Contacts of the helix formed by residues 136 - 161 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 4.6 4.0 + - - +
85A TYR* 3.5 36.2 + - + +
88A HIS* 3.8 14.3 + - + -
92A ARG* 4.2 5.0 + - - -
134A HIS* 3.8 4.8 + - - +
135A LEU* 1.3 77.2 - - - +
137A VAL* 1.3 70.3 + - - +
138A GLU* 2.8 33.2 - - - +
139A ASP* 3.1 24.4 + - - +
140A TYR* 3.1 20.1 + - - +
86E ARG* 3.2 13.4 + - - -
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 3.8 32.5 - - - +
128A ASP* 5.2 1.1 - - - +
135A LEU 3.4 1.9 + - - -
136A ASP* 1.3 75.8 + - - +
138A GLU* 1.3 68.8 + - - +
140A TYR* 3.2 4.0 + - - +
141A LEU* 3.0 34.6 + - + +
10E LEU* 4.2 14.6 - - + -
13E PHE* 4.0 24.5 - - + -
14E LEU* 3.5 31.4 - - + -
17E GLU* 5.2 3.8 - - - +
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Residues in contact with GLU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 4.4 7.9 - - - +
96A GLN* 5.1 0.2 - - - -
136A ASP* 2.8 29.0 - - - +
137A VAL* 1.3 78.8 + - - +
139A ASP* 1.3 64.1 + - - +
141A LEU* 3.1 4.3 + - - +
142A SER* 3.0 26.8 + - - +
188A ASN* 3.5 38.3 + - + +
191A LEU* 3.8 20.5 - - + +
14E LEU* 4.3 11.4 - - - +
17E GLU* 2.9 27.7 - - - +
21E ARG* 4.6 5.1 + - - -
86E ARG* 3.3 11.3 + - - -
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A HIS* 3.1 26.0 - - - -
92A ARG* 3.0 27.0 + - - +
95A LEU* 3.3 19.9 - - + +
96A GLN* 3.2 30.8 + - + +
99A VAL* 4.2 6.1 - - - +
135A LEU* 4.0 12.3 - - + -
136A ASP* 3.1 22.9 + - + +
138A GLU* 1.3 75.5 - - - +
140A TYR* 1.3 62.5 + - - +
142A SER* 3.3 3.3 + - - -
143A GLY* 3.0 19.6 + - - -
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 3.7 20.9 - - + +
113A LEU* 3.8 10.7 - - + +
114A VAL* 2.6 26.7 + - + -
115A THR 4.0 0.7 - - - -
116A ARG* 3.5 52.7 + - + -
119A VAL* 4.1 10.1 - - + -
135A LEU* 4.4 5.7 - - + +
136A ASP 3.1 13.4 + - - +
137A VAL 3.4 8.1 - - - +
139A ASP* 1.3 76.5 - - - +
141A LEU* 1.3 70.4 + - + +
143A GLY* 3.1 4.3 + - - -
144A VAL* 3.0 42.8 + - + +
6E ILE* 3.7 18.1 - - + +
7E PHE* 5.7 0.9 - + - -
10E LEU* 3.7 31.2 - - + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 3.0 29.1 + - + +
138A GLU 3.7 6.5 - - - +
140A TYR* 1.3 82.0 - - + +
142A SER* 1.3 61.8 + - - +
144A VAL* 3.3 7.4 + - + +
145A LEU* 3.0 27.4 + - - +
181A PHE* 3.9 25.4 - - + -
184A LEU* 3.7 24.2 - - + -
186A LEU* 4.6 2.0 - - + -
191A LEU* 4.2 24.9 - - + -
7E PHE* 4.0 14.6 - - + -
10E LEU* 3.5 27.4 - - + -
14E LEU* 4.5 5.2 - - + -
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Residues in contact with SER 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG* 4.9 2.6 + - - -
96A GLN* 3.3 34.0 + - - -
138A GLU 3.0 13.6 + - - -
139A ASP 3.5 8.1 - - - -
141A LEU* 1.3 75.3 - - - +
143A GLY* 1.3 66.9 + - - +
145A LEU* 3.0 13.7 + - - +
146A ILE* 3.0 18.9 + - - +
191A LEU* 3.4 19.9 - - - +
194A ARG* 4.3 15.6 + - - +
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Residues in contact with GLY 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 3.6 23.7 + - - +
99A VAL* 3.8 11.7 - - - -
100A PHE* 3.6 14.0 - - - -
139A ASP 3.0 8.5 + - - -
140A TYR 3.1 3.8 + - - -
142A SER* 1.3 78.5 - - - +
144A VAL* 1.3 56.6 + - - +
146A ILE* 3.4 9.6 + - - +
147A LEU* 3.0 23.6 + - - +
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Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 5.0 2.5 - - + -
113A LEU* 4.3 14.8 - - + -
114A VAL* 6.4 0.4 - - + -
140A TYR* 3.0 51.6 + - + +
141A LEU* 3.4 10.5 - - + +
142A SER 3.0 0.2 - - - -
143A GLY* 1.3 75.4 - - - +
145A LEU* 1.3 59.8 + - - +
147A LEU* 3.0 12.7 - - + +
148A ALA* 3.0 25.1 + - - +
177A LEU* 4.0 32.0 - - + +
181A PHE* 4.3 14.8 - - + -
7E PHE* 4.9 4.0 - - + -
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Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU 3.0 18.2 + - - +
142A SER 3.0 6.8 + - - +
144A VAL* 1.3 71.9 - - - +
146A ILE* 1.3 65.1 + - - +
148A ALA* 3.1 6.6 + - - +
149A SER* 3.0 22.9 + - - -
181A PHE* 3.6 32.1 - - + -
191A LEU* 4.2 13.9 - - + -
194A ARG* 3.8 26.5 - - + +
195A TYR* 3.6 33.4 - - + +
198A LEU* 4.0 32.3 - - + +
201A ASP* 4.5 1.4 - - - +
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Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 4.5 16.6 - - + +
97A ARG* 4.9 11.9 - - + +
100A PHE* 3.5 32.3 - - + -
142A SER 3.0 16.9 + - - +
143A GLY* 3.5 15.9 - - - +
145A LEU* 1.3 72.7 - - - +
147A LEU* 1.3 67.0 + - - +
149A SER* 3.1 12.8 + - - +
150A GLU* 3.0 21.4 + - + +
194A ARG* 3.7 36.3 - - - +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.4 13.2 - - + -
103A ALA* 3.9 23.6 - - + +
104A PHE* 3.6 39.3 - - + +
107A TYR* 4.8 3.6 - - + -
112A THR 5.9 0.2 - - - +
113A LEU* 4.4 11.4 - - + -
143A GLY 3.0 13.7 + - - +
144A VAL* 3.0 16.6 - - - +
146A ILE* 1.3 76.7 - - - +
148A ALA* 1.3 60.9 + - - +
150A GLU* 3.0 4.9 + - - +
151A LEU* 2.9 41.4 + - + +
173A PHE* 4.3 26.2 - - + -
177A LEU* 5.2 2.5 - - + -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL 3.0 11.4 + - - +
145A LEU* 3.1 10.3 + - - +
147A LEU* 1.3 78.0 - - - +
149A SER* 1.3 58.4 + - - +
151A LEU* 2.9 18.8 + - - -
152A SER* 3.0 12.0 + - - -
174A ILE* 3.6 20.6 - - + +
177A LEU* 4.2 15.7 - - + +
198A LEU* 3.6 31.0 - - + -
201A ASP* 3.8 2.9 - - - +
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU 3.0 11.9 + - - -
146A ILE* 3.1 18.6 + - - +
148A ALA* 1.3 76.2 - - - +
150A GLU* 1.3 57.6 + - - +
152A SER* 3.1 13.6 + - - -
153A ARG* 3.8 5.7 + - - +
201A ASP* 3.1 27.3 + - - -
203B LYS* 3.7 27.3 + - - -
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 2.6 35.4 + - - +
46A HIS* 3.1 12.1 + - - -
100A PHE* 3.5 30.4 - - + -
104A PHE* 4.1 19.7 - - + -
146A ILE* 3.0 13.2 + - + +
147A LEU* 3.3 9.9 - - + +
148A ALA 3.0 0.6 - - - -
149A SER* 1.3 81.1 - - - +
151A LEU* 1.3 59.2 + - + +
152A SER 3.4 0.2 - - - -
153A ARG* 3.5 19.7 + - - +
154A LEU* 3.0 23.6 + - - +
203B LYS* 5.4 3.5 + - - -
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PHE* 4.0 20.6 - - + -
107A TYR* 4.0 27.8 - - + -
147A LEU* 2.9 31.9 + - + +
148A ALA* 2.9 6.4 + - - +
150A GLU* 1.3 77.3 - - - +
152A SER* 1.3 60.7 + - - +
154A LEU* 3.6 26.9 - - + -
155A SER 2.9 21.1 + - - -
170A ILE* 3.2 21.4 - - + +
173A PHE* 3.8 34.3 - - + -
174A ILE* 4.1 8.7 - - + -
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Residues in contact with SER 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 3.0 7.8 + - - -
149A SER 3.1 8.7 + - - -
151A LEU* 1.3 76.8 - - - +
153A ARG* 1.3 64.1 + - - +
155A SER* 3.1 13.0 + - - -
156A VAL* 3.1 17.2 + - - +
174A ILE* 4.2 1.0 - - - +
201A ASP* 3.0 30.8 + - - -
204A LYS* 3.6 27.9 + - - +
205A VAL* 3.8 25.1 - - - -
208A VAL* 5.4 0.2 - - - +
203B LYS* 5.4 0.5 + - - -
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Residues in contact with ARG 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 3.7 26.7 + - - +
46A HIS* 4.0 23.2 + - + +
149A SER 4.0 9.4 - - - +
150A GLU* 3.5 22.3 + - - +
151A LEU 3.3 0.6 - - - -
152A SER* 1.3 82.0 + - - +
154A LEU* 1.3 63.1 + - - +
156A VAL* 3.2 6.4 + - + +
157A ASN* 3.0 31.6 + - - +
204A LYS* 4.0 10.5 - - - +
175B ASN* 4.0 6.7 + - - -
178B ASP* 4.6 10.3 + - - -
202B VAL* 3.7 17.8 - - - +
203B LYS* 4.3 29.3 - - + +
206B GLU* 3.0 41.9 + - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.9 26.0 - - + +
46A HIS* 3.5 22.8 - - + +
104A PHE* 4.4 5.2 - - + -
107A TYR* 5.2 2.5 - - + -
108A LEU* 4.0 23.8 - - + -
150A GLU 3.0 15.3 + - - +
151A LEU* 3.5 32.1 - - + +
152A SER 3.3 0.4 - - - -
153A ARG* 1.3 75.0 - - - +
155A SER* 1.3 58.1 + - - +
157A ASN* 3.9 1.5 - - + -
158A SER* 2.9 38.7 + - - +
166A ARG* 4.7 15.5 - - - +
170A ILE* 4.2 9.9 - - + -
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Residues in contact with SER 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU 2.9 14.2 + - - -
152A SER* 3.1 13.0 + - - -
154A LEU* 1.3 76.6 - - - +
156A VAL* 1.3 63.8 + - - +
158A SER* 3.1 8.3 + - - -
159A VAL* 3.1 24.5 + - - +
167A PRO* 3.5 20.6 - - - +
170A ILE* 3.7 22.0 - - - -
205A VAL* 3.9 8.1 - - - +
208A VAL* 3.6 20.4 - - - +
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A SER 3.1 3.8 + - - +
153A ARG* 3.6 7.4 - - + +
155A SER* 1.3 79.0 - - - +
157A ASN* 1.3 70.6 + - - +
159A VAL 3.1 3.1 + - - -
160A THR* 3.1 18.1 + - - +
204A LYS* 3.8 30.3 - - + +
208A VAL* 3.9 19.3 - - + -
206B GLU* 3.9 17.0 - - + +
207B GLU* 4.4 10.3 - - + +
210B TYR* 3.5 44.3 - - + -
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Residues in contact with ASN 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL 5.7 0.2 - - - +
46A HIS* 2.9 47.4 + - + +
153A ARG* 3.0 15.2 + - - +
154A LEU* 4.1 3.1 - - + +
156A VAL* 1.3 77.1 - - - +
158A SER* 1.3 57.6 + - - +
160A THR* 3.3 13.0 + - - +
161A ALA* 3.0 27.5 + - - +
206B GLU* 2.9 53.5 + - - +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 2.9 23.5 + - - +
155A SER* 3.1 9.9 - - - -
157A ASN* 1.3 75.3 - - - +
159A VAL* 1.3 60.8 + - - +
161A ALA* 3.0 20.6 + - - +
163A ASP* 2.9 46.5 + - - +
166A ARG* 3.5 23.6 - - - +
167A PRO* 3.5 4.0 - - - +
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A SER 3.1 4.1 + - - +
156A VAL 3.6 1.3 - - - +
158A SER* 1.3 73.7 - - - +
160A THR* 1.3 65.7 + - - +
161A ALA 3.2 0.5 + - - -
162A GLY* 3.2 9.0 + - - -
163A ASP 4.0 5.4 - - - +
164A TYR* 3.5 17.8 + - + +
167A PRO* 3.3 29.2 - - + -
208A VAL* 3.6 21.3 - - + -
212A LEU* 4.1 25.4 - - + -
210B TYR* 3.5 26.9 - - + -
213B SER* 4.2 5.2 + - - -
214B ILE* 4.4 15.3 - - + +
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A VAL 3.1 7.4 + - - -
157A ASN* 3.4 17.5 + - - +
158A SER 3.2 0.2 - - - -
159A VAL* 1.3 77.5 - - - +
161A ALA* 1.3 59.8 + - - +
162A GLY 3.6 0.3 + - - -
206B GLU 4.5 1.6 + - - -
209B VAL* 3.8 23.7 + - + +
210B TYR* 3.3 32.7 + - - +
213B SER* 3.7 21.0 + - - +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS 6.1 0.4 - - - +
52A GLN* 5.6 10.8 - - + +
157A ASN 3.0 15.0 + - - +
158A SER* 3.0 11.4 + - - +
160A THR* 1.3 77.9 - - + +
162A GLY* 1.3 57.7 + - - +
163A ASP* 3.3 3.9 + - + +
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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