Contacts of the helix formed by residues 136 - 161 (chain B) in PDB entry 3PJA
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 136 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B HIS* 3.5 21.7 + - + +
92B ARG* 4.2 2.9 + - - -
134B HIS* 3.8 5.1 + - - +
135B LEU* 1.3 76.1 - - - +
137B VAL* 1.3 76.8 + - - +
138B GLU* 3.0 31.1 + - - +
139B ASP* 3.0 25.6 + - - +
140B TYR* 2.8 27.0 + - - +
17D GLU* 4.0 0.7 - - - +
86D ARG* 3.0 35.7 + - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 3.6 35.2 - - - +
135B LEU 3.4 0.8 + - - -
136B ASP* 1.3 72.5 + - - +
138B GLU* 1.3 67.1 + - - +
140B TYR* 3.6 6.2 - - + +
141B LEU* 3.0 41.4 + - + +
10D LEU* 3.9 22.4 - - + +
13D PHE* 4.2 17.3 - - + -
14D LEU* 3.9 25.4 - - + -
17D GLU* 4.8 7.0 - - - +
86D ARG* 4.7 1.6 - - - +
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 3.8 15.5 - - - +
136B ASP* 3.0 23.8 + - - +
137B VAL* 1.3 77.4 - - - +
139B ASP* 1.3 63.0 + - - +
141B LEU* 3.3 2.4 + - - +
142B SER* 3.0 26.9 + - - -
188B ASN* 3.2 40.3 + - - +
191B LEU* 3.9 23.5 - - + +
14D LEU* 4.0 14.0 - - - +
17D GLU* 3.4 19.2 - - - +
21D ARG* 4.7 10.0 + - - -
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Residues in contact with ASP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B HIS* 2.9 25.3 - - - -
91B TRP* 4.9 0.5 - - - -
92B ARG* 3.2 21.3 + - - +
95B LEU* 3.7 18.2 - - + +
96B GLN* 3.1 39.0 + - + +
99B VAL* 4.8 1.4 - - - +
135B LEU* 3.8 14.6 - - + -
136B ASP* 3.0 22.6 + - + +
138B GLU* 1.3 75.9 - - - +
140B TYR* 1.3 69.7 + - - +
142B SER* 3.1 5.0 + - - -
143B GLY* 3.0 16.5 + - - -
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Residues in contact with TYR 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.9 19.8 - - + +
103B ALA* 6.3 0.2 - - + -
113B LEU* 3.8 18.9 - - + +
114B VAL* 2.7 26.2 + - + -
115B THR 4.1 0.2 - - - -
116B ARG* 3.6 53.1 + - + -
119B VAL* 4.3 8.5 - - + -
135B LEU* 4.0 9.7 - - + +
136B ASP 2.8 18.2 + - - +
137B VAL 3.6 3.4 - - - +
139B ASP* 1.3 72.8 - - - +
141B LEU* 1.3 70.3 + - + +
143B GLY* 2.9 14.2 + - - -
144B VAL* 3.0 33.6 + - + +
6D ILE* 3.9 8.3 - - + +
7D PHE* 5.8 1.6 - + - -
10D LEU* 3.7 31.0 - - + -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B VAL* 3.0 37.0 + - + +
138B GLU* 3.6 4.3 - - - +
140B TYR* 1.3 80.8 - - + +
142B SER* 1.3 62.6 + - - +
144B VAL* 3.1 6.1 + - + +
145B LEU* 3.0 25.8 + - - +
181B PHE* 3.8 23.5 - - + -
184B LEU* 3.9 20.2 - - + -
186B LEU* 4.4 2.0 - - + -
191B LEU* 4.1 26.5 - - + -
7D PHE* 3.9 15.3 - - + -
10D LEU* 3.6 24.9 - - + -
14D LEU* 4.3 8.3 - - + -
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Residues in contact with SER 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 5.0 1.9 + - - -
96B GLN* 3.4 38.8 + - - -
138B GLU 3.0 14.7 + - - -
139B ASP 3.1 3.6 + - - -
141B LEU* 1.3 75.8 - - - +
143B GLY* 1.3 64.0 + - - +
145B LEU* 3.1 3.7 + - - +
146B ILE* 3.0 29.1 + - - +
191B LEU* 3.3 21.1 - - - +
194B ARG* 3.8 15.6 + - - +
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLN* 3.6 24.9 + - - +
99B VAL* 4.1 4.7 - - - -
100B PHE* 3.5 21.3 - - - +
103B ALA* 5.7 0.7 - - - -
139B ASP 3.0 8.3 + - - -
140B TYR 2.9 8.4 + - - -
142B SER* 1.3 77.0 - - - +
144B VAL* 1.3 57.9 + - - +
146B ILE* 3.4 6.5 + - - +
147B LEU* 3.0 22.7 + - - +
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 5.2 2.5 - - + -
103B ALA* 5.4 4.5 - - + -
113B LEU* 4.2 17.0 - - + -
140B TYR* 3.0 50.8 + - + +
141B LEU* 3.5 10.1 - - + +
142B SER 3.1 0.2 - - - -
143B GLY* 1.3 75.3 - - - +
145B LEU* 1.3 62.2 + - - +
147B LEU* 3.2 10.2 - - + +
148B ALA* 3.0 23.6 + - - +
177B LEU* 4.0 29.9 - - + +
181B PHE* 4.1 16.8 - - + -
7D PHE* 4.8 4.3 - - + -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU 3.0 17.0 + - - +
142B SER 3.1 6.3 + - - +
144B VAL* 1.3 74.1 - - - +
146B ILE* 1.3 66.2 + - - +
148B ALA* 3.0 15.7 + - + +
149B SER* 3.1 14.4 + - - -
177B LEU* 6.5 0.2 - - + -
181B PHE* 3.4 34.3 - - + -
191B LEU* 4.1 16.8 - - + +
194B ARG* 3.4 36.3 - - + +
195B TYR* 3.7 20.6 - - - +
198B LEU* 4.0 32.3 - - + -
201B ASP* 4.4 1.0 - - - +
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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
----------------------------------------------------------
96B GLN* 4.5 13.7 - - + +
97B ARG* 4.9 4.5 - - + +
100B PHE* 3.4 34.5 - - + -
142B SER 3.0 15.6 + - - +
143B GLY* 3.5 15.0 - - - +
144B VAL 3.3 0.2 - - - -
145B LEU* 1.3 75.5 - - - +
147B LEU* 1.3 62.8 + - - +
149B SER* 3.3 7.7 + - - +
150B GLU* 3.0 21.8 + - - +
194B ARG* 3.9 32.5 - - - +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 3.5 12.0 - - + -
103B ALA* 3.7 29.2 - - + +
104B PHE* 3.7 42.0 - - + +
107B TYR* 5.0 2.9 - - + -
112B THR 5.9 0.2 - - - +
113B LEU* 4.4 14.1 - - + -
143B GLY 3.0 13.7 + - - +
144B VAL* 3.2 14.1 - - + +
146B ILE* 1.3 76.1 - - - +
148B ALA* 1.3 63.9 + - - +
150B GLU* 3.1 2.8 + - + +
151B LEU* 2.9 36.0 + - + +
173B PHE* 4.2 22.0 - - + -
177B LEU* 5.5 0.2 - - + -
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL 3.0 12.2 + - - +
145B LEU* 3.0 12.7 + - + +
147B LEU* 1.3 75.7 - - - +
149B SER* 1.3 61.0 + - - +
151B LEU* 3.2 3.2 + - - -
152B SER* 3.0 19.9 + - - -
174B ILE* 3.4 19.6 - - + +
177B LEU* 4.1 15.3 - - + -
198B LEU* 3.6 31.9 - - + -
201B ASP* 3.8 5.3 - - - +
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Residues in contact with SER 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU 3.1 11.3 + - - -
146B ILE* 3.7 9.6 - - - -
147B LEU 3.2 0.2 - - - -
148B ALA* 1.3 72.7 - - - +
150B GLU* 1.3 66.7 + - - +
152B SER* 2.9 17.7 + - - -
153B ARG* 3.1 10.9 + - - +
197B GLY 5.7 0.2 - - - -
201B ASP* 3.0 28.9 + - - -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 5.9 3.3 - - - +
46B HIS* 2.9 29.7 + - - +
100B PHE* 3.6 35.9 - - + -
104B PHE* 3.9 29.6 - - + -
146B ILE* 3.0 7.7 + - + +
147B LEU* 3.5 9.2 - - + +
149B SER* 1.3 77.2 - - - +
151B LEU* 1.3 57.1 + - - +
153B ARG* 3.5 18.2 + - - +
154B LEU* 3.0 26.0 + - - +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 4.0 15.9 - - + -
107B TYR* 3.9 37.5 - - + +
147B LEU* 2.9 27.4 + - + +
148B ALA* 3.6 5.6 - - - +
149B SER 3.1 0.4 - - - -
150B GLU* 1.3 75.6 - - - +
152B SER* 1.3 60.0 + - - +
154B LEU* 3.4 21.9 + - + -
155B SER 3.0 21.1 + - - -
170B ILE* 3.3 28.7 - - + +
173B PHE* 3.6 37.9 - - + -
174B ILE* 4.1 5.6 - - + -
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ALA 3.0 11.1 + - - -
149B SER 2.9 17.7 + - - -
151B LEU* 1.3 72.8 - - - +
153B ARG* 1.3 66.5 + - - +
155B SER* 3.0 13.0 + - - -
156B VAL* 3.1 17.0 + - - +
174B ILE* 4.1 0.8 - - - +
200B TYR* 5.5 0.2 - - - -
201B ASP* 3.1 27.5 + - - -
204B LYS* 3.8 23.6 + - - +
205B VAL* 3.6 27.1 - - - +
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 3.3 40.3 + - - +
149B SER 3.1 8.4 + - - +
150B GLU* 3.6 22.3 + - - +
152B SER* 1.3 82.2 + - - +
154B LEU* 1.3 57.4 + - - +
156B VAL* 3.4 4.4 + - - +
157B ASN* 3.0 44.6 + - - +
204B LYS* 4.1 16.6 - - - +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.9 29.2 - - + +
46B HIS* 3.6 27.3 - - + +
104B PHE* 4.4 7.2 - - + -
107B TYR* 5.7 0.9 - - + -
108B LEU* 4.4 18.2 - - + -
150B GLU 3.0 18.2 + - - +
151B LEU* 3.7 24.9 - - + +
152B SER 3.1 0.2 - - - -
153B ARG* 1.3 73.6 - - - +
155B SER* 1.3 66.9 + - - +
157B ASN* 4.5 0.4 - - - +
158B SER* 2.9 34.7 + - - +
166B ARG* 3.8 29.6 - - - +
170B ILE* 4.2 1.8 - - + -
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Residues in contact with SER 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU 3.0 13.8 + - - -
152B SER* 3.0 14.1 + - - -
154B LEU* 1.3 75.6 - - - +
156B VAL* 1.3 64.6 - - - +
158B SER* 3.1 7.4 + - - -
159B VAL* 3.1 25.4 + - - +
167B PRO* 3.5 23.9 - - - +
170B ILE* 3.9 18.4 - - - +
205B VAL* 4.1 12.7 - - - +
208B VAL* 3.8 14.6 - - - +
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B SER 3.1 5.4 + - - +
153B ARG* 3.7 7.6 - - - +
155B SER* 1.3 82.3 - - - +
157B ASN* 1.3 71.9 + - - +
159B VAL* 3.2 6.6 + - - +
160B THR* 3.1 25.5 + - - +
204B LYS* 3.8 31.4 - - + -
208B VAL* 3.8 24.9 - - + -
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Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS* 3.3 58.4 + - - +
153B ARG* 3.0 38.4 + - - +
154B LEU* 4.2 1.6 - - + +
156B VAL* 1.3 85.4 - - - +
158B SER* 1.3 62.0 + - - +
160B THR* 3.3 13.0 + - - -
161B ALA* 3.2 18.0 + - - +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS 5.2 0.9 - - - -
154B LEU* 2.9 22.4 + - - +
155B SER* 3.1 9.9 + - - -
157B ASN* 1.3 74.0 - - - +
159B VAL* 1.3 69.8 + - - +
161B ALA* 3.0 11.8 + - - +
162B GLY 3.3 0.2 + - - -
163B ASP* 3.0 43.1 + - - +
166B ARG* 4.0 21.9 - - - +
167B PRO* 3.6 12.0 - - - +
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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
----------------------------------------------------------
155B SER 3.1 4.4 + - - +
156B VAL* 3.2 8.7 + - - +
158B SER* 1.3 82.3 + - - +
160B THR* 1.3 65.1 + - - +
162B GLY* 2.9 11.6 + - - -
163B ASP 3.8 6.7 - - - +
164B TYR* 3.4 25.7 + - + +
167B PRO* 3.3 28.7 - - + -
208B VAL* 3.5 22.4 - - + -
212B LEU* 4.1 21.1 - - + -
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Residues in contact with THR 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 3.1 19.4 + - - +
157B ASN* 3.4 19.1 + - - -
158B SER 3.2 0.2 - - - -
159B VAL* 1.3 79.8 - - - +
161B ALA* 1.3 56.9 + - - +
162B GLY 3.4 2.3 + - - -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B HIS 4.8 0.7 - - - +
47B GLN 4.0 22.7 - - - +
48B GLY* 4.4 14.1 - - - +
49B ALA* 5.1 2.0 - - + +
157B ASN 3.2 13.6 + - - +
158B SER* 3.0 8.5 + - - +
159B VAL 3.0 1.2 - - - -
160B THR* 1.3 77.0 - - + +
162B GLY* 1.3 58.4 + - - +
163B ASP* 3.3 5.3 + - + +
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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