Contacts of the helix formed by residues 136 - 161 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 4.0 3.1 - - - +
86A ARG* 2.7 37.2 + - - +
88E HIS* 3.1 25.4 + - + +
91E TRP* 6.3 0.9 - - + -
92E ARG* 4.3 1.2 + - - -
134E HIS* 3.5 7.2 + - - +
135E LEU* 1.3 75.4 - - - +
137E VAL* 1.3 75.5 + - - +
138E GLU* 3.1 26.9 + - - +
139E ASP* 3.1 26.2 + - - +
140E TYR* 3.0 19.9 + - - +
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Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.0 22.2 - - + +
13A PHE* 4.0 21.8 - - + -
14A LEU* 4.0 25.4 - - + -
17A GLU* 4.4 14.8 - - - +
86A ARG* 4.4 1.2 - - - +
116E ARG* 3.7 36.8 - - - +
135E LEU 3.3 2.0 + - - -
136E ASP* 1.3 78.4 + - - +
138E GLU* 1.3 60.9 + - - +
140E TYR* 3.2 5.7 + - - +
141E LEU* 3.0 30.3 + - + +
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Residues in contact with GLU 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.4 13.4 - - + +
17A GLU* 4.3 18.9 - - - +
21A ARG* 4.6 10.3 + - - -
92E ARG* 3.4 17.9 + - - +
96E GLN* 5.1 0.2 - - - -
136E ASP* 3.1 13.4 + - - +
137E VAL* 1.3 76.6 - - - +
139E ASP* 1.3 63.9 + - - +
141E LEU* 3.3 4.9 + - - +
142E SER* 3.0 26.4 + - - -
188E ASN* 3.3 40.8 + - - +
191E LEU* 4.1 22.5 - - + +
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Residues in contact with ASP 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E HIS* 2.9 25.2 - - - -
91E TRP* 4.9 0.2 - - - -
92E ARG* 3.1 28.6 + - - +
95E LEU* 3.7 18.3 - - + +
96E GLN* 3.1 30.1 + - + +
99E VAL* 4.8 1.9 - - - +
135E LEU* 4.3 12.1 - - + -
136E ASP* 3.1 23.4 + - + +
138E GLU* 1.3 74.1 - - - +
140E TYR* 1.3 68.4 + - - +
142E SER* 3.1 5.2 + - - -
143E GLY* 3.0 17.2 + - - -
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Residues in contact with TYR 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.0 7.4 - - + +
7A PHE* 5.9 1.1 - + - -
10A LEU* 3.6 33.0 - - + -
99E VAL* 3.9 21.1 - - + +
113E LEU* 3.8 18.9 - - + +
114E VAL* 2.7 26.2 + - + -
115E THR 4.1 0.7 - - - -
116E ARG* 3.6 56.6 + - + -
119E VAL* 4.3 8.5 - - + -
135E LEU* 4.3 9.9 - - + +
136E ASP 3.0 7.6 + - - +
137E VAL 3.2 9.9 - - - +
139E ASP* 1.3 74.9 - - - +
141E LEU* 1.3 66.8 + - + +
143E GLY* 3.0 14.0 + - - -
144E VAL* 3.0 34.8 + - + +
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Residues in contact with LEU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.9 13.0 - - + -
10A LEU* 3.4 30.1 - - + -
14A LEU* 4.2 14.6 - - + -
137E VAL* 3.0 22.5 + - + +
138E GLU* 3.6 8.3 - - - +
139E ASP 3.3 0.2 - - - -
140E TYR* 1.3 82.5 - - + +
142E SER* 1.3 61.9 + - - +
144E VAL* 3.2 6.3 + - + +
145E LEU* 3.0 26.2 + - - +
181E PHE* 3.8 24.0 - - + -
184E LEU* 3.9 19.7 - - + -
186E LEU* 4.3 2.0 - - + -
191E LEU* 4.1 25.6 - - + -
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Residues in contact with SER 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E GLN* 3.4 32.5 + - - -
138E GLU 3.0 14.9 + - - -
139E ASP 3.1 8.3 + - - -
141E LEU* 1.3 71.9 - - - +
143E GLY* 1.3 66.7 + - - +
145E LEU* 3.2 4.3 + - - +
146E ILE* 3.0 28.8 + - - +
191E LEU* 3.4 19.6 - - - +
194E ARG* 3.8 17.5 + - - +
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Residues in contact with GLY 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E GLN* 3.6 24.5 + - - +
99E VAL* 4.2 4.5 - - - -
100E PHE* 3.5 20.7 - - - +
103E ALA* 5.7 0.4 - - - -
139E ASP 3.0 7.9 + - - -
140E TYR 3.0 8.0 + - - -
142E SER* 1.3 76.4 - - - +
144E VAL* 1.3 58.2 + - - +
146E ILE* 3.4 6.3 + - - +
147E LEU* 3.0 23.4 + - - +
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Residues in contact with VAL 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 4.6 4.3 - - + -
99E VAL* 5.2 2.2 - - + -
103E ALA* 5.4 5.2 - - + -
113E LEU* 4.2 15.7 - - + -
140E TYR* 3.0 52.0 + - + +
141E LEU* 3.5 9.9 - - + +
142E SER 3.1 0.2 - - - -
143E GLY* 1.3 75.4 - - - +
145E LEU* 1.3 60.4 + - - +
147E LEU* 3.2 11.0 - - + +
148E ALA* 3.0 23.9 + - - +
177E LEU* 4.0 29.1 - - + +
181E PHE* 4.2 16.6 - - + -
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Residues in contact with LEU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E LEU 3.0 17.5 + - - +
142E SER 3.2 7.4 + - - +
144E VAL* 1.3 75.6 - - - +
146E ILE* 1.3 64.5 + - - +
148E ALA* 3.0 15.8 + - + +
149E SER* 3.1 15.1 + - - -
177E LEU* 6.5 0.2 - - + -
181E PHE* 3.5 32.8 - - + -
191E LEU* 4.1 16.6 - - + +
194E ARG* 3.4 35.9 - - + +
195E TYR* 3.7 20.6 - - + +
198E LEU* 4.0 32.5 - - + -
201E ASP* 4.5 1.2 - - - +
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Residues in contact with ILE 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E GLN* 4.5 16.8 - - + +
97E ARG* 4.9 4.3 - - + +
100E PHE* 3.4 32.3 - - + -
142E SER 3.0 16.2 + - - +
143E GLY* 3.5 14.4 - - - +
144E VAL 3.3 0.2 - - - -
145E LEU* 1.3 71.2 - - - +
147E LEU* 1.3 66.2 + - - +
149E SER* 3.3 8.3 + - - -
150E GLU* 3.0 21.4 + - + +
194E ARG* 3.9 33.0 - - - +
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E PHE* 3.5 11.6 - - + -
103E ALA* 3.7 29.4 - - + +
104E PHE* 3.7 42.4 - - + +
107E TYR* 5.0 3.1 - - + -
113E LEU* 4.3 14.6 - - + -
143E GLY 3.0 14.0 + - - +
144E VAL* 3.2 13.9 - - + +
146E ILE* 1.3 76.7 - - - +
148E ALA* 1.3 64.1 + - - +
150E GLU* 3.1 3.2 + - + +
151E LEU* 2.9 36.2 + - + +
173E PHE* 4.2 22.2 - - + -
177E LEU* 5.5 0.7 - - + -
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Residues in contact with ALA 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E VAL 3.0 11.6 + - - +
145E LEU* 3.0 13.3 + - + +
147E LEU* 1.3 77.2 - - - +
149E SER* 1.3 61.7 + - - +
151E LEU* 3.1 3.4 + - - -
152E SER* 3.0 19.6 + - - -
174E ILE* 3.4 20.0 - - + +
177E LEU* 4.1 15.7 - - + +
198E LEU* 3.6 31.6 - - + -
201E ASP* 3.9 5.7 - - - +
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Residues in contact with SER 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E LEU 3.1 10.6 + - - -
146E ILE* 3.7 10.1 - - - -
148E ALA* 1.3 72.9 - - - +
150E GLU* 1.3 66.5 + - - +
152E SER* 2.8 17.8 + - - -
153E ARG* 3.1 10.6 + - - +
197E GLY 5.8 0.5 - - - -
201E ASP* 3.0 28.9 + - - -
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Residues in contact with GLU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E GLN* 3.7 26.0 + - - +
46E HIS* 2.9 29.8 + - - +
100E PHE* 3.6 35.0 - - + -
104E PHE* 3.8 29.9 - - + -
146E ILE* 3.0 7.5 + - + +
147E LEU* 3.5 9.2 - - + +
149E SER* 1.3 76.6 - - - +
151E LEU* 1.3 56.9 + - - +
153E ARG* 3.5 12.5 + - - +
154E LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E PHE* 4.1 15.9 - - + -
107E TYR* 3.9 35.9 - - + -
147E LEU* 2.9 27.5 + - + +
148E ALA* 3.6 4.7 - - - +
149E SER 3.1 0.4 - - - -
150E GLU* 1.3 76.0 - - - +
152E SER* 1.3 60.8 + - - +
154E LEU* 4.0 22.0 - - + -
155E SER 3.0 21.3 + - - -
170E ILE* 3.4 29.8 - - + +
173E PHE* 3.6 37.5 - - + -
174E ILE* 4.1 6.1 - - + -
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Residues in contact with SER 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148E ALA 3.0 9.5 + - - -
149E SER 2.8 18.4 + - - -
151E LEU* 1.3 73.1 - - - +
153E ARG* 1.3 66.4 + - - +
155E SER* 3.0 12.6 + - - -
156E VAL* 3.1 16.6 + - - +
174E ILE* 4.1 0.6 - - - +
201E ASP* 3.1 25.9 + - - -
204E LYS* 3.8 24.8 + - - +
205E VAL* 3.6 27.5 - - - +
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Residues in contact with ARG 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E GLN* 3.5 29.1 + - - +
46E HIS* 3.3 40.6 + - + +
149E SER 3.1 8.3 + - - +
150E GLU* 3.6 15.9 + - - +
152E SER* 1.3 84.2 + - - +
154E LEU* 1.3 55.8 + - - +
156E VAL* 3.4 3.8 + - - +
157E ASN* 3.0 44.3 + - - +
204E LYS* 4.1 15.0 - - - +
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Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E VAL* 3.9 30.3 - - + +
46E HIS* 3.6 26.7 - - + +
104E PHE* 4.4 7.4 - - + -
107E TYR* 5.7 0.9 - - + -
108E LEU* 4.4 18.2 - - + -
150E GLU 3.0 18.0 + - - +
151E LEU* 3.7 25.1 - - + +
152E SER 3.1 0.4 - - - -
153E ARG* 1.3 74.6 - - - +
155E SER* 1.3 65.3 + - - +
157E ASN 4.5 0.2 - - - +
158E SER* 2.9 36.3 + - - +
166E ARG* 3.9 30.1 - - - +
170E ILE* 4.2 1.6 - - + -
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Residues in contact with SER 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E LEU 3.0 14.7 + - - -
152E SER* 3.3 12.8 - - - -
154E LEU* 1.3 76.7 - - - +
156E VAL* 1.3 64.9 + - - +
158E SER* 3.1 7.5 + - - -
159E VAL* 3.1 25.4 + - - +
167E PRO* 3.5 23.7 - - - +
170E ILE* 3.9 19.3 - - - +
205E VAL* 4.2 11.7 - - - +
208E VAL* 3.8 15.1 - - - +
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Residues in contact with VAL 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E SER 3.1 5.1 + - - +
153E ARG* 3.7 7.6 - - - +
155E SER* 1.3 82.3 - - - +
157E ASN* 1.3 73.5 + - - +
159E VAL* 3.2 6.1 + - - +
160E THR* 3.0 24.6 + - - +
204E LYS* 3.8 30.3 - - + -
208E VAL* 3.8 24.9 - - + -
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Residues in contact with ASN 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E HIS* 3.3 59.7 + - + +
153E ARG* 3.0 37.1 + - - +
154E LEU 4.2 1.1 - - - +
156E VAL* 1.3 85.2 - - - +
158E SER* 1.3 61.7 + - - +
160E THR* 3.3 13.1 + - - -
161E ALA* 3.2 18.2 + - - +
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Residues in contact with SER 158 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E HIS 5.3 0.9 - - - -
154E LEU* 2.9 23.6 + - - +
155E SER* 3.1 9.2 + - - -
157E ASN* 1.3 74.6 - - - +
159E VAL* 1.3 69.1 + - - +
161E ALA* 3.0 13.0 + - - +
163E ASP* 3.0 44.0 + - - +
166E ARG* 4.0 21.9 - - - +
167E PRO* 3.5 12.5 - - - +
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Residues in contact with VAL 159 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E SER 3.1 3.1 + - - +
156E VAL* 3.5 8.5 - - - +
158E SER* 1.3 82.2 + - - +
160E THR* 1.3 65.8 + - - +
162E GLY 2.9 12.0 + - - -
163E ASP 3.8 6.7 - - - +
164E TYR* 3.4 26.0 + - + +
167E PRO* 3.3 29.6 - - + -
208E VAL* 3.5 22.2 - - + -
212E LEU* 4.0 20.6 - - + -
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Residues in contact with THR 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E VAL* 3.0 20.1 + - - +
157E ASN* 3.4 18.7 + - - -
158E SER 3.2 0.2 - - - -
159E VAL* 1.3 78.9 - - - +
161E ALA* 1.3 57.7 + - + +
162E GLY 3.4 2.3 + - - -
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Residues in contact with ALA 161 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E HIS 4.9 1.3 - - - +
47E GLN 4.8 2.0 - - - -
48E GLY* 4.3 33.4 - - - +
157E ASN 3.2 13.0 + - - +
158E SER* 3.0 8.8 + - - +
159E VAL 3.0 1.2 - - - -
160E THR* 1.3 77.1 - - + +
162E GLY* 1.3 57.5 + - - +
163E ASP* 3.3 6.7 + - + +
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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