Contacts of the helix formed by residues 141 - 166 (chain B) in PDB entry 4MBS
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 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LEU* 3.4 23.4 - - + +
64B MET* 3.8 12.1 - - - +
138B LYS 4.2 11.2 - - - +
139B ALA 3.1 16.8 + - - +
140B ARG* 1.3 74.7 - - - +
142B VAL* 1.4 66.7 + - - +
143B THR* 3.0 16.0 + - - +
144B PHE* 3.5 18.1 + - + +
145B GLY 3.1 17.0 + - - -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 6.3 2.7 - - + -
61B LEU 3.8 9.4 - - - +
62B LYS* 3.4 35.9 - - - +
63B SER* 3.8 10.8 - - - +
64B MET* 4.3 2.2 - - - +
67B ILE* 3.9 26.6 - - + +
141B THR* 1.4 71.7 + - - +
143B THR* 1.3 63.1 + - + +
145B GLY* 3.1 3.5 + - - +
146B VAL* 2.9 33.0 + - + +
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.9 15.0 - - + +
309A LEU* 3.0 35.8 - - + +
312A PHE* 3.7 47.0 - - + -
141B THR* 3.0 5.0 + - - -
142B VAL* 1.3 77.6 - - + +
144B PHE* 1.4 49.9 + - - -
146B VAL* 3.2 8.1 + - - +
147B VAL* 2.8 42.3 + - - +
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Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 3.5 34.8 - + - -
305A ARG* 6.6 0.4 - - + -
64B MET* 4.0 19.1 - - + -
68B TYR* 4.6 3.6 - - - -
139B ALA* 3.9 17.9 - - + +
141B THR* 3.5 24.6 + - + +
142B VAL 3.4 0.6 - - - -
143B THR* 1.4 78.7 + - - +
145B GLY* 1.3 49.4 + - - +
147B VAL* 3.4 6.9 + - + +
148B THR* 2.9 61.7 + - + +
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Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 4.3 7.4 - - - -
67B ILE* 3.8 13.0 - - - -
68B TYR* 3.6 16.6 - - - -
141B THR 3.1 14.8 + - - -
142B VAL 3.1 5.3 + - - -
144B PHE* 1.3 75.9 - - - +
146B VAL* 1.3 51.8 + - - +
148B THR* 2.9 17.4 + - - -
149B SER* 2.8 26.9 + - - -
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 4.3 28.0 - - + -
67B ILE* 4.1 26.2 - - + -
142B VAL* 2.9 21.1 + - + +
143B THR* 3.6 11.0 - - - +
145B GLY* 1.3 73.9 - - - +
147B VAL* 1.4 67.1 + - + +
149B SER* 3.2 5.2 + - - -
150B VAL* 3.1 31.9 + - + +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ALA* 4.4 18.8 - - + +
299A PHE* 3.6 30.1 - - + -
308A LEU* 5.7 9.0 - - + -
312A PHE* 6.3 3.4 - - + -
143B THR* 2.8 27.7 + - - +
144B PHE* 3.8 8.7 - - + +
146B VAL* 1.4 75.0 - - + +
148B THR* 1.4 60.3 + - - +
150B VAL* 3.5 7.6 + - - +
151B ILE* 3.2 32.0 + - + +
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Residues in contact with THR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE* 3.6 30.1 - - + -
68B TYR* 2.8 25.9 + - - +
121B LEU* 4.8 10.8 - - + -
144B PHE* 2.9 37.1 + - + +
145B GLY 2.9 10.2 + - - -
147B VAL* 1.4 71.8 - - - +
149B SER* 1.4 54.3 + - - +
151B ILE* 3.5 4.1 + - - +
152B THR* 2.6 40.9 + - - -
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 3.5 6.3 - - - +
68B TYR* 3.9 4.3 - - - -
71B ASN* 3.2 34.4 + - - -
118B PHE* 3.7 17.1 - - - -
145B GLY 2.8 22.0 + - - -
146B VAL* 3.2 9.6 + - - -
148B THR* 1.4 74.1 + - - +
150B VAL* 1.3 61.5 + - - +
152B THR* 3.4 2.6 + - - -
153B TRP* 2.9 33.8 + - - -
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 5.2 6.5 - - + -
146B VAL* 3.1 23.2 + - + +
147B VAL* 3.6 9.9 - - - +
148B THR 3.4 0.2 - - - -
149B SER* 1.3 73.1 - - - +
151B ILE* 1.3 69.0 + - + +
153B TRP* 3.3 10.4 + - - +
154B VAL* 3.1 34.9 + - + +
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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
----------------------------------------------------------
43A PHE* 4.6 10.5 - - + -
295A ILE* 4.3 26.0 - - + -
298A ALA* 5.8 0.9 - - + -
299A PHE* 3.4 32.8 - - + -
1107A OLC 4.6 11.4 - - + -
147B VAL* 3.2 28.6 + - + +
148B THR* 4.0 6.1 - - - +
150B VAL* 1.3 78.2 - - + +
152B THR* 1.3 53.5 + - - +
154B VAL* 3.1 9.9 + - - +
155B VAL* 2.8 47.7 + - + +
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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
----------------------------------------------------------
114B SER* 4.9 0.9 - - - -
117B PHE* 3.5 35.3 - - + -
118B PHE* 3.6 28.3 - - + -
121B LEU* 3.4 18.9 - - + +
148B THR* 2.6 22.3 + - - -
149B SER 3.5 5.6 - - - -
150B VAL 3.3 0.4 - - - -
151B ILE* 1.3 77.1 - - - +
153B TRP* 1.4 54.6 + - - +
155B VAL* 3.4 8.1 + - - +
156B ALA* 3.0 27.4 + - - +
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Residues in contact with TRP 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN* 2.7 44.2 + - - -
74B ILE* 4.0 19.1 - - + -
75B SER* 3.7 19.5 - - - -
78B PHE* 3.8 24.7 - + - -
110B ILE* 3.9 18.6 - - + -
114B SER* 3.3 28.5 - - - -
118B PHE* 3.5 14.8 - + - -
149B SER 2.9 30.4 + - - -
150B VAL* 3.3 9.8 + - - +
152B THR* 1.4 73.4 - - - +
154B VAL* 1.4 58.3 + - + +
156B ALA* 3.3 5.0 + - - +
157B VAL* 3.0 35.5 + - + +
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Residues in contact with VAL 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.9 4.7 - - + -
43A PHE* 3.9 44.2 - - + -
1107A OLC 4.9 4.9 - - + -
150B VAL* 3.1 21.3 + - + +
151B ILE* 3.1 9.7 + - - +
153B TRP* 1.4 72.5 - - + +
155B VAL* 1.3 65.3 + - + +
157B VAL* 3.3 8.3 + - - +
158B PHE* 3.0 52.4 + - + -
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1107A OLC 4.0 29.6 - - + -
117B PHE* 3.9 20.6 - - + -
151B ILE* 2.8 28.4 + - + +
152B THR* 3.4 7.8 + - - +
154B VAL* 1.3 75.9 - - - +
156B ALA* 1.4 56.3 + - - +
158B PHE* 3.3 9.4 + - + +
159B ALA* 2.9 29.3 + - + +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ILE* 4.2 12.3 - - + +
113B PHE* 4.2 3.0 - - + -
114B SER* 3.9 35.2 - - - +
117B PHE* 3.9 12.3 - - + -
152B THR 3.0 13.8 + - - +
153B TRP* 3.6 9.0 - - - +
154B VAL 3.3 0.2 - - - -
155B VAL* 1.4 76.2 - - - +
157B VAL* 1.4 56.8 + - - +
159B ALA* 3.4 5.1 + - - +
160B SER* 2.8 33.0 + - - -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.7 33.0 - - + -
110B ILE* 4.1 33.9 - - + -
153B TRP* 3.0 22.4 + - + +
154B VAL* 3.3 9.4 + - - +
156B ALA* 1.4 71.9 - - - +
158B PHE* 1.3 63.7 + - - +
160B SER* 3.3 2.9 + - - -
161B LEU* 3.1 28.3 + - + +
164B ILE* 4.9 1.6 - - + +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.7 25.8 - - + -
39A LEU* 3.4 44.0 - - + -
40A VAL* 4.1 16.2 - - + -
43A PHE* 5.3 4.7 - + + -
291A CYS* 5.7 0.2 - - - -
1107A OLC 3.7 54.3 - - + +
154B VAL* 3.0 41.6 + - + -
155B VAL* 3.6 9.4 - - - +
157B VAL* 1.3 78.1 - - - +
159B ALA* 1.3 59.3 + - - +
160B SER 3.5 0.2 + - - -
161B LEU* 3.6 21.0 + - + +
162B PRO* 3.9 5.9 - - - +
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.8 18.2 - - + -
117B PHE* 5.1 2.9 - - + -
155B VAL* 2.9 18.4 + - + +
156B ALA* 3.7 8.3 - - - +
157B VAL 3.3 0.2 - - - -
158B PHE* 1.3 76.9 - - - +
160B SER* 1.3 56.8 + - - +
161B LEU 3.5 0.2 - - - -
163B ASN* 3.4 2.3 + - - -
197B LYS* 2.8 38.0 + - + +
201B LEU* 4.1 20.9 - - + -
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.3 22.9 - - - +
110B ILE* 3.3 32.4 + - - -
113B PHE* 3.3 6.9 - - - -
156B ALA 2.8 20.9 + - - -
157B VAL 3.8 2.0 - - - -
158B PHE 3.3 0.2 - - - -
159B ALA* 1.3 73.7 - - - +
161B LEU* 1.3 64.4 + - - +
163B ASN* 3.2 19.8 + - - +
164B ILE* 3.3 24.2 + - - +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 4.5 9.9 - - + -
36A LEU* 3.8 32.8 - - + +
39A LEU* 3.7 33.9 - - + -
157B VAL* 3.1 15.4 + - + +
158B PHE* 3.6 24.9 - - + +
160B SER* 1.3 72.3 - - - +
162B PRO* 1.4 73.7 - - + +
163B ASN 3.2 0.7 + - - -
164B ILE* 3.2 25.0 + - + +
165B ILE* 3.2 30.4 + - + +
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Residues in contact with PRO 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.3 21.1 - - + -
158B PHE 3.9 7.6 - - - +
161B LEU* 1.4 89.3 - - + +
163B ASN* 1.3 57.0 + - - +
165B ILE* 3.2 4.4 + - + +
166B PHE* 3.1 36.2 + - + -
190B TRP* 4.4 15.5 - - + -
193B PHE* 5.8 2.7 - - + -
194B GLN* 3.5 20.4 - - - +
197B LYS* 3.6 24.5 - - - +
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Residues in contact with ASN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B THR* 4.8 2.0 - - - -
109B PHE* 3.4 44.3 - - + -
113B PHE* 5.0 0.4 - - - -
159B ALA 3.4 7.5 + - - -
160B SER* 3.2 17.8 + - - +
161B LEU 3.2 0.2 - - - -
162B PRO* 1.3 74.7 - - - +
164B ILE* 1.4 54.7 + - - +
166B PHE* 3.5 4.2 + - - +
167B THR* 2.6 33.4 + - - -
180B SER* 4.9 4.7 + - - -
182B PHE* 5.4 2.6 - - - -
194B GLN* 3.0 33.3 + - - +
197B LYS* 3.4 25.5 - - - +
198B ILE* 5.4 0.2 - - - +
1101B MRV 4.9 1.0 - - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 2.8 55.0 + - + +
105B THR* 4.8 5.6 - - + +
106B GLY* 3.6 29.6 - - - +
109B PHE* 5.6 0.7 - - + -
110B ILE* 4.4 10.1 - - + -
157B VAL* 4.9 1.6 - - + +
160B SER* 3.4 31.6 - - - +
161B LEU* 3.2 21.4 + - + +
163B ASN* 1.4 75.1 - - + +
165B ILE* 1.3 57.5 + - + +
167B THR* 3.4 13.5 + - - +
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Residues in contact with ILE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.3 50.2 + - + +
32A LEU* 3.9 24.5 - - + +
35A PRO* 3.8 26.7 - - + -
102B GLN* 3.9 8.1 + - - +
161B LEU* 3.2 34.4 + - + +
162B PRO* 3.2 9.2 + - + +
164B ILE* 1.3 80.1 - - + +
166B PHE* 1.3 76.3 + - + +
167B THR 3.2 8.2 + - - +
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 4.5 18.8 - - + -
31A ARG* 4.8 11.7 - - + -
32A LEU* 3.7 31.4 - - + -
162B PRO* 3.1 25.9 + - + +
163B ASN* 3.5 2.6 + - - +
164B ILE 3.4 0.2 - - - -
165B ILE* 1.3 86.7 - - + +
167B THR* 1.3 58.9 + - - +
168B ARG* 4.1 1.0 + - - +
180B SER* 3.5 3.3 - - - +
181B HIS* 2.7 58.2 + - - +
182B PHE* 4.3 16.8 - + + -
183B PRO* 3.8 29.6 - - + -
190B TRP* 4.2 20.4 - + - -
194B GLN* 5.3 0.2 - - - -
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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
------------------------------------------------------------
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