - + -
163B ILE* 3.2 25.6 + - + +
164B LEU 4.1 6.3 - - - +
165B GLU 3.0 9.8 + - - +
166B GLY* 1.3 88.7 - - - +
----------------------------------------------------------
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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