Contacts of the helix formed by residues 154 - 182 (chain A) in PDB entry 1JB0
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 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A TYR* 5.2 2.7 - - - -
101A GLU* 3.3 13.7 - - - +
152A ILE* 3.8 2.1 - - - +
153A THR* 1.3 88.5 + - - +
155A GLU* 1.3 64.0 + - - +
156A PHE* 3.0 22.2 + - - +
157A GLN* 2.9 47.5 + - - +
158A LEU* 3.6 11.2 + - - +
238A LEU* 4.5 14.5 - - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY 3.7 11.1 - - - +
95A ALA* 3.3 37.4 - - + +
98A SER* 4.3 12.5 + - - +
100A TYR* 4.8 2.8 - - - +
101A GLU* 2.8 44.1 + - - +
154A ASN* 1.3 71.7 - - - +
156A PHE* 1.3 62.3 + - - +
158A LEU* 3.4 5.9 + - - +
159A TYR* 3.1 23.8 + - - +
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ASN* 3.0 13.7 + - - +
155A GLU* 1.3 80.7 - - - +
157A GLN* 1.3 61.0 + - + +
159A TYR* 3.3 17.0 + + - +
160A CYS* 3.0 51.0 + - - -
1114A CLA 3.5 64.6 - + + -
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Residues in contact with GLN 157 (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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151A GLY 4.4 0.4 + - - -
152A ILE* 3.4 11.8 - - + -
153A THR* 2.6 35.3 + - - +
154A ASN* 2.9 33.5 + - - +
156A PHE* 1.3 78.4 - - + +
158A LEU* 1.3 61.5 + - - +
160A CYS* 3.3 7.2 + - - +
161A THR* 2.8 29.0 + - - -
238A LEU* 5.0 2.8 - - - +
239A PRO* 3.9 19.2 - - - +
1112A CLA 3.1 43.6 + - + +
1114A CLA 4.6 13.0 - - + -
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Residues in contact with LEU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 3.6 24.8 - - + +
94A GLY* 3.4 36.8 - - - +
95A ALA* 3.5 4.9 - - + +
100A TYR* 4.3 15.5 - - + -
147A TRP* 4.0 28.7 - - + +
152A ILE* 3.5 35.2 - - + -
154A ASN 4.0 9.2 - - - +
155A GLU* 3.4 11.2 + - - +
156A PHE 3.3 0.2 - - - -
157A GLN* 1.3 77.1 - - - +
159A TYR* 1.3 57.8 + - - +
161A THR* 3.1 7.6 + - - -
162A ALA* 2.9 28.8 + - - +
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.8 29.4 - + - -
95A ALA* 3.9 8.6 - - + +
96A LYS* 3.8 27.6 - - - -
155A GLU 3.1 14.7 + - - +
156A PHE* 3.5 21.3 - + - +
158A LEU* 1.3 79.3 - - - +
160A CYS* 1.3 60.5 + - - +
162A ALA* 3.4 6.9 + - - +
163A ILE* 3.1 58.8 + - + +
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Residues in contact with CYS 160 (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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156A PHE* 3.0 55.4 + - - +
157A GLN 3.6 2.9 - - - +
159A TYR* 1.3 77.6 - - - +
161A THR* 1.3 60.9 + - - +
163A ILE* 3.4 7.9 + - - +
164A GLY* 3.0 24.6 + - - -
1112A CLA 3.4 20.5 + - - +
1114A CLA 3.8 24.7 - - + -
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Residues in contact with THR 161 (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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91A TYR* 3.4 40.6 - - + -
152A ILE* 4.9 1.2 - - - +
157A GLN 2.8 15.8 + - - -
158A LEU 3.1 1.8 + - - -
160A CYS* 1.3 73.1 - - - +
162A ALA* 1.3 60.7 + - - +
164A GLY* 3.2 1.9 + - - -
165A GLY* 2.8 27.4 + - - -
1112A CLA 3.3 28.6 + - + +
4002A BCR 3.6 41.8 - - + +
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 3.2 38.9 - - - +
91A TYR* 4.0 1.7 - - - +
92A PHE* 3.7 27.8 - - + +
158A LEU 2.9 13.2 + - - +
159A TYR* 3.4 12.3 - - - +
161A THR* 1.3 77.1 - - - +
163A ILE* 1.3 63.5 + - + +
166A LEU* 3.1 23.3 + - - +
1105A CLA 6.2 0.4 - - + -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 5.8 3.6 - - + -
159A TYR* 3.1 48.0 + - + +
160A CYS* 3.7 8.1 - - - +
161A THR 3.3 0.2 - - - -
162A ALA* 1.3 76.7 - - + +
164A GLY* 1.3 65.2 + - - +
166A LEU* 3.0 18.2 + - + +
167A VAL* 2.9 32.8 + - + +
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Residues in contact with GLY 164 (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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160A CYS 3.0 15.1 + - - -
161A THR 3.2 3.1 + - - -
163A ILE* 1.3 78.4 - - - +
165A GLY* 1.3 56.4 + - - +
167A VAL* 3.3 10.5 + - - +
168A MET* 3.0 33.4 + - - +
1112A CLA 5.1 1.8 - - - -
4002A BCR 3.6 13.9 - - - -
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.7 10.2 - - - +
88A SER* 3.9 13.0 - - - -
161A THR 2.8 14.1 + - - -
162A ALA 3.3 4.0 + - - -
163A ILE 3.1 0.4 - - - -
164A GLY* 1.3 74.1 - - - +
166A LEU* 1.3 58.9 + - - +
168A MET* 3.2 6.3 + - - +
169A ALA* 2.8 28.9 + - - +
4002A BCR 3.6 19.0 - - - +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.3 21.3 - - + -
88A SER* 3.2 23.3 - - - +
162A ALA 3.1 9.2 + - - +
163A ILE* 3.0 19.3 + - + +
165A GLY* 1.3 72.1 - - - +
167A VAL* 1.3 67.0 + - + +
169A ALA* 3.2 5.7 + - + +
170A GLY* 3.0 19.2 + - - -
1105A CLA 4.0 37.5 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 2.9 31.6 + - + +
164A GLY* 3.5 9.9 - - - +
165A GLY 3.2 0.2 - - - -
166A LEU* 1.3 76.9 - - + +
168A MET* 1.3 57.4 + - + +
170A GLY* 3.0 4.5 + - - -
171A LEU* 2.8 45.3 + - + +
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Residues in contact with MET 168 (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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84A PHE* 3.8 22.9 - - + -
164A GLY 3.0 17.5 + - - +
165A GLY 3.4 7.6 - - - +
167A VAL* 1.3 81.6 - - + +
169A ALA* 1.3 52.1 + - - +
171A LEU* 3.2 37.2 - - + -
172A MET* 2.6 52.0 + - + +
1103A CLA 3.6 30.1 - - + -
1111A CLA 4.8 3.8 - - + -
4002A BCR 3.9 15.9 - - + -
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ALA* 3.4 24.7 - - + +
84A PHE* 3.8 10.7 - - + +
85A ILE* 3.8 19.1 - - + +
165A GLY 2.8 16.3 + - - +
166A LEU* 3.3 14.8 - - + +
167A VAL 3.1 0.2 - - - -
168A MET* 1.3 72.9 - - - +
170A GLY* 1.3 52.1 + - - +
172A MET* 3.2 6.2 + - - +
173A LEU* 2.7 37.0 + - - +
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Residues in contact with GLY 170 (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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166A LEU 3.0 9.1 + - - -
167A VAL 3.0 6.6 + - - -
169A ALA* 1.3 73.3 - - - +
171A LEU* 1.3 56.7 + - - +
173A LEU* 3.1 9.6 + - - +
174A PHE* 2.7 36.7 + - - +
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Residues in contact with LEU 171 (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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167A VAL* 2.8 24.2 + - + +
168A MET* 3.2 35.4 - - + +
170A GLY* 1.3 74.7 - - - +
172A MET* 1.3 67.6 + - + +
174A PHE* 3.2 9.7 + - + +
175A ALA* 3.1 19.1 + - - +
1108A CLA 3.5 38.5 - - + +
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Residues in contact with MET 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.5 22.3 - - + +
80A LEU* 3.3 44.2 - - + -
81A ALA* 3.8 13.2 - - + +
84A PHE* 4.1 18.4 - - + -
168A MET* 2.6 53.9 + - + +
169A ALA 3.3 4.7 - - - +
171A LEU* 1.3 81.2 - - + +
173A LEU* 1.3 64.7 + - - +
174A PHE 3.2 0.9 + - - -
175A ALA* 3.3 12.7 + - - +
176A GLY 3.3 9.0 + - - -
1108A CLA 4.4 13.9 - - + -
1111A CLA 4.3 22.9 - - + -
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Residues in contact with LEU 173 (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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77A PHE 4.9 0.9 - - - -
78A GLY* 4.3 12.3 - - - -
81A ALA* 3.9 11.4 - - + +
85A ILE* 6.4 0.2 - - + -
169A ALA 2.7 20.4 + - - +
170A GLY* 3.5 9.9 - - - +
172A MET* 1.3 72.7 - - - +
174A PHE* 1.3 61.6 + - - +
176A GLY* 3.7 1.5 + - - +
177A TRP 3.6 3.8 + - - -
1102A CLA 4.7 11.7 - - + -
1107A CLA 3.6 44.9 - - + -
1109A CLA 3.2 48.7 - - + +
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Residues in contact with PHE 174 (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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170A GLY 2.7 20.4 + - - +
171A LEU* 3.4 11.0 - - + +
172A MET 3.1 0.2 - - - -
173A LEU* 1.3 71.8 - - - +
175A ALA* 1.3 59.3 + - - +
177A TRP* 3.2 41.7 + + + +
178A PHE* 2.9 48.0 + + + +
1108A CLA 3.2 33.9 - - + -
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Residues in contact with ALA 175 (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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77A PHE* 3.7 25.8 - - + -
171A LEU 3.1 2.9 + - - +
172A MET 3.7 3.4 - - - +
174A PHE* 1.3 75.8 - - - +
176A GLY* 1.3 58.0 + - - +
178A PHE* 3.6 8.2 - - - +
179A HIS* 2.7 40.6 + - + +
1108A CLA 3.6 43.1 - - + -
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Residues in contact with GLY 176 (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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74A SER* 3.2 22.2 + - - -
77A PHE* 3.4 24.6 - - - +
172A MET 3.3 7.7 + - - -
173A LEU 3.7 1.1 + - - -
174A PHE 3.2 1.0 - - - -
175A ALA* 1.3 81.0 - - - +
177A TRP* 1.3 64.3 + - - +
180A TYR* 3.2 6.4 + - - +
1109A CLA 3.3 21.1 - - - -
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Residues in contact with TRP 177 (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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23A THR* 2.9 34.4 + - + +
173A LEU 3.6 1.9 + - - +
174A PHE* 3.2 45.2 + + + +
176A GLY* 1.3 72.0 - - - +
178A PHE* 1.3 74.5 + + - +
180A TYR 3.1 1.2 + - - -
181A HIS* 2.8 61.6 + + + +
182A LYS* 3.4 44.9 - - + -
1109A CLA 3.2 59.3 - + + +
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Residues in contact with PHE 178 (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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174A PHE* 2.9 32.6 + + + +
175A ALA* 3.6 6.5 - - - +
177A TRP* 1.3 94.0 - + + +
179A HIS* 1.3 78.1 + + - +
182A LYS* 3.0 38.3 + - + +
183A ARG* 2.8 49.3 + - + -
1108A CLA 3.3 61.7 - + + -
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Residues in contact with HIS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 6.1 0.2 - - + -
70A ARG* 4.8 3.8 - - - +
73A PHE* 4.0 24.4 - + + -
74A SER* 3.8 5.7 + - - +
77A PHE* 3.9 19.3 - + + -
175A ALA* 2.7 27.8 + - + +
176A GLY 3.2 2.0 + - - +
178A PHE* 1.3 85.8 - + - +
180A TYR* 1.3 58.3 + - - +
183A ARG 2.8 24.0 + - - -
184A ALA* 3.2 21.9 - - - +
185A PRO* 3.8 8.4 - - + +
1108A CLA 2.3 75.4 + + + -
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 4.0 5.9 - - - +
21A VAL* 3.8 28.8 - - + +
67A ASP* 2.8 29.7 + - - -
70A ARG* 3.6 27.1 - - + -
71A LYS* 3.3 32.5 + - + -
74A SER* 3.1 14.8 - - - +
176A GLY 3.2 7.3 + - - +
177A TRP 3.1 3.2 + - - +
179A HIS* 1.3 80.3 - - - +
181A HIS* 1.3 72.3 + + + +
184A ALA* 3.9 13.6 - - - +
1109A CLA 3.3 64.3 + + + -
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Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP* 3.0 26.7 - - - +
20A PRO* 3.0 6.7 - - - +
21A VAL* 2.7 46.8 + - + +
22A PRO 3.8 9.6 + - - -
23A THR* 3.7 19.9 + - - +
177A TRP* 2.8 47.3 + + + +
180A TYR* 1.3 80.5 - + + +
182A LYS* 1.3 59.9 + - + +
1109A CLA 2.4 54.2 + + - -
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASN* 3.3 0.7 - - - -
19A ASP* 2.7 52.7 + - - +
20A PRO* 4.3 0.2 - - - -
23A THR* 5.6 1.7 + - - -
177A TRP* 3.4 45.5 + - + -
178A PHE* 3.0 32.0 + - + +
181A HIS* 1.3 80.8 - - - +
183A ARG* 1.3 76.1 + - + +
184A ALA 4.0 0.9 - - - -
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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